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2287086eaa91efa682a8bb3fd41bc185c78df14a
shiny/revdep/problems.md
Barret Schloerke 231c13d9a5 run revdep. updates redep_cran notes
2020-06-19 11:09:15 -04:00

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aaSEA

Run revdep_details(,"aaSEA") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.

ADAMgui

Run revdep_details(,"ADAMgui") for more info

In both

  • checking dependencies in R code ... NOTE

    Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

  • checking data for non-ASCII characters ... NOTE

      Note: found 3 marked UTF-8 strings

adapr

Run revdep_details(,"adapr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::clean_source’

adegenet

Run revdep_details(,"adegenet") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.3Mb
    files   1.7Mb

adepro

Run revdep_details(,"adepro") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.

AdhereRViz

Run revdep_details(,"AdhereRViz") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘lubridate’ ‘parallel’ ‘rsvg’ ‘scales’
  All declared Imports should be used.

alevinQC

Run revdep_details(,"alevinQC") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  11.6Mb

AMPLE

Run revdep_details(,"AMPLE") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.

analysisPipelines

Run revdep_details(,"analysisPipelines") for more info

In both

  • checking package dependencies ... NOTE 
    Package which this enhances but not available for checking: ‘SparkR’

animalcules

Run revdep_details(,"animalcules") for more info

Newly fixed

  • checking examples ... ERROR 
    Running examples in ‘animalcules-Ex.R’ failed
The error most likely occurred in:

> ### Name: find_taxonomy_300
> ### Title: Find the taxonomy for maximum 300 tids
> ### Aliases: find_taxonomy_300
> 
> ### ** Examples
> 
> taxonLevels <- find_taxonomy_300(tids=1200)
Error: HTTP failure: 429
{"error":"API rate limit exceeded","api-key":"100.36.143.38","count":"4","limit":"3"}
Execution halted

In both

  • checking installed package size ... NOTE

      installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc     4.4Mb
    shiny   1.9Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.

  • checking R code for possible problems ... NOTE

    alpha_div_boxplot: no visible binding for global variable ‘richness’
differential_abundance: no visible binding for global variable ‘padj’
differential_abundance: no visible binding for global variable ‘pValue’
differential_abundance: no visible binding for global variable
  ‘log2FoldChange’
diversities_help: no visible binding for global variable ‘x’
find_biomarker: no visible binding for global variable ‘rowname’
find_biomarker: no visible binding for global variable ‘importance’
find_biomarker: no visible binding for global variable ‘.’
find_biomarker: no visible binding for global variable ‘Overall’
find_biomarker: no visible binding for global variable ‘y’
find_biomarker: no visible binding for global variable ‘m’
find_biomarker: no visible binding for global variable ‘d’
relabu_barplot: no visible binding for global variable ‘.’
relabu_boxplot: no visible binding for global variable ‘.’
relabu_heatmap: no visible binding for global variable ‘.’
upsample_counts: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . Overall d importance log2FoldChange m pValue padj richness rowname
  x y

  • checking for unstated dependencies in vignettes ... NOTE

    '::' or ':::' import not declared from: ‘devtools’

animaltracker

Run revdep_details(,"animaltracker") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘V8’
  All declared Imports should be used.

animint2

Run revdep_details(,"animint2") for more info

In both

  • checking examples ... ERROR

    Running examples in ‘animint2-Ex.R’ failed
The error most likely occurred in:

> ### Name: aes
> ### Title: Define aesthetic mappings.
> ### Aliases: aes
> 
> ### ** Examples
> 
> aes(x = mpg, y = wt)

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 732 | SKIPPED: 7 | WARNINGS: 14 | FAILED: 19 ]
  1. Failure: grid: facet order follows default data frame order (@test-compiler-facet-locate.r#118) 
  2. Failure: grid: facet order follows default data frame order (@test-compiler-facet-locate.r#119) 
  3. Failure: grid: facet order follows default data frame order (@test-compiler-facet-locate.r#126) 
  4. Failure: grid: facet order follows default data frame order (@test-compiler-facet-locate.r#127) 
  5. Failure: grid: facet order follows default data frame order (@test-compiler-facet-locate.r#134) 
  6. Failure: grid: facet order follows default data frame order (@test-compiler-facet-locate.r#135) 
  7. Failure: wrap: facet order follows default data frame order (@test-compiler-facet-locate.r#148) 
  8. Failure: wrap: facet order follows default data frame order (@test-compiler-facet-locate.r#154) 
  9. Failure: wrap: facet order follows default data frame order (@test-compiler-facet-locate.r#160) 
  1. ...

  Error: testthat unit tests failed
  Execution halted

  • checking installed package size ... NOTE

      installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.0Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘tibble’
  All declared Imports should be used.

ANOVAIREVA

Run revdep_details(,"ANOVAIREVA") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.

ANOVAShiny

Run revdep_details(,"ANOVAShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.

antitrust

Run revdep_details(,"antitrust") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘MASS’ ‘evd’
  All declared Imports should be used.

apexcharter

Run revdep_details(,"apexcharter") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 230 marked UTF-8 strings

appreci8R

Run revdep_details(,"appreci8R") for more info

In both

  • checking package dependencies ... ERROR 
    Packages required but not available:
  'PolyPhen.Hsapiens.dbSNP131', 'SIFT.Hsapiens.dbSNP137'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ArchaeoPhases

Run revdep_details(,"ArchaeoPhases") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.

arena2r

Run revdep_details(,"arena2r") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.

ASSOCShiny

Run revdep_details(,"ASSOCShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.

AUCell

Run revdep_details(,"AUCell") for more info

In both

  • checking package dependencies ... NOTE

    Package which this enhances but not available for checking: ‘doMC’

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘S4Vectors’
  All declared Imports should be used.

  • checking R code for possible problems ... NOTE

    AUCell_createViewerApp : <anonymous>: no visible global function
  definition for ‘%>%’
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable ‘tsne1’
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable ‘tsne2’
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable ‘cell’
Undefined global functions or variables:
  %>% cell tsne1 tsne2

  • checking Rd cross-references ... NOTE

    Package unavailable to check Rd xrefs: ‘SingleCellExperiment’

autoTS

Run revdep_details(,"autoTS") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.

BARIS

Run revdep_details(,"BARIS") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.

BatchQC

Run revdep_details(,"BatchQC") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  fbatch3      -0.1891     0.3385  -0.559   0.5787  
  fcond1        0.5066     0.2764   1.833   0.0721 .
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

  Residual standard error: 1.071 on 56 degrees of freedom
  Multiple R-squared:  0.06516,	Adjusted R-squared:  0.01508 
  F-statistic: 1.301 on 3 and 56 DF,  p-value: 0.2831

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: batchQC (@test_batchQC.R#25) 

  Error: testthat unit tests failed
  Execution halted

  • checking R code for possible problems ... NOTE

    gene_plot: no visible global function definition for ‘boxplot’
gene_plot: no visible binding for global variable ‘batch’
gls.series.C: no visible global function definition for ‘lm.fit’
sample_plot: no visible global function definition for ‘boxplot’
sample_plot: no visible binding for global variable ‘batch’
Undefined global functions or variables:
  batch boxplot lm.fit
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "lm.fit")
to your NAMESPACE file.

BayesBD

Run revdep_details(,"BayesBD") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

BayesianNetwork

Run revdep_details(,"BayesianNetwork") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.

BayesNetBP

Run revdep_details(,"BayesNetBP") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘cyjShiny’

BBEST

Run revdep_details(,"BBEST") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘wmtsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

BCEA

Run revdep_details(,"BCEA") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘INLA’

bdchecks

Run revdep_details(,"bdchecks") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 72 marked UTF-8 strings

bdclean

Run revdep_details(,"bdclean") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.

bde

Run revdep_details(,"bde") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.

bea.R

Run revdep_details(,"bea.R") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.

beanz

Run revdep_details(,"beanz") for more info

In both

  • checking installed package size ... NOTE

      installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

bestSDP

Run revdep_details(,"bestSDP") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.

BETS

Run revdep_details(,"BETS") for more info

In both

  • checking whether the package can be unloaded cleanly ... WARNING

    Error: package or namespace load failed for ‘BETS’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so':
  dlopen(/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so
Execution halted

  • checking whether the namespace can be loaded with stated dependencies ... WARNING

    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so':
  dlopen(/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

  • checking dependencies in R code ... NOTE

    Error: package or namespace load failed for ‘BETS’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so':
  dlopen(/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/BETS/RMySQL/libs/RMySQL.so
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   },
Execution halted

bibliometrix

Run revdep_details(,"bibliometrix") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb

bigPint

Run revdep_details(,"bigPint") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data             2.1Mb
    doc              2.7Mb
    shiny-examples   3.0Mb

bigQueryR

Run revdep_details(,"bigQueryR") for more info

In both

  • checking Rd cross-references ... NOTE 
    Package unavailable to check Rd xrefs: ‘bigrquery’

billboarder

Run revdep_details(,"billboarder") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb

binovisualfields

Run revdep_details(,"binovisualfields") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.

bioCancer

Run revdep_details(,"bioCancer") for more info

In both

  • checking Rd files ... WARNING

    checkRd: (5) bioCancer.Rd:0-20: Must have a \description

  • checking installed package size ... NOTE

      installed size is  8.3Mb
  sub-directories of 1Mb or more:
    app       3.3Mb
    doc       2.8Mb
    extdata   1.6Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘import’ ‘methods’ ‘shinythemes’
  All declared Imports should be used.

BiocOncoTK

Run revdep_details(,"BiocOncoTK") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Execution halted
  ── 3. Error: rbind utilities work (@test_dockstore_scripts.R#29)  ──────────────
  cannot open the connection
  Backtrace:
   1. base::readRDS("demo.rds")
   2. base::gzfile(file, "rb")

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 3 ]
  1. Failure: exprByMSI_csv produces expected CSV (@test_dockstore_scripts.R#10) 
  2. Error: exprByMSI_csv produces expected CSV (@test_dockstore_scripts.R#11) 
  3. Error: rbind utilities work (@test_dockstore_scripts.R#29) 

  Error: testthat unit tests failed
  Execution halted

  • checking installed package size ... NOTE

      installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data        6.1Mb
    doc         3.6Mb
    pamphlets   4.5Mb

  • checking R code for possible problems ... NOTE

    ...
ggscat_av: no visible binding for global variable ‘symbol’
ggscat_av: no visible binding for global variable ‘msival’
ggscat_av: no visible binding for global variable ‘tmsi’
ggscat_av: no visible binding for global variable ‘log2exa’
mc3toGR : <anonymous>: no visible binding for global variable
  ‘Consequence’
multiviz: no visible binding for global variable ‘acronym’
multiviz: no visible binding for global variable ‘msival’
prc: no visible binding for global variable ‘acronym’
prc: no visible global function definition for ‘right_join’
rainfall: no visible global function definition for ‘genome’
tumNorSet : <anonymous>: no visible global function definition for
  ‘pancan_SE’
Undefined global functions or variables:
  BiocFileCache Consequence acronym genome log2ex log2exa mapIds
  map_tcga_ncit msicode msival new pancan_SE project_short_name
  right_join seqlengths symbol tfstart tmsi v1 v2
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

  • checking data for non-ASCII characters ... NOTE

      Note: found 46 marked UTF-8 strings

BioInstaller

Run revdep_details(,"BioInstaller") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb

BioNetStat

Run revdep_details(,"BioNetStat") for more info

In both

  • checking installed package size ... NOTE

      installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.9Mb
    shiny     1.9Mb

  • checking package subdirectories ... NOTE

    Found the following CITATION file in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘RColorBrewer’ ‘RJSONIO’ ‘ggplot2’ ‘knitr’ ‘pheatmap’
  ‘plyr’ ‘stats’ ‘utils’ ‘whisker’ ‘yaml’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘DT’ ‘shiny’ ‘shinyBS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

  • checking R code for possible problems ... NOTE

    ...
  for ‘bplapply’
gaussianDensity: no visible global function definition for ‘bw.nrd0’
gaussianDensity: no visible global function definition for ‘density’
pathPlot: no visible binding for global variable ‘median’
readVarFile: no visible global function definition for ‘read.table’
resInt : <anonymous>: no visible global function definition for ‘dist’
retEdgesTable: no visible global function definition for ‘p.adjust’
retTable: no visible global function definition for ‘p.adjust’
spectralDistributionTest: no visible global function definition for
  ‘bplapply’
spectralEntropyTest: no visible global function definition for
  ‘bplapply’
var.list: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  adjacencyMatrix1 aggregate bplapply bw.nrd0 cor density dist expr
  median p.adjust read.csv read.table
Consider adding
  importFrom("stats", "aggregate", "bw.nrd0", "cor", "density", "dist",
             "median", "p.adjust")
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.

BIRDS

Run revdep_details(,"BIRDS") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘esquisse’ ‘rgdal’
  All declared Imports should be used.

  • checking data for non-ASCII characters ... NOTE

      Note: found 27976 marked UTF-8 strings

biva

Run revdep_details(,"biva") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘corrgram’ ‘rpivotTable’ ‘shinyAce’
  All declared Imports should be used.

blkbox

Run revdep_details(,"blkbox") for more info

In both

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘bigrf’

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’

blockCV

Run revdep_details(,"blockCV") for more info

In both

  • checking Rd cross-references ... NOTE 
    Package unavailable to check Rd xrefs: ‘biomod2’

BLRShiny

Run revdep_details(,"BLRShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.

bsplus

Run revdep_details(,"bsplus") for more info

Newly broken

  • checking tests ... 
     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  y[1]: "col-sm-3 col-sm-offset-1"

  ── 2. Failure: constructor with different column-specs (@test-accordion_sidebar.
  tagGetAttribute(acc_sidebar_main, "class") not identical to "col-sm-7 col-sm-offset-1".
  1/1 mismatches
  x[1]: "col-sm-7 offset-md-1 col-sm-offset-1"
  y[1]: "col-sm-7 col-sm-offset-1"

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 102 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: constructor with different column-specs (@test-accordion_sidebar.R#57) 
  2. Failure: constructor with different column-specs (@test-accordion_sidebar.R#59) 

  Error: testthat unit tests failed
  Execution halted

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.

caffsim

Run revdep_details(,"caffsim") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.

canvasXpress

Run revdep_details(,"canvasXpress") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb

CaPO4Sim

Run revdep_details(,"CaPO4Sim") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.

cartools

Run revdep_details(,"cartools") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’
  ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’
  All declared Imports should be used.

ChAMP

Run revdep_details(,"ChAMP") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘IlluminaHumanMethylation450kmanifest’

Depends: includes the non-default packages:
  'minfi', 'ChAMPdata', 'FEM', 'DMRcate',
  'Illumina450ProbeVariants.db',
  'IlluminaHumanMethylationEPICmanifest', 'DT'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CHETAH

Run revdep_details(,"CHETAH") for more info

In both

  • checking installed package size ... NOTE

      installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  11.0Mb
    doc    1.8Mb

  • checking dependencies in R code ... NOTE

    Package in Depends field not imported from: ‘SingleCellExperiment’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

chipPCR

Run revdep_details(,"chipPCR") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
plot,refMFI-refMFI: no visible global function definition for ‘mtext’
plot,refMFI-refMFI: no visible global function definition for ‘abline’
plot,refMFI-refMFI: no visible global function definition for ‘legend’
plot,refMFI-refMFI: no visible global function definition for ‘lines’
qqline,refMFI: no visible binding for global variable ‘qnorm’
Undefined global functions or variables:
  abline adjustcolor arrows axis coef cor head layout legend lines lm
  mad matplot median mtext na.omit par points polygon predict
  predict.lm qnorm quantile rect rnorm rstudent rug sd shapiro.test
  smooth.spline tail text wilcox.test
Consider adding
  importFrom("grDevices", "adjustcolor")
  importFrom("graphics", "abline", "arrows", "axis", "layout", "legend",
             "lines", "matplot", "mtext", "par", "points", "polygon",
             "rect", "rug", "text")
  importFrom("stats", "coef", "cor", "lm", "mad", "median", "na.omit",
             "predict", "predict.lm", "qnorm", "quantile", "rnorm",
             "rstudent", "sd", "shapiro.test", "smooth.spline",
             "wilcox.test")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.

chromoMap

Run revdep_details(,"chromoMap") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.

cicerone

Run revdep_details(,"cicerone") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.

cjoint

Run revdep_details(,"cjoint") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.

  • checking data for non-ASCII characters ... NOTE

      Note: found 29 marked UTF-8 strings

clustDRM

Run revdep_details(,"clustDRM") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.

CLUSTShiny

Run revdep_details(,"CLUSTShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.

CMShiny

Run revdep_details(,"CMShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.

CNVPanelizer

Run revdep_details(,"CNVPanelizer") for more info

In both

  • checking dependencies in R code ... NOTE 
    Unexported object imported by a ':::' call: ‘utils:::format.object_size’
  See the note in ?`:::` about the use of this operator.

cocktailApp

Run revdep_details(,"cocktailApp") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 14661 marked UTF-8 strings

codebook

Run revdep_details(,"codebook") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.

  • checking data for non-ASCII characters ... NOTE

      Note: found 65 marked UTF-8 strings

cognitoR

Run revdep_details(,"cognitoR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.

COMPASS

Run revdep_details(,"COMPASS") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘rmarkdown’
  All declared Imports should be used.
':::' call which should be '::': ‘flowWorkspace:::.getNodeInd’
  See the note in ?`:::` about the use of this operator.

  • checking R code for possible problems ... NOTE

    .CellCounts: no visible binding for global variable
  ‘_COMPASS_CellCounts’
COMPASSfitToCountsTable: no visible binding for global variable
  ‘population’
COMPASSfitToCountsTable: no visible binding for global variable ‘Count’
COMPASSfitToCountsTable: no visible binding for global variable ‘id’
CellCounts_character: no visible binding for global variable
  ‘_COMPASS_CellCounts_character’
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for ‘gh_pop_is_bool_gate’
Undefined global functions or variables:
  Count _COMPASS_CellCounts _COMPASS_CellCounts_character
  gh_pop_is_bool_gate id population

competitiontoolbox

Run revdep_details(,"competitiontoolbox") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.

conflr

Run revdep_details(,"conflr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.

CoRegNet

Run revdep_details(,"CoRegNet") for more info

In both

  • checking for unstated dependencies in ‘tests’ ... WARNING

    '::' or ':::' import not declared from: ‘BiocGenerics’

  • checking dependencies in R code ... NOTE

    'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘gplots’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

  • checking R code for possible problems ... NOTE

    ...
refine,coregnet: no visible global function definition for ‘glm’
refine,coregnet: no visible global function definition for ‘abline’
regulatorInfluence,coregnet : <anonymous> : <anonymous>: no visible
  global function definition for ‘t.test’
regulators,coregnet: no visible global function definition for
  ‘na.omit’
repressors,coregnet: no visible global function definition for
  ‘na.omit’
targets,coregnet: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  abline arrows as.dist axis coef colorRampPalette cor fisher.test glm
  hclust heatmap.2 lines lm mtext na.omit p.adjust par pchisq pnorm
  quantile rainbow sd segments symbols t.test text vcount wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "abline", "arrows", "axis", "lines", "mtext",
             "par", "segments", "symbols", "text")
  importFrom("stats", "as.dist", "coef", "cor", "fisher.test", "glm",
             "hclust", "lm", "na.omit", "p.adjust", "pchisq", "pnorm",
             "quantile", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.

corporaexplorer

Run revdep_details(,"corporaexplorer") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘rmarkdown’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinyjs’
  All declared Imports should be used.

cosinor

Run revdep_details(,"cosinor") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.

coveffectsplot

Run revdep_details(,"coveffectsplot") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘data.table’ ‘dplyr’ ‘markdown’ ‘shinyjs’ ‘table1’
  ‘tidyr’
  All declared Imports should be used.

CRANsearcher

Run revdep_details(,"CRANsearcher") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings

crawl

Run revdep_details(,"crawl") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘gdistance’ ‘raster’
  All declared Imports should be used.

crispRdesignR

Run revdep_details(,"crispRdesignR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.

crisprseekplus

Run revdep_details(,"crisprseekplus") for more info

In both

  • checking R code for possible problems ... NOTE 
    installpack: no visible global function definition for
  'install.packages'
Undefined global functions or variables:
  install.packages
Consider adding
  importFrom("utils", "install.packages")
to your NAMESPACE file.

CrossICC

Run revdep_details(,"CrossICC") for more info

In both

  • checking R code for possible problems ... NOTE 
    .mergemodel: no visible global function definition for ‘coxph’
CrossICC: no visible global function definition for ‘.’
FAIME: no visible binding for global variable ‘SampleExp’
get.max.var.rows: no visible binding for global variable ‘V1’
predictor: no visible global function definition for ‘assay’
runFAIME: no visible global function definition for ‘assay’
Undefined global functions or variables:
  . SampleExp V1 assay coxph

crossmeta

Run revdep_details(,"crossmeta") for more info

In both

  • checking dependencies in R code ... WARNING

    '::' or ':::' import not declared from: ‘shinyBS’
Unexported object imported by a ':::' call: ‘GEOquery:::parseGSEMatrix’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getDirListing’ ‘getGEO’ ‘getGEOSuppFiles’

  • checking R code for possible problems ... NOTE

    ...
  ‘download.file’
getDirListing: no visible global function definition for ‘read.table’
getGEOSuppFiles: no visible global function definition for
  ‘download.file’
get_dfs: no visible global function definition for ‘head’
load_agil_plat : <anonymous>: no visible global function definition for
  ‘capture.output’
load_agil_plat: no visible global function definition for ‘as’
load_illum_plat: no visible global function definition for ‘as’
padog: no visible global function definition for ‘is’
symbol_annot: no visible binding for global variable ‘SYMBOL_9606’
which_max_iqr: no visible binding for global variable ‘iqrange’
Undefined global functions or variables:
  SYMBOL_9606 as capture.output download.file head iqrange is
  read.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "capture.output", "download.file", "head",
             "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

  • checking Rd cross-references ... NOTE

    Packages unavailable to check Rd xrefs: ‘PADOG’, ‘GeneMeta’

CSUV

Run revdep_details(,"CSUV") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘parcor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CTAShiny

Run revdep_details(,"CTAShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.

ctsem

Run revdep_details(,"ctsem") for more info

In both

  • checking installed package size ... NOTE

      installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.3Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘pkgbuild’
  All declared Imports should be used.

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

CTShiny

Run revdep_details(,"CTShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.

CVE

Run revdep_details(,"CVE") for more info

In both

  • checking examples ... ERROR

    Running examples in ‘CVE-Ex.R’ failed
The error most likely occurred in:

> ### Name: get.oncotator.anno
> ### Title: Open Cancer Variant Explorer (CVE) Shiny app
> ### Aliases: get.oncotator.anno
> 
> ### ** Examples
> 
> exCase <- data.frame(chr = rep(10, 3),
+     start = c("100894110", "100985376", "101137905"),
+     end = c("100894110", "100985376", "101137905"),
+     ref_allele = c("T", "C", "G"),
+     obs_allele = c("G", "A", "A"))
> get.oncotator.anno(exCase)
Error in open.connection(con, "rb") : HTTP error 502.
Calls: get.oncotator.anno ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted

  • checking data for ASCII and uncompressed saves ... WARNING

    
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                old_size new_size compress
  WGCNAmelanoma_extension.RData    2.4Mb    2.1Mb       xz
  crcCase.RData                    1.1Mb    678Kb       xz
  melanomaCase.RData               654Kb    473Kb       xz

  • checking installed package size ... NOTE

      installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    doc    1.5Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘RTCGAToolbox’
  All declared Imports should be used.
Package in Depends field not imported from: ‘tidyverse’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

d3Tree

Run revdep_details(,"d3Tree") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.

datacheck

Run revdep_details(,"datacheck") for more info

In both

  • checking R code for possible problems ... NOTE

    ...
heatmap_quality: no visible global function definition for ‘heatmap’
is.oneOf: no visible global function definition for ‘read.csv’
is_one_of: no visible global function definition for ‘read.csv’
pkg.version: no visible global function definition for ‘citation’
pkg_version: no visible global function definition for ‘citation’
ruleCoverage: no visible global function definition for ‘dotchart’
ruleCoverage: no visible global function definition for ‘abline’
rule_coverage: no visible global function definition for ‘dotchart’
rule_coverage: no visible global function definition for ‘abline’
shortSummary: no visible global function definition for ‘sd’
short_summary: no visible global function definition for ‘sd’
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.

  • checking files in ‘vignettes’ ... NOTE

    Package has no Sweave vignette sources and no VignetteBuilder field.

datadigest

Run revdep_details(,"datadigest") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.

dataesgobr

Run revdep_details(,"dataesgobr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘shinyFiles’ ‘shinycssloaders’ ‘shinyjs’ ‘shinythemes’
  All declared Imports should be used.

debrowser

Run revdep_details(,"debrowser") for more info

In both

  • checking R code for possible problems ... NOTE 
    checkCountData : <anonymous>: no visible binding for global variable
  ‘err’
debrowserdataload: no visible binding for global variable ‘demodata’
debrowserhistogram: no visible global function definition for ‘config’
getBarMainPlot: no visible global function definition for ‘config’
getBoxMainPlot: no visible global function definition for ‘config’
getDensityPlot: no visible binding for global variable ‘samples’
getDensityPlot: no visible global function definition for ‘config’
getIQRPlot: no visible global function definition for ‘config’
mainScatterNew: no visible global function definition for ‘config’
plot_pca: no visible binding for global variable ‘x’
plot_pca: no visible binding for global variable ‘y’
plot_pca: no visible binding for global variable ‘samples’
plot_pca: no visible global function definition for ‘config’
runHeatmap: no visible global function definition for ‘config’
Undefined global functions or variables:
  config demodata err samples x y

delayed

Run revdep_details(,"delayed") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘assertthat’
  All declared Imports should be used.

DEP

Run revdep_details(,"DEP") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.0Mb

detzrcr

Run revdep_details(,"detzrcr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.

DiscoRhythm

Run revdep_details(,"DiscoRhythm") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.

  • checking R code for possible problems ... NOTE

    discoApp: no visible binding for global variable ‘.discorhythm_ncores’
discoBatch: no visible binding for global variable ‘discoODAres’
Undefined global functions or variables:
  .discorhythm_ncores discoODAres

diveRsity

Run revdep_details(,"diveRsity") for more info

In both

  • checking package dependencies ... NOTE 
    Packages suggested but not available for checking: 'sendplot', 'HWxtest'

DLMtool

Run revdep_details(,"DLMtool") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.3Mb
    libs   1.1Mb

Doscheda

Run revdep_details(,"Doscheda") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data             2.1Mb
    doc              1.6Mb
    shiny-examples   2.0Mb

dosedesignR

Run revdep_details(,"dosedesignR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘ggplot2’ ‘lattice’ ‘latticeExtra’ ‘shinyjs’
  All declared Imports should be used.

dplyrAssist

Run revdep_details(,"dplyrAssist") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.

dragon

Run revdep_details(,"dragon") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘broom’ ‘colorspace’ ‘colourpicker’ ‘cowplot’
  ‘igraph’ ‘magrittr’ ‘shinyBS’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinythemes’ ‘tidyverse’ ‘visNetwork’
  All declared Imports should be used.

dropR

Run revdep_details(,"dropR") for more info

In both

  • checking R code for possible problems ... NOTE 
    compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.

dtwclust

Run revdep_details(,"dtwclust") for more info

In both

  • checking for GNU extensions in Makefiles ... NOTE 
    GNU make is a SystemRequirements.

DVHmetrics

Run revdep_details(,"DVHmetrics") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.

dynamichazard

Run revdep_details(,"dynamichazard") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    doc    1.7Mb
    libs   2.7Mb

EBImage

Run revdep_details(,"EBImage") for more info

In both

  • checking whether package ‘EBImage’ can be installed ... WARNING

    Found the following significant warnings:
  morphology.cpp:163:14: warning: expression result unused [-Wunused-value]
  morphology.cpp:166:14: warning: expression result unused [-Wunused-value]
  morphology.cpp:170:14: warning: expression result unused [-Wunused-value]
  morphology.cpp:196:14: warning: expression result unused [-Wunused-value]
  morphology.cpp:199:14: warning: expression result unused [-Wunused-value]
  morphology.cpp:203:14: warning: expression result unused [-Wunused-value]
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex/EBImage/new/EBImage.Rcheck/00install.out’ for details.

  • checking installed package size ... NOTE

      installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc      5.1Mb
    images   1.7Mb

effectR

Run revdep_details(,"effectR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.

elementR

Run revdep_details(,"elementR") for more info

In both

  • checking examples ... ERROR 
    Running examples in ‘elementR-Ex.R’ failed
The error most likely occurred in:

> ### Name: elementR_project
> ### Title: Object elementR_project
> ### Aliases: elementR_project
> 
> ### ** Examples
> 
> ## create a new elementR_repStandard object based on the "filePath" 
> ## from a folder containing sample replicate
> 
> filePath <- system.file("Example_Session", package="elementR")
> 
> exampleProject <- elementR_project$new(filePath)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: <Anonymous> ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted

embryogrowth

Run revdep_details(,"embryogrowth") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 5 marked UTF-8 strings

EML

Run revdep_details(,"EML") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘EML’

ENCODExplorer

Run revdep_details(,"ENCODExplorer") for more info

In both

  • checking R code for possible problems ... NOTE 
    createDesign: no visible binding for global variable ‘file_format’
createDesign: no visible binding for global variable ‘status’
createDesign: no visible binding for global variable ‘accession’
createDesign: no visible binding for global variable ‘controls’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘accession’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘href’
createDesign: no visible global function definition for ‘.’
createDesign: no visible binding for global variable ‘href’
createDesign: no visible binding for global variable ‘Experiment’
createDesign: no visible binding for global variable ‘Value’
downloadEncode: no visible binding for global variable ‘file_accession’
downloadEncode: no visible binding for global variable ‘file_format’
downloadEncode: no visible binding for global variable ‘accession’
shinyEncode: no visible binding for global variable ‘ui’
shinyEncode: no visible binding for global variable ‘server’
Undefined global functions or variables:
  . Experiment Value accession controls file_accession file_format href
  server status ui

enviGCMS

Run revdep_details(,"enviGCMS") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘xcms’

epicontacts

Run revdep_details(,"epicontacts") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.

EpiSignalDetection

Run revdep_details(,"EpiSignalDetection") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘ggplot2’ ‘knitr’ ‘pander’
  All declared Imports should be used.

epivizrChart

Run revdep_details(,"epivizrChart") for more info

In both

  • checking installed package size ... NOTE

      installed size is 25.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc   17.3Mb
    www    3.8Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: 'epivizrServer'
  All declared Imports should be used.

erma

Run revdep_details(,"erma") for more info

In both

  • checking installed package size ... NOTE

      installed size is 218.3Mb
  sub-directories of 1Mb or more:
    bed_tabix  178.2Mb
    data        37.1Mb
    doc          2.1Mb

  • checking R code for possible problems ... NOTE

    geneTxRange: no visible global function definition for ‘select’
genemodelOLD: no visible binding for global variable ‘exonsBy’
stateProfile: no visible binding for global variable ‘states_25’
stateProfile: no visible binding for global variable ‘short_celltype’
stateProfile: no visible binding for global variable ‘name’
statesByRange: no visible binding for global variable ‘mod’
statesByRange: no visible binding for global variable ‘upstream’
statesByRange: no visible binding for global variable ‘downstream’
statesByRange : <anonymous>: no visible binding for global variable
  ‘tss’
statesByRange: no visible binding for global variable ‘states_25’
Undefined global functions or variables:
  downstream exonsBy mod name select short_celltype states_25 tss
  upstream

EventStudy

Run revdep_details(,"EventStudy") for more info

In both

  • checking installed package size ... NOTE

      installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.

ezplot

Run revdep_details(,"ezplot") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.

farrell

Run revdep_details(,"farrell") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.

FastqCleaner

Run revdep_details(,"FastqCleaner") for more info

In both

  • checking for portable file names ... NOTE

    Found the following non-portable file paths:
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-11-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-12-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-13-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-14-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-7-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-8-1.png

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

  • checking installed package size ... NOTE

      installed size is  5.7Mb
  sub-directories of 1Mb or more:
    application   4.2Mb
    doc           1.1Mb

FELLA

Run revdep_details(,"FELLA") for more info

In both

  • checking running R code from vignettes ...

      ‘musmusculus.Rmd’ using ‘UTF-8’... OK
  ‘quickstart.Rmd’ using ‘UTF-8’... OK
  ‘zebrafish.Rmd’ using ‘UTF-8’... OK
  ‘FELLA.Rnw’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘FELLA.Rnw’
  ...

> g.go <- addGOToGraph(graph = g, GOterm = "GO:0005739", 
+     godata.options = list(OrgDb = "org.Hs.eg.db", ont = "CC"), 
+     mart.options = list( .... [TRUNCATED] 
Ensembl site unresponsive, trying useast mirror
Ensembl site unresponsive, trying uswest mirror

  When sourcing ‘FELLA.R’:
Error: Multiple cache results found
Execution halted

  • checking R code for possible problems ... NOTE

    buildGraphFromKEGGREST: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.

firebase

Run revdep_details(,"firebase") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.

fitteR

Run revdep_details(,"fitteR") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘ExtDist’

fitur

Run revdep_details(,"fitur") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.

flair

Run revdep_details(,"flair") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘dplyr’ ‘evaluate’ ‘ggplot2’
  All declared Imports should be used.

flora

Run revdep_details(,"flora") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb

flowAI

Run revdep_details(,"flowAI") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb

flowcatchR

Run revdep_details(,"flowcatchR") for more info

In both

  • checking installed package size ... NOTE

      installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    9.5Mb

  • checking dependencies in R code ... NOTE

    'library' or 'require' call to ‘EBImage’ which was already attached by Depends.
  Please remove these calls from your code.

frailtypack

Run revdep_details(,"frailtypack") for more info

In both

  • checking whether package ‘frailtypack’ can be installed ... ERROR 
    Installation failed.
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/frailtypack/new/frailtypack.Rcheck/00install.out’ for details.

Installation

Devel

* installing *source* package ‘frailtypack’ ...
** package ‘frailtypack’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  Adonnees.f90 -o Adonnees.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  AparamMultive.f90 -o AparamMultive.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  Aparameters.f90 -o Aparameters.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  aGhermite.f90 -o aGhermite.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  ahrmsym.f90 -o ahrmsym.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  funcpajsplinesIndiv.f90 -o funcpajsplinesIndiv.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c init.c -o init.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  risque.f90 -o risque.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  somme.f90 -o somme.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  test.f90 -o test.o
funcpajsplinesIndiv.f90:6:8:

     use comon,only:mm,mm3,mm2,mm1,& !m3m3,m2m2,m1m1,mmm,m3m2,m3m1,m3m,m2m1,m2m,m1m
        1
Fatal Error: Can't open module file ‘comon.mod’ for reading at (1): No such file or directory
compilation terminated.
make: *** [funcpajsplinesIndiv.o] Error 1
make: *** Waiting for unfinished jobs....
somme.f90:7:47:

     integer:: i,num_thread,num_proc,nb_thread,d
                                               1
Warning: Unused variable ‘d’ declared at (1) [-Wunused-variable]
somme.f90:7:45:

     integer:: i,num_thread,num_proc,nb_thread,d
                                             1
Warning: Unused variable ‘nb_thread’ declared at (1) [-Wunused-variable]
somme.f90:1:31:

 subroutine somme(ab,s,nboot,nbr,vOut)
                               1
Warning: Unused dummy argument ‘nbr’ at (1) [-Wunused-dummy-argument]
somme.f90:7:35:

     integer:: i,num_thread,num_proc,nb_thread,d
                                   1
Warning: Unused variable ‘num_proc’ declared at (1) [-Wunused-variable]
ERROR: compilation failed for package ‘frailtypack’
* removing ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/frailtypack/new/frailtypack.Rcheck/frailtypack’

CRAN

* installing *source* package ‘frailtypack’ ...
** package ‘frailtypack’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  Adonnees.f90 -o Adonnees.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  AparamMultive.f90 -o AparamMultive.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  Aparameters.f90 -o Aparameters.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  aGhermite.f90 -o aGhermite.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  ahrmsym.f90 -o ahrmsym.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  funcpajsplinesIndiv.f90 -o funcpajsplinesIndiv.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c init.c -o init.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  risque.f90 -o risque.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  somme.f90 -o somme.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls   -fPIC  -Wall -g -O2  -c  test.f90 -o test.o
funcpajsplinesIndiv.f90:4:8:

     use tailles
        1
Fatal Error: Can't open module file ‘tailles.mod’ for reading at (1): No such file or directory
compilation terminated.
somme.f90:7:47:

     integer:: i,num_thread,num_proc,nb_thread,d
                                               1
Warning: Unused variable ‘d’ declared at (1) [-Wunused-variable]
somme.f90:7:45:

     integer:: i,num_thread,num_proc,nb_thread,d
                                             1
Warning: Unused variable ‘nb_thread’ declared at (1) [-Wunused-variable]
somme.f90:1:31:

 subroutine somme(ab,s,nboot,nbr,vOut)
                               1
Warning: Unused dummy argument ‘nbr’ at (1) [-Wunused-dummy-argument]
somme.f90:7:35:

     integer:: i,num_thread,num_proc,nb_thread,d
                                   1
Warning: Unused variable ‘num_proc’ declared at (1) [-Wunused-variable]
make: *** [funcpajsplinesIndiv.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘frailtypack’
* removing ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/frailtypack/old/frailtypack.Rcheck/frailtypack’

FSK2R

Run revdep_details(,"FSK2R") for more info

In both

  • checking package dependencies ... ERROR 
    Packages required but not available: 'googlesheets', 'readtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

FunChIP

Run revdep_details(,"FunChIP") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

g3viz

Run revdep_details(,"g3viz") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb

GA4GHshiny

Run revdep_details(,"GA4GHshiny") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 12 ]
  1. Error: app works (@test-app.R#5) 
  2. Error: initializeReferences works (@test-initializeReferences.R#6) 
  3. Error: initializeVariantSet works (@test-initializeVariantSet.R#6) 
  4. Error: searchVariantsByGeneSymbol works (@test-searchVariantsByGeneSymbol.R#9) 
  5. Error: searchVariantsByGeneSymbol feature=transcripts works (@test-searchVariantsByGeneSymbol.R#22) 
  6. Error: searchVariantsByGeneSymbol feature=exons works (@test-searchVariantsByGeneSymbol.R#35) 
  7. Error: searchVariantsByGeneSymbol feature=cds works (@test-searchVariantsByGeneSymbol.R#48) 
  8. Error: searchVariantsByGeneSymbol feature=promoters works (@test-searchVariantsByGeneSymbol.R#60) 
  9. Error: searchVariantsByGeneSymbol multiple genes works (@test-searchVariantsByGeneSymbol.R#72) 
  1. ...

  Error: testthat unit tests failed
  Execution halted

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

gamesGA

Run revdep_details(,"gamesGA") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.

gastempt

Run revdep_details(,"gastempt") for more info

In both

  • checking installed package size ... NOTE

      installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

GDCRNATools

Run revdep_details(,"GDCRNATools") for more info

In both

  • checking installed package size ... NOTE

      installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    data   1.1Mb
    doc    2.6Mb

  • checking top-level files ... NOTE

    File
  LICENSE
is not mentioned in the DESCRIPTION file.

  • checking R code for possible problems ... NOTE

    ...
gdcRNAMerge: no visible global function definition for ‘read.table’
gdcRNAMerge : <anonymous>: no visible global function definition for
  ‘read.delim’
gdcRNAMerge: no visible global function definition for ‘read.delim’
hyperTestFun: no visible global function definition for ‘phyper’
kmTestFun: no visible global function definition for ‘pchisq’
kmTestFun: no visible global function definition for ‘qnorm’
manifestDownloadFun: no visible global function definition for
  ‘read.table’
mirCorTestFun: no visible global function definition for ‘cor.test’
multiRegFun: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  Category Counts FDR Regulation Terms URLencode aggregate cor.test
  download.file foldEnrichment model.matrix p.adjust pchisq phyper
  qnorm read.delim read.table unzip write.table
Consider adding
  importFrom("stats", "aggregate", "cor.test", "model.matrix",
             "p.adjust", "pchisq", "phyper", "qnorm")
  importFrom("utils", "URLencode", "download.file", "read.delim",
             "read.table", "unzip", "write.table")
to your NAMESPACE file.

genBart

Run revdep_details(,"genBart") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.

GeneNetworkBuilder

Run revdep_details(,"GeneNetworkBuilder") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data          2.8Mb
    doc           6.5Mb
    htmlwidgets   1.8Mb

GenEst

Run revdep_details(,"GenEst") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.

GeneTonic

Run revdep_details(,"GeneTonic") for more info

In both

  • checking installed package size ... NOTE

      installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc  12.7Mb

  • checking Rd cross-references ... NOTE

    Package unavailable to check Rd xrefs: ‘pcaExplorer’

GenomicScores

Run revdep_details(,"GenomicScores") for more info

In both

  • checking examples ... ERROR

    ...
+   score(gsco, gr1)
+   gscores(gsco, gr2)
+   populations(gsco)
+   gscores(gsco, gr2, pop="DP2")
+ }
Loading required package: phastCons100way.UCSC.hg19
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘phastCons100way.UCSC.hg19’
> 
> ## supporting AnnotationHub resources
> ## Not run: 
> ##D availableGScores()
> ##D gsco <- getGScores("phastCons100way.UCSC.hg19")
> ##D gsco
> ##D gscores(gsco, gr1)
> ## End(Not run)
> 
> ## metadata from a GScores object
> name(gsco)
Error in name(gsco) : object 'gsco' not found
Execution halted

  • checking package dependencies ... NOTE

    Packages suggested but not available for checking:
  'phastCons100way.UCSC.hg19', 'MafDb.1Kgenomes.phase1.hs37d5'

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  inst/gscores-template/inst/extdata/.gitkeep
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking installed package size ... NOTE

      installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   2.8Mb

  • checking Rd cross-references ... NOTE

    Packages unavailable to check Rd xrefs: ‘phastCons100way.UCSC.hg19’, ‘MafDb.1Kgenomes.phase1.hs37d5’

GerminaR

Run revdep_details(,"GerminaR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘assertthat’ ‘shinydashboard’
  All declared Imports should be used.

ggedit

Run revdep_details(,"ggedit") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.

ggExtra

Run revdep_details(,"ggExtra") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.

ggplotAssist

Run revdep_details(,"ggplotAssist") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.

ggquickeda

Run revdep_details(,"ggquickeda") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’
  ‘ggpubr’ ‘ggrepel’ ‘ggstance’ ‘grDevices’ ‘grid’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjqui’
  ‘shinyjs’ ‘survival’ ‘survminer’ ‘table1’ ‘tidyr’
  All declared Imports should be used.

gmDatabase

Run revdep_details(,"gmDatabase") for more info

In both

  • checking whether the package can be unloaded cleanly ... WARNING

    Error: package ‘RMySQL’ could not be loaded
Execution halted

  • checking whether the namespace can be loaded with stated dependencies ... WARNING

    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/gmDatabase/RMySQL/libs/RMySQL.so':
  dlopen(/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/gmDatabase/RMySQL/libs/RMySQL.so, 6): Symbol not found: _GSS_C_NT_USER_NAME
  Referenced from: /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/gmDatabase/RMySQL/libs/RMySQL.so
  Expected in: flat namespace
 in /Users/barret/Documents/git/rstudio/shiny/shiny/revdep/library.noindex/gmDatabase/RMySQL/libs/RMySQL.so
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

  • checking dependencies in R code ... NOTE

    Error: package ‘RMySQL’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted

GmicR

Run revdep_details(,"GmicR") for more info

In both

  • checking DESCRIPTION meta-information ... NOTE

    License components with restrictions not permitted:
  GPL-2 + file LICENSE

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.

  • checking R code for possible problems ... NOTE

    GSEAGO_Builder: no visible binding for global variable ‘ex’
Undefined global functions or variables:
  ex

GOFShiny

Run revdep_details(,"GOFShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.

GPA

Run revdep_details(,"GPA") for more info

In both

  • checking for GNU extensions in Makefiles ... NOTE 
    GNU make is a SystemRequirements.

gQTLstats

Run revdep_details(,"gQTLstats") for more info

In both

  • checking installed package size ... NOTE

      installed size is 65.7Mb
  sub-directories of 1Mb or more:
    data        11.0Mb
    doc          1.1Mb
    registries  18.8Mb
    vcf         33.8Mb

  • checking R code for possible problems ... NOTE

    ...
  ‘permScore_3’
storeToMaxAssocBySNP: no visible global function definition for ‘nth’
storeToMaxAssocBySNP: no visible binding for global variable ‘MAF’
storeToMaxAssocBySNP: no visible binding for global variable ‘probeid’
storeToMaxAssocBySNP: no visible binding for global variable ‘mindist’
tqbrowser: no visible global function definition for ‘experiments’
tqbrowser : server: no visible global function definition for
  ‘experiments’
tqbrowser : server: no visible global function definition for
  ‘TabixFile’
tqbrowser : server: no visible binding for global variable ‘assoc’
tqbrowser : server: no visible binding for global variable ‘stateid’
tqbrowser : server: no visible binding for global variable ‘state’
transTable: no visible binding for global variable ‘i’
tsByRank_sing: no visible binding for global variable ‘i’
tsByRank_sing : <anonymous>: no visible binding for global variable ‘i’
boxswarm,SnpToGeneQTL: no visible binding for global variable ‘g1’
Undefined global functions or variables:
  DNAStringSetList MAF TabixFile TxDb assoc calls ch chisq criterion ex
  exonsBy experiments g1 geom_boxplot gt i id maf mindist ml10fdr nth
  permScore_1 permScore_2 permScore_3 probeid snp state stateid value x

  • checking contents of ‘data’ directory ... NOTE

    Output for data("bigfiltFDR", package = "gQTLstats"):


Output for data("bigrawFDR", package = "gQTLstats"):


Output for data("filtFDR", package = "gQTLstats"):


Output for data("rawFDR", package = "gQTLstats"):


Output for data("sensByProbe", package = "gQTLstats"):

  • checking data for non-ASCII characters ... NOTE

      Note: found 8 marked Latin-1 strings
  Note: found 12 marked UTF-8 strings

gravitas

Run revdep_details(,"gravitas") for more info

In both

  • checking examples ... ERROR

    ...
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(ggplot2)
> library(lvplot)
> # Search for granularities
> smart_meter10 %>%
+   search_gran(highest_unit = "week")
Error in if (tsibble::is_regular(.data)) { : argument is of length zero
Calls: %>% ... freduce -> withVisible -> <Anonymous> -> search_gran
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("gravitas")
  ── 1. Error: norun check runs in create_gran (@test-harmony.R#48)  ─────────────
  argument is of length zero
  Backtrace:
    1. testthat::expect_equal(...)
   10. gravitas::harmony(., ugran = "day", filter_in = "wknd_wday")
   13. gravitas::search_gran(...)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 126 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: norun check runs in create_gran (@test-harmony.R#48) 

  Error: testthat unit tests failed
  Execution halted

gridsampler

Run revdep_details(,"gridsampler") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.

GSCA

Run revdep_details(,"GSCA") for more info

In both

  • checking package dependencies ... NOTE

    Depends: includes the non-default packages:
  'shiny', 'sp', 'gplots', 'ggplot2', 'reshape2', 'RColorBrewer',
  'rhdf5'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

  • checking dependencies in R code ... NOTE

    'library' or 'require' calls in package code:
  ‘Affyhgu133A2Expr’ ‘Affyhgu133Plus2Expr’ ‘Affyhgu133aExpr’
  ‘Affymoe4302Expr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

  • checking R code for possible problems ... NOTE

    ...
GSCAplot: no visible global function definition for ‘title’
GSCAplot: no visible global function definition for ‘dev.off’
annotatePeaks: no visible binding for global variable ‘allreffile’
tabSearch: no visible global function definition for ‘data’
tabSearch: no visible binding for global variable ‘Affyhgu133aExprtab’
tabSearch: no visible binding for global variable ‘Affymoe4302Exprtab’
tabSearch: no visible binding for global variable ‘Affyhgu133A2Exprtab’
tabSearch: no visible binding for global variable
  ‘Affyhgu133Plus2Exprtab’
Undefined global functions or variables:
  Affyhgu133A2Exprtab Affyhgu133Plus2Exprtab Affyhgu133aExprtab
  Affymoe4302Exprtab P.value SampleType Var1 Var2 allreffile
  colorRampPalette data dev.off fisher.test geneid hist par pdf qnorm
  quantile sd str t.stat t.test title value variable write.csv
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "fisher.test", "qnorm", "quantile", "sd", "t.test")
  importFrom("utils", "data", "str", "write.csv", "write.table")
to your NAMESPACE file.

gt

Run revdep_details(,"gt") for more info

In both

  • checking installed package size ... NOTE

      installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   5.5Mb

  • checking data for non-ASCII characters ... NOTE

      Note: found 116 marked UTF-8 strings

gwdegree

Run revdep_details(,"gwdegree") for more info

In both

  • checking R code for possible problems ... NOTE 
    simCCCent : <anonymous>: no visible global function definition for
  ‘simulate.formula’
Undefined global functions or variables:
  simulate.formula

HaDeX

Run revdep_details(,"HaDeX") for more info

In both

  • checking installed package size ... NOTE

      installed size is  5.0Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.

hchinamap

Run revdep_details(,"hchinamap") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb

highcharter

Run revdep_details(,"highcharter") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb

HumanTranscriptomeCompendium

Run revdep_details(,"HumanTranscriptomeCompendium") for more info

In both

  • checking examples ... ERROR

    ...
Running examples in ‘HumanTranscriptomeCompendium-Ex.R’ failed
The error most likely occurred in:

> ### Name: htx_query_by_study_accession
> ### Title: retrieve 'restfulSE' SummarizedExperiment instance for selected
> ###   studies in htx compendium
> ### Aliases: htx_query_by_study_accession
> 
> ### ** Examples
> 
> htx_query_by_study_accession("ERP011411")
acquiring base restfulSE...
adding RDS to local cache, future invocations will use local image
adding rname 'https://s3.amazonaws.com/bcfound-bigrna/rangedHtxGeneSE.rds'
Loading required package: rhdf5client
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rhdf5client’
Error in .requirePackage(package) : 
  unable to find required package ‘rhdf5client’
Calls: htx_query_by_study_accession ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   12. S4Vectors::lapply(X, FUN, ...)
   14. base::lapply(as.list(X), match.fun(FUN), ...)
   15. SummarizedExperiment:::FUN(X[[i]], ...)
   16. methods:::dim(a)
   18. methods:::.findInheritedMethods(classes, fdef, mtable)
   19. methods::getClass(cl1, where = where, .Force = TRUE)
   20. methods::getClassDef(Class, where)
   21. methods:::.requirePackage(package)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: query resolution works (@test_htc.R#42) 

  Error: testthat unit tests failed
  Execution halted

hwordcloud

Run revdep_details(,"hwordcloud") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.

ideal

Run revdep_details(,"ideal") for more info

In both

  • checking R code for possible problems ... NOTE 
    ideal: no visible binding for '<<-' assignment to ‘ideal_env’
ideal : <anonymous>: no visible binding for global variable ‘airway’
ideal : <anonymous>: no visible binding for global variable ‘pvalue’
ideal : <anonymous>: no visible binding for global variable ‘baseMean’
ideal : <anonymous>: no visible binding for global variable ‘ideal_env’
Undefined global functions or variables:
  airway baseMean ideal_env pvalue

idefix

Run revdep_details(,"idefix") for more info

In both

  • checking Rd cross-references ... NOTE 
    Packages unavailable to check Rd xrefs: ‘ChoiceModelR’, ‘RSGHB’

idem

Run revdep_details(,"idem") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

immunarch

Run revdep_details(,"immunarch") for more info

In both

  • checking installed package size ... NOTE

      installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.6Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.

IMWatson

Run revdep_details(,"IMWatson") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.

IncucyteDRC

Run revdep_details(,"IncucyteDRC") for more info

In both

  • checking examples ... ERROR 
    ...
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
     █
  1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
  2.   └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
  3.     └─`%>%`(...)
  4.       ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  7.           └─IncucyteDRC:::`_fseq`(`_lhs`)
  8.             └─magrittr::freduce(value, `_function_list`)
  9.               └─function_list[[i]](value)
 10.                 ├─dplyr::mutate(., idx = row_number())
 11.                 └─dplyr:::mutate.data.frame(., idx = row_number())
 12.                   └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted

INDperform

Run revdep_details(,"INDperform") for more info

In both

  • checking examples ... ERROR

    Running examples in ‘INDperform-Ex.R’ failed
The error most likely occurred in:

> ### Name: merge_models
> ### Title: Merging two model output tibbles.
> ### Aliases: merge_models
> 
> ### ** Examples
> 
> # Using some models of the Baltic Sea demo data:
> # Merging GAM and GAMM tibbles
> test_ids <- 47:50 # choose subset
> gam_tbl <- model_gam_ex[test_ids,]
> gamm_tbl <- model_gamm(ind_init_ex[test_ids,], filter= gam_tbl$tac)
Error in model_gamm(ind_init_ex[test_ids, ], filter = gam_tbl$tac) : 
  No IND~pressure GAMM could be fitted! Check if you chose the correct error distribution (default is gaussian()).
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   4. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   5. base::tryCatch(...)
   6. base:::tryCatchList(expr, classes, parentenv, handlers)
   7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8. value[[3L]](cond)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 475 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 4 ]
  1. Error: (unknown) (@test_calc_deriv.R#6) 
  2. Error: (unknown) (@test_cond_boot.R#112) 
  3. Error: (unknown) (@test_model_gamm.R#4) 
  4. Error: (unknown) (@test_scoring.R#15) 

  Error: testthat unit tests failed
  Execution halted

  • checking installed package size ... NOTE

      installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    help   1.6Mb

inlabru

Run revdep_details(,"inlabru") for more info

In both

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘INLA’

  • checking Rd cross-references ... NOTE

    Package unavailable to check Rd xrefs: ‘INLA’

INSPEcT

Run revdep_details(,"INSPEcT") for more info

In both

  • checking installed package size ... NOTE

      installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.8Mb
    doc    3.5Mb

  • checking R code for possible problems ... NOTE

    output_pars: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  plot.new
Consider adding
  importFrom("graphics", "plot.new")
to your NAMESPACE file.

interactiveDisplay

Run revdep_details(,"interactiveDisplay") for more info

In both

  • checking dependencies in R code ... WARNING

    '::' or ':::' import not declared from: ‘.interactiveDisplayBase’

  • checking package dependencies ... NOTE

    Package which this enhances but not available for checking: ‘rstudio’

  • checking R code for possible problems ... NOTE

    ...
  for global variable ‘Var1’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable ‘Var2’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable ‘value’
Undefined global functions or variables:
  AnnotationTrack GO.db GRanges GRangesList GenomeAxisTrack IRanges
  IdeogramTrack MRcounts Var1 Var2 as.dendrogram assays cim
  colorRampPalette coord_flip cutree dendrapply dev.off dist
  elementMetadata experimentData exprs fData hclust installed.packages
  is.leaf layout_circle legend libSize mcols pData plotFeature plotOrd
  plotTracks png rainbow ranges rowRanges seqlengths seqlengths<-
  seqlevels<- seqnames ucscGenomes value
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png",
             "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "as.dendrogram", "cutree", "dendrapply", "dist",
             "hclust", "is.leaf")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.

interAdapt

Run revdep_details(,"interAdapt") for more info

In both

  • checking DESCRIPTION meta-information ... NOTE

    Malformed Description field: should contain one or more complete sentences.

  • checking R code for possible problems ... NOTE

    ...
compute_design_performance : expected_duration_plot: no visible global
  function definition for ‘legend’
compute_design_performance : boundary_adapt_plot: no visible global
  function definition for ‘matplot’
compute_design_performance : boundary_adapt_plot: no visible global
  function definition for ‘legend’
compute_design_performance : boundary_standard_H0C_plot: no visible
  global function definition for ‘matplot’
compute_design_performance : boundary_standard_H0C_plot: no visible
  global function definition for ‘legend’
compute_design_performance : boundary_standard_H01_plot: no visible
  global function definition for ‘matplot’
compute_design_performance : boundary_standard_H01_plot: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  legend lines matplot read.csv rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "matplot")
  importFrom("stats", "rnorm")
  importFrom("utils", "read.csv")
to your NAMESPACE file.

IOHanalyzer

Run revdep_details(,"IOHanalyzer") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘reshape2’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.

  • checking data for non-ASCII characters ... NOTE

      Note: found 75 marked UTF-8 strings

iSEE

Run revdep_details(,"iSEE") for more info

In both

  • checking examples ... ERROR

    ...
+   return(qc_colors)
+ }
> 
> ecm <- ExperimentColorMap(
+     assays = list(
+         tophat_counts = count_colors
+     ),
+     colData = list(
+         passes_qc_checks_s = qc_color_fun
+     )
+ )
> 
> # Example SingleCellExperiment ----
> 
> library(scRNAseq)
> sce <- ReprocessedAllenData(assays="tophat_counts")
Error: Corrupt Cache: sqlite file
  See vignette section on corrupt cache
  cache: /Users/barret/Library/Caches/ExperimentHub
  filename: experimenthub.sqlite3
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  The following objects are masked from 'package:base':

      aperm, apply, rowsum

  Loading required package: SingleCellExperiment
  > 
  > test_check("iSEE")
  Loading required package: scRNAseq
  Loading required package: scater
  Loading required package: ggplot2
  Error: Corrupt Cache: sqlite file
    See vignette section on corrupt cache
    cache: /Users/barret/Library/Caches/ExperimentHub
    filename: experimenthub.sqlite3
  Execution halted

  • checking installed package size ... NOTE

      installed size is 26.3Mb
  sub-directories of 1Mb or more:
    doc  24.6Mb

  • checking dependencies in R code ... NOTE

    Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.

iSEEu

Run revdep_details(,"iSEEu") for more info

In both

  • checking examples ... ERROR

    ...
> ###   .panelColor,DifferentialStatisticsTable-method
> ###   .defineDataInterface,DifferentialStatisticsTable-method
> ###   .hideInterface,DifferentialStatisticsTable-method
> ###   .generateTable,DifferentialStatisticsTable-method
> ###   .createObservers,DifferentialStatisticsTable-method
> ###   .cacheCommonInfo,DifferentialStatisticsTable-method
> ###   .refineParameters,DifferentialStatisticsTable-method
> ###   .multiSelectionInvalidated,DifferentialStatisticsTable-method
> 
> ### ** Examples
> 
> library(scRNAseq)
> library(scater)
Loading required package: ggplot2
> 
> sce <- ReprocessedAllenData(assays="tophat_counts")
Error: Corrupt Cache: sqlite file
  See vignette section on corrupt cache
  cache: /Users/barret/Library/Caches/ExperimentHub
  filename: experimenthub.sqlite3
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:

      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

  The following objects are masked from 'package:base':

      aperm, apply, rowsum

  Loading required package: SingleCellExperiment
  > 
  > test_check("iSEEu")
  Error: Corrupt Cache: sqlite file
    See vignette section on corrupt cache
    cache: /Users/barret/Library/Caches/ExperimentHub
    filename: experimenthub.sqlite3
  Execution halted

iSTATS

Run revdep_details(,"iSTATS") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb

ivygapSE

Run revdep_details(,"ivygapSE") for more info

In both

  • checking installed package size ... NOTE

      installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data  13.9Mb
    doc    2.4Mb

  • checking R code for possible problems ... NOTE

    exprByType: no visible binding for global variable ‘ivySE’
ivyGlimpse: no visible binding for global variable ‘ivySE’
ivyGlimpse : server: no visible binding for global variable ‘ivySE’
Undefined global functions or variables:
  ivySE

jpmesh

Run revdep_details(,"jpmesh") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 176 marked UTF-8 strings

jpndistrict

Run revdep_details(,"jpndistrict") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 188 marked UTF-8 strings

jsmodule

Run revdep_details(,"jsmodule") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘Cairo’ ‘survC1’
  All declared Imports should be used.

KNNShiny

Run revdep_details(,"KNNShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.

kokudosuuchi

Run revdep_details(,"kokudosuuchi") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 52458 marked UTF-8 strings

koRpus

Run revdep_details(,"koRpus") for more info

In both

  • checking package dependencies ... NOTE 
    Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’

leaflet.extras2

Run revdep_details(,"leaflet.extras2") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.

learnstats

Run revdep_details(,"learnstats") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
qqsim: no visible global function definition for ‘hist’
qqsim: no visible global function definition for ‘mtext’
qqsim: no visible global function definition for ‘jpeg’
qqsim: no visible global function definition for ‘dev.off’
timeseressim: no visible global function definition for ‘rnorm’
timeseressim: no visible global function definition for ‘par’
timeseressim: no visible global function definition for ‘mtext’
timeseressim: no visible global function definition for ‘jpeg’
timeseressim: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  axis dchisq dev.off dnorm dt hist jpeg legend mtext par pchisq pf
  pnorm polygon pt qchisq qf qqline qqnorm qt rchisq rnorm rt runif
  segments title
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "axis", "hist", "legend", "mtext", "par",
             "polygon", "segments", "title")
  importFrom("stats", "dchisq", "dnorm", "dt", "pchisq", "pf", "pnorm",
             "pt", "qchisq", "qf", "qqline", "qqnorm", "qt", "rchisq",
             "rnorm", "rt", "runif")
to your NAMESPACE file.

levi

Run revdep_details(,"levi") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.

  • checking R code for possible problems ... NOTE

    LEVIui: no visible global function definition for ‘is’
levi_function: no visible binding for global variable ‘x’
Undefined global functions or variables:
  is x
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

likert

Run revdep_details(,"likert") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 7 marked UTF-8 strings

live

Run revdep_details(,"live") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.

lmviz

Run revdep_details(,"lmviz") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.

mapdeck

Run revdep_details(,"mapdeck") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   1.9Mb
    libs          2.9Mb

mapedit

Run revdep_details(,"mapedit") for more info

In both

  • checking package dependencies ... NOTE 
    Package which this enhances but not available for checking: ‘geojsonio’

MDSPCAShiny

Run revdep_details(,"MDSPCAShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.

memapp

Run revdep_details(,"memapp") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.

memery

Run revdep_details(,"memery") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.

meta4diag

Run revdep_details(,"meta4diag") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘INLA’

MetCirc

Run revdep_details(,"MetCirc") for more info

In both

  • checking dependencies in R code ... NOTE

    Unexported objects imported by ':::' calls:
  ‘MSnbase:::bin_Spectra’ ‘circlize:::get.sector.data’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘recordPlotFill_degreeFeatures’ ‘recordPlotHighlight’ ‘replayPlotAdd’
  ‘replayPlotOrder’ ‘select’ ‘spectraCond’ ‘typeMatch_link0’

  • checking R code for possible problems ... NOTE

    plotSpectra: no visible binding for global variable ‘mz’
plotSpectra: no visible binding for global variable ‘int’
Undefined global functions or variables:
  int mz

MethylAid

Run revdep_details(,"MethylAid") for more info

In both

  • checking examples ... ERROR

    Running examples in ‘MethylAid-Ex.R’ failed
The error most likely occurred in:

> ### Name: summarize
> ### Title: summarization of Illumina Human DNA Methylation array data
> ### Aliases: summarize
> 
> ### ** Examples
> 
> library(minfiData)
Error in library(minfiData) : there is no package called ‘minfiData’
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  ERROR in test_summarize: Error in library(minfiData) : there is no package called 'minfiData'
  ERROR in test_visualize: Error in library(minfiData) : there is no package called 'minfiData'

  Test files with failing tests

     test_summarize.R 
       test_summarize 

     test_visualize.R 
       test_visualize 


  Error in BiocGenerics:::testPackage("MethylAid") : 
    unit tests failed for package MethylAid
  Execution halted

  • checking package dependencies ... NOTE

    Packages suggested but not available for checking:
  'MethylAidData', 'minfiData'

methylGSA

Run revdep_details(,"methylGSA") for more info

In both

  • checking R code for possible problems ... NOTE 
    getAnnot: no visible global function definition for ‘getAnnotation’
getAnnot: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
getAnnot: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
Undefined global functions or variables:
  IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylationEPICanno.ilm10b4.hg19 getAnnotation

mgcViz

Run revdep_details(,"mgcViz") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb

microhaplot

Run revdep_details(,"microhaplot") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.

miniMeta

Run revdep_details(,"miniMeta") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.

miRcomp

Run revdep_details(,"miRcomp") for more info

In both

  • checking data for ASCII and uncompressed saves ... WARNING 
    
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                  old_size new_size compress
  lifetech.rda       350Kb    276Kb       xz
  qpcRb4.rda         290Kb    243Kb       xz
  qpcRb5.rda         288Kb    242Kb       xz
  qpcRdefault.rda    290Kb    242Kb       xz
  qpcRl5.rda         287Kb    239Kb       xz
  qpcRlinexp.rda     235Kb    199Kb       xz

MLDAShiny

Run revdep_details(,"MLDAShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.

MLInterfaces

Run revdep_details(,"MLInterfaces") for more info

In both

  • checking package dependencies ... NOTE

    Package which this enhances but not available for checking: ‘rda’

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘fpc’ ‘gbm’ ‘ggvis’ ‘hwriter’ ‘mlbench’ ‘pls’ ‘shiny’ ‘stats4’
  ‘threejs’ ‘tools’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘BiocGenerics’ ‘Rcpp’ ‘annotate’ ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘MASS:::predict.lda’ ‘ada:::predict.ada’ ‘e1071:::predict.svm’
  ‘rpart:::predict.rpart’ ‘stats:::plot.hclust’
  See the note in ?`:::` about the use of this operator.

  • checking S3 generic/method consistency ... NOTE

    Found the following apparent S3 methods exported but not registered:
  predict.RAB predict.classifierOutput predict.dlda2 predict.gbm2
  predict.knn.cv2 predict.knn2 predict.lvq predict.rdaML
  predict.rdacvML print.rdaML print.rdacvML
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

  • checking R code for possible problems ... NOTE

    ...
plspinHcube : <anonymous>: no visible global function definition for
  ‘points3d’
predict.classifierOutput: no visible global function definition for
  ‘exprs’
predict.gbm2: no visible global function definition for ‘predict.gbm’
rab: no visible global function definition for ‘rpart’
getGrid,ExpressionSet: no visible global function definition for
  ‘exprs’
planarPlot,classifierOutput-ExpressionSet-character: no visible global
  function definition for ‘exprs’
predScore,classifierOutput: no visible global function definition for
  ‘rowMax’
Undefined global functions or variables:
  %>% := abstract actionButton add_tooltip annotation bind_shiny br
  brewer.pal clusterboot column div em exprs featureNames fluidPage
  fluidRow gbm ggvis ggvisOutput h1 hclustCBI htmlOutput hwrite isolate
  key layer_points lookUp mainPanel mlbench.hypercube numericInput
  observe p pData plotOutput plotcp points3d predict.gbm reactive
  renderPlot renderScatterplotThree renderTable renderText rowMax rpart
  scatterplot3js scatterplotThreeOutput selectInput shinyApp
  sidebarLayout sidebarPanel stopApp strong tableOutput textOutput

  • checking Rd files ... NOTE

    prepare_Rd: plspinHcube.Rd:17-19: Dropping empty section \details

mlr3shiny

Run revdep_details(,"mlr3shiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.

MLRShiny

Run revdep_details(,"MLRShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.

MLRShiny2

Run revdep_details(,"MLRShiny2") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.

MMDiff2

Run revdep_details(,"MMDiff2") for more info

In both

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm9’

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.

  • checking R code for possible problems ... NOTE

    DBAmmd: no visible global function definition for ‘new’
getReads: no visible global function definition for ‘IRangesList’
Undefined global functions or variables:
  IRangesList new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

MNLR

Run revdep_details(,"MNLR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.

MSEtool

Run revdep_details(,"MSEtool") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  15.9Mb

MSGFgui

Run revdep_details(,"MSGFgui") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘MSGFplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

MSnbase

Run revdep_details(,"MSnbase") for more info

In both

  • checking installed package size ... NOTE

      installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.9Mb
    doc    7.7Mb

  • checking DESCRIPTION meta-information ... NOTE

    Authors@R field gives more than one person with maintainer role:
  Laurent Gatto <laurent.gatto@uclouvain.be> [aut, cre] (<https://orcid.org/0000-0002-1520-2268>)
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] (<https://orcid.org/0000-0002-6977-7147>)
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]

  • checking dependencies in R code ... NOTE

    ':::' call which should be '::': ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
  ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
  ‘MALDIquant:::.savitzkyGolay’
  ‘S4Vectors:::makeClassinfoRowForCompactPrinting’
  ‘mzR:::.hasChromatograms’ ‘mzR:::.hasSpectra’
  See the note in ?`:::` about the use of this operator.

mstrio

Run revdep_details(,"mstrio") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.

MuChPoint

Run revdep_details(,"MuChPoint") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.

nbc4va

Run revdep_details(,"nbc4va") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 4. Error: nbc() can handle incorrect column data types in the correct positio
  The train data IDs are not unique (duplicates found:)
  Backtrace:
   1. testthat::expect_warning(...)
   6. nbc4va:::internalCheckNBC(trainTypes, testTypes)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 68 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
  1. Failure: (unknown) (@test_nbc4va.R#29) 
  2. Failure: (unknown) (@test_nbc4va.R#32) 
  3. Failure: nbc() sets the out$test.known to correctly indicate whether or not the test causes are known (@test_nbc4va.R#46) 
  4. Error: nbc() can handle incorrect column data types in the correct positions (@test_nbc4va.R#67) 

  Error: testthat unit tests failed
  Execution halted

  • checking package dependencies ... NOTE

    Package which this enhances but not available for checking: ‘openVA’

NBShiny

Run revdep_details(,"NBShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.

NBShiny2

Run revdep_details(,"NBShiny2") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.

NDP

  • Version: 0.1.0
  • Source code: https://github.com/cran/NDP
  • Date/Publication: 2019-03-30 15:00:02 UTC
  • Number of recursive dependencies: 29

Run revdep_details(,"NDP") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.

neo4r

Run revdep_details(,"neo4r") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.

nprcgenekeepr

Run revdep_details(,"nprcgenekeepr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.

oceanis

Run revdep_details(,"oceanis") for more info

In both

  • checking installed package size ... NOTE

      installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.9Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.

omicplotR

Run revdep_details(,"omicplotR") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    Package in Depends field not imported from: ‘ALDEx2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

oneSENSE

Run revdep_details(,"oneSENSE") for more info

In both

  • checking examples ... WARNING

    Found the following significant warnings:

  Warning: 'export' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.

  • checking top-level files ... NOTE

    File
  LICENSE
is not mentioned in the DESCRIPTION file.

ontoProc

Run revdep_details(,"ontoProc") for more info

In both

  • checking examples ... ERROR

    ...
> ### Name: common_classes
> ### Title: list and count samples with common ontological annotation in two
> ###   SEs
> ### Aliases: common_classes
> 
> ### ** Examples
> 
> if (requireNamespace("SingleR")) {
+   imm = SingleR::ImmGenData()
+   if ("label.ont" %in% names(colData(imm))) {
+     cl = getCellOnto()
+     blu = SingleR::BlueprintEncodeData()
+     common_classes( cl, imm, blu )
+     }
+   }
Loading required namespace: SingleR
Error: Corrupt Cache: sqlite file
  See vignette section on corrupt cache
  cache: /Users/barret/Library/Caches/ExperimentHub
  filename: experimenthub.sqlite3
Execution halted

  • checking installed package size ... NOTE

      installed size is 39.6Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      2.0Mb
    doc       1.8Mb
    ontoRda  33.5Mb

  • checking R code for possible problems ... NOTE

    CLfeat : prupdate: no visible binding for global variable ‘PRID’
CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’
bind_formal_tags: no visible global function definition for ‘colData’
bind_formal_tags: no visible global function definition for ‘colData<-’
common_classes: no visible global function definition for ‘colData’
connect_classes: no visible global function definition for ‘colData’
ctmarks: no visible binding for '<<-' assignment to ‘pr’
ctmarks: no visible binding for '<<-' assignment to ‘go’
ctmarks : server: no visible binding for global variable ‘text’
cyclicSigset: no visible binding for global variable ‘sigels’
ldfToTerm: no visible binding for global variable ‘PROSYM’
subset_descendants: no visible global function definition for ‘colData’
sym2CellOnto: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  PRID PROSYM SYMBOL colData colData<- sigels text
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.

  • checking data for non-ASCII characters ... NOTE

      Note: found 162 marked UTF-8 strings

oolong

Run revdep_details(,"oolong") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘R6’ ‘digest’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.

openmetrics

Run revdep_details(,"openmetrics") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.

openPrimeRui

Run revdep_details(,"openPrimeRui") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    Package in Depends field not imported from: ‘openPrimeR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

oppr

Run revdep_details(,"oppr") for more info

In both

  • checking package dependencies ... NOTE 
    Packages suggested but not available for checking: 'gurobi', 'Rsymphony'

pairsD3

Run revdep_details(,"pairsD3") for more info

In both

  • checking R code for possible problems ... NOTE 
    pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.

PanVizGenerator

Run revdep_details(,"PanVizGenerator") for more info

In both

  • checking for hidden files and directories ... NOTE 
    Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

PathoStat

Run revdep_details(,"PathoStat") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘ComplexHeatmap’ ‘RColorBrewer’
  All declared Imports should be used.

pcaExplorer

Run revdep_details(,"pcaExplorer") for more info

In both

  • checking installed package size ... NOTE

      installed size is 21.3Mb
  sub-directories of 1Mb or more:
    doc  20.1Mb

  • checking R code for possible problems ... NOTE

    pcaExplorer: no visible binding for '<<-' assignment to
  ‘pcaexplorer_env’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘airway’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘pcaexplorer_env’
Undefined global functions or variables:
  airway pcaexplorer_env

pcFactorStan

Run revdep_details(,"pcFactorStan") for more info

In both

  • checking installed package size ... NOTE

      installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   9.7Mb

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

pepStat

Run revdep_details(,"pepStat") for more info

In both

  • checking DESCRIPTION meta-information ... NOTE

    Malformed Description field: should contain one or more complete sentences.

  • checking whether the namespace can be loaded with stated dependencies ... NOTE

    Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

  • checking R code for possible problems ... NOTE

    ...
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
end,peptideSet: no visible global function definition for ‘end’
position,peptideSet: no visible global function definition for ‘start’
position,peptideSet: no visible global function definition for ‘end’
start,peptideSet: no visible global function definition for ‘start’
write.pSet,peptideSet: no visible global function definition for
  ‘start’
write.pSet,peptideSet: no visible global function definition for ‘end’
write.pSet,peptideSet: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  annotation dev.flush dev.hold dev.interactive devAskNewPage end
  lm.fit lm.wfit mcols mcols<- median read.csv sd start write.csv
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive",
             "devAskNewPage")
  importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd",
             "start")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.

phenocamr

Run revdep_details(,"phenocamr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.

piano

Run revdep_details(,"piano") for more info

In both

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘rsbml’

  • checking Rd cross-references ... NOTE

    Packages unavailable to check Rd xrefs: ‘PGSEA’, ‘samr’, ‘GSA’
Unknown package ‘HTSanalyzeR’ in Rd xrefs

pitchRx

Run revdep_details(,"pitchRx") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘ggsubplot’

pivottabler

Run revdep_details(,"pivottabler") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.0Mb

plethem

Run revdep_details(,"plethem") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  You are now using PLETHEM.
                          If you have installed PLETHEM for the first time or have just updated it, please run setUserDb() to select an existing database or createUserDb() to create a new one.
  > 
  > test_check("plethem")
  ── 1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19)
  invalid 'type' (list) of argument
  Backtrace:
   1. plethem::getLifecourseTissueVolumes(...)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19) 

  Error: testthat unit tests failed
  Execution halted

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘V8’ ‘devtools’ ‘formatR’ ‘gdata’ ‘rhandsontable’ ‘shinythemes’
  ‘sqldf’
  All declared Imports should be used.

plotGrouper

Run revdep_details(,"plotGrouper") for more info

In both

  • checking R code for possible problems ... NOTE 
    gplot: no visible binding for global variable ‘max_value’
gplot: no visible binding for global variable ‘max_error’
Undefined global functions or variables:
  max_error max_value

plotly

Run revdep_details(,"plotly") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  6.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb

pmd

Run revdep_details(,"pmd") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 62 marked UTF-8 strings

pogos

Run revdep_details(,"pogos") for more info

In both

  • checking R code for possible problems ... NOTE 
    compoundsByCell: no visible binding for global variable ‘cell_lines_v1’
compoundsByCell: no visible binding for global variable ‘compounds_v1’
compoundsByCell: no visible binding for global variable ‘datasets_v1’
lkc: no visible binding for global variable ‘cell_lines_v1’
lkc: no visible binding for global variable ‘compounds_v1’
lkc: no visible binding for global variable ‘datasets_v1’
plot,DRProfSet-missing: no visible binding for global variable ‘dose’
plot,DRProfSet-missing: no visible binding for global variable
  ‘response’
plot,DRProfSet-missing: no visible binding for global variable ‘drug’
plot,DRTraceSet-missing: no visible binding for global variable ‘dose’
plot,DRTraceSet-missing: no visible binding for global variable
  ‘response’
plot,DRTraceSet-missing: no visible binding for global variable
  ‘cell_line’
Undefined global functions or variables:
  cell_line cell_lines_v1 compounds_v1 datasets_v1 dose drug response

polaroid

Run revdep_details(,"polaroid") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.

polmineR

Run revdep_details(,"polmineR") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.9Mb

precisely

Run revdep_details(,"precisely") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.

PrecisionTrialDrawer

Run revdep_details(,"PrecisionTrialDrawer") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘LowMACAAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

predictoR

Run revdep_details(,"predictoR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.

PREPShiny

Run revdep_details(,"PREPShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.

primirTSS

Run revdep_details(,"primirTSS") for more info

In both

  • checking dependencies in R code ... WARNING

    '::' or ':::' import not declared from: 'magrittr'

  • checking R code for possible problems ... NOTE

    ...
plot_primiRNA_track: no visible binding for global variable
  ‘symbol_name’
plot_primiRNA_track: no visible binding for global variable
  ‘stem_loop_p1’
plot_primiRNA_track: no visible binding for global variable
  ‘stem_loop_p2’
plot_primiRNA_track: no visible binding for global variable ‘gene_id’
plot_primiRNA_track: no visible binding for global variable ‘gene_p1’
plot_primiRNA_track: no visible binding for global variable ‘gene_p2’
plot_primiRNA_track: no visible binding for global variable ‘tss_p1’
plot_primiRNA_track: no visible binding for global variable ‘tss_p2’
require_fa: no visible binding for global variable ‘arrow’
tss_filter: no visible binding for global variable ‘gene_id’
tss_filter: no visible binding for global variable ‘new_info’
tss_filter: no visible binding for global variable ‘predicted_tss’
tss_filter: no visible binding for global variable ‘tss_type’
Undefined global functions or variables:
  TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank
  gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci
  mir_name new_info phast_rank predicted_tss previous seqname start1
  stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type

prioritizr

Run revdep_details(,"prioritizr") for more info

In both

  • checking package dependencies ... NOTE

    Packages suggested but not available for checking: 'gurobi', 'Rsymphony'

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘exactextractr’
  All declared Imports should be used.

PROBShiny

Run revdep_details(,"PROBShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.

processanimateR

Run revdep_details(,"processanimateR") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb

psichomics

Run revdep_details(,"psichomics") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.2Mb

pwrEWAS

Run revdep_details(,"pwrEWAS") for more info

In both

  • checking examples ... ERROR

    ...
> 
> ### ** Examples
> 
> outDelta <- pwrEWAS(minTotSampleSize = 10,
+     maxTotSampleSize = 20,
+     SampleSizeSteps = 10,
+     NcntPer = 0.5,
+     targetDelta = c(0.2, 0.5),
+     J = 1000,
+     targetDmCpGs = 10,
+     tissueType = "Adult (PBMC)",
+     detectionLimit = 0.01,
+     DMmethod = "limma",
+     FDRcritVal = 0.05,
+     core = 2,
+     sims = 30)
Error: Corrupt Cache: sqlite file
  See vignette section on corrupt cache
  cache: /Users/barret/Library/Caches/ExperimentHub
  filename: experimenthub.sqlite3
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  pwrEWAS RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_pwrEWAS: Error : Corrupt Cache: sqlite file
    See vignette section on corrupt cache
    cache: /Users/barret/Library/Caches/ExperimentHub
    filename: experimenthub.sqlite3

  Test files with failing tests

     test_pwrEWAS.R 
       test_pwrEWAS 


  Error in BiocGenerics:::testPackage("pwrEWAS") : 
    unit tests failed for package pwrEWAS
  Execution halted

QCA

  • Version: 3.8.2
  • Source code: https://github.com/cran/QCA
  • Date/Publication: 2020-06-03 06:30:09 UTC
  • Number of recursive dependencies: 20

Run revdep_details(,"QCA") for more info

In both

  • checking installed package size ... NOTE

      installed size is  6.3Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

qlcData

Run revdep_details(,"qlcData") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 1459 marked UTF-8 strings

qqplotr

Run revdep_details(,"qqplotr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.

questionr

Run revdep_details(,"questionr") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘haven’
  All declared Imports should be used.

  • checking data for non-ASCII characters ... NOTE

      Note: found 4145 marked UTF-8 strings

R3CPET

Run revdep_details(,"R3CPET") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘clues’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

RagGrid

Run revdep_details(,"RagGrid") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.

rAmCharts

Run revdep_details(,"rAmCharts") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 11.8Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.0Mb

rangeModelMetadata

Run revdep_details(,"rangeModelMetadata") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.

rapbase

Run revdep_details(,"rapbase") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.

Rariant

Run revdep_details(,"Rariant") for more info

In both

  • checking whether package ‘Rariant’ can be installed ... ERROR 
    Installation failed.
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/Rariant/new/Rariant.Rcheck/00install.out’ for details.

Installation

Devel

* installing *source* package ‘Rariant’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object 'rbind_all' is not exported by 'namespace:dplyr'
Execution halted
ERROR: lazy loading failed for package ‘Rariant’
* removing ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/Rariant/new/Rariant.Rcheck/Rariant’

CRAN

* installing *source* package ‘Rariant’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object 'rbind_all' is not exported by 'namespace:dplyr'
Execution halted
ERROR: lazy loading failed for package ‘Rariant’
* removing ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/Rariant/old/Rariant.Rcheck/Rariant’

rcellminer

Run revdep_details(,"rcellminer") for more info

In both

  • checking data for non-ASCII characters ... WARNING

      Error loading dataset 'fingerprintList':
   Error in .requirePackage(package) : 
    unable to find required package 'fingerprint'

  The dataset(s) may use package(s) not declared in the DESCRIPTION file.

  • checking installed package size ... NOTE

      installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    5.9Mb

  • checking whether the namespace can be loaded with stated dependencies ... NOTE

    Warning: no function found corresponding to methods exports from ‘rcellminer’ for: ‘initialize’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

  • checking R code for possible problems ... NOTE

    plotCellMiner: no visible global function definition for ‘par’
plotCellMiner: no visible global function definition for ‘layout’
plotCellMiner: no visible global function definition for ‘lcm’
plotCellMiner: no visible global function definition for ‘axis’
plotDrugSets: no visible global function definition for ‘par’
plotDrugSets: no visible global function definition for ‘axis’
plotDrugSets: no visible global function definition for ‘segments’
Undefined global functions or variables:
  axis layout lcm par segments
Consider adding
  importFrom("graphics", "axis", "layout", "lcm", "par", "segments")
to your NAMESPACE file.

rCGH

Run revdep_details(,"rCGH") for more info

In both

  • checking installed package size ... NOTE

      installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    extdata   1.2Mb

  • checking files in ‘vignettes’ ... NOTE

    The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.

Rcwl

Run revdep_details(,"Rcwl") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(yaml)
  > test_check("Rcwl")
  ── 1. Error: extensions (@test_all.R#94)  ──────────────────────────────────────
  invalid 'description' argument
  Backtrace:
   1. testthat::expect_true(all(ext %in% read_yaml(cwlfile)))
   5. yaml::read_yaml(cwlfile)
   6. base::file(file, "rt", encoding = fileEncoding)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 16 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: extensions (@test_all.R#94) 

  Error: testthat unit tests failed
  Execution halted

  • checking S3 generic/method consistency ... WARNING

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

  • checking replacement functions ... WARNING

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

  • checking for missing documentation entries ... WARNING

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

  • checking for code/documentation mismatches ... WARNING

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
/usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
/usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)

  • checking foreign function calls ... NOTE

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

  • checking R code for possible problems ... NOTE

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)

  • checking Rd \usage sections ... NOTE

    /usr/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

rddapp

Run revdep_details(,"rddapp") for more info

In both

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:

  Attaching package: 'zoo'

  The following objects are masked from 'package:base':

      as.Date, as.Date.numeric

  Loading required package: AER
  Loading required package: car
  Loading required package: carData
  Loading required package: survival
  Loading required package: Formula
  > library(rddtools)
  Error in library(rddtools) : there is no package called 'rddtools'
  Execution halted

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘rddtools’

  • checking Rd cross-references ... NOTE

    Unknown package ‘rddtools’ in Rd xrefs

recmap

Run revdep_details(,"recmap") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 1036 marked UTF-8 strings

ReDaMoR

Run revdep_details(,"ReDaMoR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.

RefNet

Run revdep_details(,"RefNet") for more info

In both

  • checking whether package ‘RefNet’ can be installed ... WARNING 
    Found the following significant warnings:
  Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/RefNet/new/RefNet.Rcheck/00install.out’ for details.

regressoR

Run revdep_details(,"regressoR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘ROCR’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’ ‘gbm’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘rattle’ ‘rpart’ ‘shinyWidgets’
  ‘shinydashboardPlus’ ‘shinyjs’ ‘xgboost’ ‘zip’
  All declared Imports should be used.

ReportingTools

Run revdep_details(,"ReportingTools") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
  'fData'
.marrayLM.to.html: no visible global function definition for
  'featureNames'
.marrayLM.to.html: no visible global function definition for 'fData'
check.ids: no visible binding for global variable 'org.Hs.eg.db'
check.ids: no visible global function definition for 'keys'
custHeaderPanel : <anonymous>: no visible binding for global variable
  'tags'
custHeaderPanel : <anonymous>: no visible global function definition
  for 'HTML'
custHeaderPanel: no visible global function definition for 'tagList'
custHeaderPanel: no visible global function definition for 'tag'
custHeaderPanel: no visible global function definition for 'div'
custHeaderPanel: no visible global function definition for 'h1'
publish,trellis-HTMLReport: no visible binding for global variable
  'htmlRep'
toReportDF,DESeqDataSet: no visible global function definition for
  'mcols'
Undefined global functions or variables:
  HTML columns description div exprs fData featureNames h1 htmlRep keys
  keytype mcols org.Hs.eg.db tag tagList tags

reverseR

Run revdep_details(,"reverseR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.

RforProteomics

Run revdep_details(,"RforProteomics") for more info

Newly broken

  • checking R code for possible problems ... NOTE 
    shinyMA: possible error in plotOutput("plotma", clickId =
  "plotma_click", width = 400, height = 400): unused argument (clickId
  = "plotma_click")

In both

  • checking whether package ‘RforProteomics’ can be installed ... WARNING

    Found the following significant warnings:
  Note: possible error in 'plotOutput("plotma", ': unused argument (clickId = "plotma_click") 
  Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/RforProteomics/new/RforProteomics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.

  • checking package dependencies ... NOTE

    Packages suggested but not available for checking: 'xcms', 'IPPD'

  • checking installed package size ... NOTE

      installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb

Rfssa

Run revdep_details(,"Rfssa") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.

rgl

Run revdep_details(,"rgl") for more info

In both

  • checking installed package size ... NOTE

      installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb

  • checking Rd cross-references ... NOTE

    Package unavailable to check Rd xrefs: ‘heplots’

rhandsontable

Run revdep_details(,"rhandsontable") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb

RLumShiny

Run revdep_details(,"RLumShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.

rmarkdown

Run revdep_details(,"rmarkdown") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb

rmd

Run revdep_details(,"rmd") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.

RnBeads

Run revdep_details(,"RnBeads") for more info

In both

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’

Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
  'ff', 'fields', 'ggplot2', 'gplots', 'gridExtra', 'limma',
  'matrixStats', 'illuminaio', 'methylumi', 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking installed package size ... NOTE

      installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R     4.1Mb
    doc   3.7Mb

  • checking DESCRIPTION meta-information ... NOTE

    Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qvalue’
A package should be listed in only one of these fields.

  • checking whether the namespace can be loaded with stated dependencies ... NOTE

    Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

  • checking dependencies in R code ... NOTE

    Unexported objects imported by ':::' calls:
  'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
  'grDevices:::.smoothScatterCalcDensity'
  'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
  'minfi:::.normalizeFunnorm450k'
  See the note in ?`:::` about the use of this operator.

  • checking R code for possible problems ... NOTE

    ...
  Measure Mmusculus PairsBootRefFreeEwasModel Predicted Probe
  RGChannelSet Rd2HTML RefFreeEwasModel SNP Sample Segment Slide Target
  Term UcscTrack Value addSex as.profileCGH assayDataElement
  assayDataElementNames barcode browserSession bv calculateFDRs chrom
  combinedRank combinedRank.var comma covgMedian covgPercLow covgPercUp
  cv.glmnet daglad diffmeth diffmeth.p.adj.fdr diffmeth.p.val
  dinucleotideFrequency eps expectedCounts featureData featureData<-
  featureNames featureNames<- foreach geneCounts genome<- getCN
  getDoParWorkers getGreen getManifest getMeth getRed getSex getTable
  getUnmeth getVarCov glmnet grid.draw grid.newpage group group1 group2
  i impute.knn is.subsegmentation k letterFrequency lme loadRegionDB
  log10FDR log10P mapToGenome mclapply mean.diff mean.quot.log2 melt
  mergeRegionDBs muted n.sites num.sites numSites numeric.names
  oddsRatios p.vals.t.na.adj pData percent_format phenoData phenoData<-
  plotAlphaDistributionOneChr plotFinalSegmentation plotTracks
  preprocessSWAN pvalues qvalue readMethylome readSNPTable refText
  reg.type region.size registerDoParallel relative.coord removeSNPs
  report runLOLA samples segmentPMDs segmentUMRsLMRs seqlengths
  seqlevels<- sigCategories sites2ignore size solve.QP stopCluster sva
  target texthere tsne type types ucscTableQuery universeCounts useMart
  v var.diff varFit varLabels x x2 xmlValue y y2 yint

RobStatTM

Run revdep_details(,"RobStatTM") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.

rosr

Run revdep_details(,"rosr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rstudioapi’ ‘tinytex’
  All declared Imports should be used.

rpostgisLT

Run revdep_details(,"rpostgisLT") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.

Rqc

Run revdep_details(,"Rqc") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  'IRanges' 'Rcpp'
  All declared Imports should be used.

RQuantLib

Run revdep_details(,"RQuantLib") for more info

In both

  • checking examples ... ERROR

    ...
+                fixFreq="Annual",
+                floatFreq="Semiannual")
+ 
+ setEvaluationDate(as.Date("2016-2-16"))               
+ times<-times <- seq(0,14.75,.25)
+ dcurve <- DiscountCurve(params, tsQuotes, times=times,legparams)
+ 
+ # Price the Bermudan swaption
+ pricing <- AffineSwaption(params, dcurve,swaptionMaturities, swapTenors, volMatrix,legparams)
+ summary(pricing)
+ 
+ }    

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: affineWithRebuiltCurveEngine(params, matchlegs, c(ts$table$date),     ts$table$zeroRates, expiry, tenor, vol)
 2: AffineSwaption.default(params, dcurve, swaptionMaturities, swapTenors,     volMatrix, legparams)
 3: AffineSwaption(params, dcurve, swaptionMaturities, swapTenors,     volMatrix, legparams)
An irrecoverable exception occurred. R is aborting now ...

  • checking tests ...

     ERROR
Running the tests in ‘tests/RQuantlib.R’ failed.
Last 13 lines of output:
  +                             settleDate=as.Date('2002-2-15'),
  +                             dt=0.25,
  +                             interpWhat='discount', interpHow='loglinear')
  > discountCurve <- DiscountCurve(discountCurve.param, list(flat=0.05))
  > 
  > ZeroCouponBond(bond, discountCurve, dateparams)

   *** caught segfault ***
  address 0x0, cause 'memory not mapped'

  Traceback:
   1: ZeroBondWithRebuiltCurve(bond, c(discountCurve$table$date), discountCurve$table$zeroRates,     dateparams)
   2: ZeroCouponBond.default(bond, discountCurve, dateparams)
   3: ZeroCouponBond(bond, discountCurve, dateparams)
  An irrecoverable exception occurred. R is aborting now ...

  • checking whether package ‘RQuantLib’ can be installed ... WARNING

    ...
  /usr/local/include/ql/models/marketmodels/products/multistep/multistepcoinitialswaps.hpp:48:14: warning: 'auto_ptr<QuantLib::MarketModelMultiProduct>' is deprecated [-Wdeprecated-declarations]#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
  55:14: warning: 'auto_ptr<QuantLib::MarketModelMultiProduct>' is deprecated [-Wdeprecated-declarations]
  :49:14: warning: 'auto_ptr<QuantLib::MarketModelMultiProduct>' is deprecated [-Wdeprecated-declarations]In file included from calendars.cpp:20:
  :2080:28:136:22: warning: 'auto_ptr<QuantLib::MarketModelPathwiseMultiProduct>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/models/marketmodels/products/multistep/multistepratchet.hpp#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated)):51:14: warning: note'auto_ptr<QuantLib::MarketModelMultiProduct>' is deprecated [-Wdeprecated-declarations]: expanded from macro '_LIBCPP_DEPRECATED'
  /usr/local/include/ql/models/marketmodels/products/pathwise/pathwiseproductcaplet.hpp:136:22: warning: 2080:28: 'auto_ptr<QuantLib::MarketModelPathwiseMultiProduct>' is deprecated [-Wdeprecated-declarations]
  In file included from 48: warning: 'auto_ptr<QuantLib::MarketModelPathwiseMultiProduct>' is deprecated [-Wdeprecated-declarations]
  :195:22: warning: 'auto_ptr<QuantLib::MarketModelPathwiseMultiProduct>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/utilities/clone.hpp:49:20: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/fittedbonddiscountcurve.hpp:201:22: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/nonlinearfittingmethods.hpp:60:14: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/nonlinearfittingmethods.hpp:89:14: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/nonlinearfittingmethods.hpp:120:14: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/nonlinearfittingmethods.hpp:165:14: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/nonlinearfittingmethods.hpp:203:14: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  /usr/local/include/ql/termstructures/yield/nonlinearfittingmethods.hpp:223:14: warning: 'auto_ptr<QuantLib::FittedBondDiscountCurve::FittingMethod>' is deprecated [-Wdeprecated-declarations]
  affine.cpp:33:53: warning: 'CalibrationHelper' is deprecated [-Wdeprecated-declarations]
  bermudan.cpp:33:53: warning: 'CalibrationHelper' is deprecated [-Wdeprecated-declarations]
  hullwhite.cpp:43:54: warning: 'CalibrationHelper' is deprecated [-Wdeprecated-declarations]
  hullwhite.cpp:111:54: warning: 'CalibrationHelper' is deprecated [-Wdeprecated-declarations]
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/RQuantLib/new/RQuantLib.Rcheck/00install.out’ for details.

rrvgo

Run revdep_details(,"rrvgo") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking dependencies in R code ... NOTE

    Unexported object imported by a ':::' call: ‘GOSemSim:::getAncestors’
  See the note in ?`:::` about the use of this operator.

  • checking R code for possible problems ... NOTE

    scatterPlot: no visible binding for global variable ‘V1’
scatterPlot: no visible binding for global variable ‘V2’
scatterPlot: no visible binding for global variable ‘parentTerm’
scatterPlot: no visible binding for global variable ‘parent’
Undefined global functions or variables:
  V1 V2 parent parentTerm

rtimicropem

Run revdep_details(,"rtimicropem") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.

RtutoR

Run revdep_details(,"RtutoR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.

RxODE

Run revdep_details(,"RxODE") for more info

In both

  • checking package dependencies ... NOTE 
    Packages suggested but not available for checking:
  'SnakeCharmR', 'installr'

safetyGraphics

Run revdep_details(,"safetyGraphics") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.

sangerseqR

Run revdep_details(,"sangerseqR") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
chromatogram,sangerseq: no visible global function definition for
  ‘quantile’
chromatogram,sangerseq: no visible global function definition for ‘IQR’
chromatogram,sangerseq: no visible global function definition for ‘pdf’
chromatogram,sangerseq: no visible global function definition for
  ‘rect’
chromatogram,sangerseq: no visible global function definition for
  ‘lines’
chromatogram,sangerseq: no visible global function definition for
  ‘mtext’
chromatogram,sangerseq: no visible global function definition for
  ‘axis’
chromatogram,sangerseq: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  IQR axis dev.off lines mtext par pdf quantile rect
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "lines", "mtext", "par", "rect")
  importFrom("stats", "IQR", "quantile")
to your NAMESPACE file.

santaR

Run revdep_details(,"santaR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.

SC3

Run revdep_details(,"SC3") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking installed package size ... NOTE

      installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.4Mb

  • checking top-level files ... NOTE

    File
  LICENSE
is not mentioned in the DESCRIPTION file.

scone

Run revdep_details(,"scone") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
sconeReport : server: no visible global function definition for ‘theme’
sconeReport : server: no visible global function definition for
  ‘element_blank’
sconeReport : server: no visible global function definition for
  ‘ggplotly’
sconeReport : server: no visible global function definition for
  ‘geom_violin’
sconeReport : server: no visible global function definition for
  ‘coord_cartesian’
sconeReport : server: no visible global function definition for
  ‘scale_fill_manual’
sconeReport : server: no visible global function definition for
  ‘geom_point’
sconeReport : server: no visible global function definition for
  ‘guides’
Undefined global functions or variables:
  %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin
  ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork
  scale_fill_manual theme visEdges visGroups visHierarchicalLayout
  visLegend visNetwork visNetworkOutput visNetworkProxy visOptions
  visSelectNodes ylim

SDEFSR

Run revdep_details(,"SDEFSR") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.

SEA

Run revdep_details(,"SEA") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.0Mb

semdrw

Run revdep_details(,"semdrw") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.

SemNeT

Run revdep_details(,"SemNeT") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.

  • checking Rd cross-references ... NOTE

    Package unavailable to check Rd xrefs: ‘SemNetCleaner’

seqplots

Run revdep_details(,"seqplots") for more info

In both

  • checking installed package size ... NOTE

      installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    seqplots  10.1Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.

  • checking foreign function calls ... NOTE

    Foreign function call to a different package:
  .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

  • checking R code for possible problems ... NOTE

    ...
plotHeatmap,list: no visible global function definition for ‘hclust’
plotHeatmap,list: no visible global function definition for ‘dist’
plotHeatmap,list: no visible global function definition for ‘cutree’
plotHeatmap,list: no visible global function definition for
  ‘as.dendrogram’
plotHeatmap,list: no visible global function definition for ‘title’
Undefined global functions or variables:
  Var1 Var2 abline adjustcolor approx as.dendrogram axis box
  capture.output colorRampPalette cutree dist doFileOperations hclust
  image kmeans layout lines mtext par plot.new qt rainbow rect rgb text
  title value
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
             "rgb")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "mtext", "par", "plot.new", "rect", "text",
             "title")
  importFrom("stats", "approx", "as.dendrogram", "cutree", "dist",
             "hclust", "kmeans", "qt")
  importFrom("utils", "capture.output")
to your NAMESPACE file.

sglr

Run revdep_details(,"sglr") for more info

In both

  • checking DESCRIPTION meta-information ... NOTE

    Malformed Description field: should contain one or more complete sentences.

  • checking R code for possible problems ... NOTE

    .computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.

shiny.router

Run revdep_details(,"shiny.router") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.

shiny.semantic

Run revdep_details(,"shiny.semantic") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   8.0Mb

shinyAce

Run revdep_details(,"shinyAce") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb

shinyaframe

Run revdep_details(,"shinyaframe") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.

shinybrms

Run revdep_details(,"shinybrms") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘brms’
  All declared Imports should be used.

shinyBS

Run revdep_details(,"shinyBS") for more info

In both

  • checking R code for possible problems ... NOTE 
    popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.

shinyEffects

Run revdep_details(,"shinyEffects") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.

shinyhelper

Run revdep_details(,"shinyhelper") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.

ShinyItemAnalysis

Run revdep_details(,"ShinyItemAnalysis") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘shinyBS’ ‘shinydashboard’ ‘xtable’
  All declared Imports should be used.

  • checking Rd cross-references ... NOTE

    Package unavailable to check Rd xrefs: ‘WrightMap’

shinyjs

Run revdep_details(,"shinyjs") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.

shinyKGode

Run revdep_details(,"shinyKGode") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.

shinyMethyl

Run revdep_details(,"shinyMethyl") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘IlluminaHumanMethylation450kmanifest’

Package suggested but not available for checking: ‘minfiData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

shinypanels

Run revdep_details(,"shinypanels") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.

shinyr

Run revdep_details(,"shinyr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’ ‘plotly’
  All declared Imports should be used.

shinyrecap

Run revdep_details(,"shinyrecap") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.

shinyTANDEM

Run revdep_details(,"shinyTANDEM") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘rTANDEM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

sigmajs

Run revdep_details(,"sigmajs") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 28 marked UTF-8 strings

SimDesign

Run revdep_details(,"SimDesign") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘doMPI’

simplevis

Run revdep_details(,"simplevis") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘readr’ ‘rmarkdown’ ‘shinycssloaders’
  All declared Imports should be used.

singleCellTK

Run revdep_details(,"singleCellTK") for more info

In both

  • checking for hidden files and directories ... NOTE

    Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

  • checking installed package size ... NOTE

      installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    3.8Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘celda’ ‘shinyBS’ ‘shinythemes’
  All declared Imports should be used.
Missing or unexported object: ‘SingleCellExperiment::isSpike’

skeleSim

Run revdep_details(,"skeleSim") for more info

In both

  • checking whether package ‘skeleSim’ can be installed ... ERROR 
    Installation failed.
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/skeleSim/new/skeleSim.Rcheck/00install.out’ for details.

Installation

Devel

* installing *source* package ‘skeleSim’ ...
** package ‘skeleSim’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘strata<-’ is not exported by 'namespace:strataG'
Execution halted
ERROR: lazy loading failed for package ‘skeleSim’
* removing ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/skeleSim/new/skeleSim.Rcheck/skeleSim’

CRAN

* installing *source* package ‘skeleSim’ ...
** package ‘skeleSim’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘strata<-’ is not exported by 'namespace:strataG'
Execution halted
ERROR: lazy loading failed for package ‘skeleSim’
* removing ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/skeleSim/old/skeleSim.Rcheck/skeleSim’

skpr

Run revdep_details(,"skpr") for more info

In both

  • checking installed package size ... NOTE

      installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.

soc.ca

Run revdep_details(,"soc.ca") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 833 marked UTF-8 strings

soilcarbon

Run revdep_details(,"soilcarbon") for more info

In both

  • checking R code for possible problems ... NOTE

    compileDatabase: no visible global function definition for ‘use_data’
Undefined global functions or variables:
  use_data

  • checking data for non-ASCII characters ... NOTE

      Note: found 145 marked UTF-8 strings

sojourner

Run revdep_details(,"sojourner") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘rtiff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

soundgen

Run revdep_details(,"soundgen") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb

SpaDES.addins

Run revdep_details(,"SpaDES.addins") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.

spant

Run revdep_details(,"spant") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.

sparklyr

Run revdep_details(,"sparklyr") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    java   2.4Mb

sparkTable

Run revdep_details(,"sparkTable") for more info

In both

  • checking R code for possible problems ... NOTE 
    pixmapGrob: no visible global function definition for ‘imageGrob’
Undefined global functions or variables:
  imageGrob

SpatialEpiApp

Run revdep_details(,"SpatialEpiApp") for more info

In both

  • checking package dependencies ... NOTE

    Package suggested but not available for checking: ‘INLA’

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.

spatialLIBD

Run revdep_details(,"spatialLIBD") for more info

In both

  • checking examples ... ERROR

    ...
> ### Title: Check input image_path
> ### Aliases: check_image_path
> 
> ### ** Examples
> 
> 
> if (enough_ram()) {
+     ## Obtain the necessary data
+     if (!exists("sce")) sce <- fetch_data("sce")
+ 
+     ## Get the path to the images
+     img_path <- system.file("app", "www", "data", package = "spatialLIBD")
+ 
+     ## Check the object
+     check_image_path(img_path, sce)
+ }
Error: Corrupt Cache: sqlite file
  See vignette section on corrupt cache
  cache: /Users/barret/Library/Caches/ExperimentHub
  filename: experimenthub.sqlite3
Execution halted

  • checking installed package size ... NOTE

      installed size is 14.3Mb
  sub-directories of 1Mb or more:
    app    5.6Mb
    doc    5.9Mb
    help   2.3Mb

spectrolab

Run revdep_details(,"spectrolab") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.

SSDM

Run revdep_details(,"SSDM") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.

ssrch

Run revdep_details(,"ssrch") for more info

In both

  • checking R code for possible problems ... NOTE

    docset_searchapp : server : <anonymous>: no visible global function
  definition for ‘metadata<-’
docset_searchapp : server : <anonymous>: no visible global function
  definition for ‘metadata’
Undefined global functions or variables:
  metadata metadata<-

  • checking data for non-ASCII characters ... NOTE

      Note: found 4 marked UTF-8 strings

sstModel

Run revdep_details(,"sstModel") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.

STAT

Run revdep_details(,"STAT") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.

steemr

Run revdep_details(,"steemr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.

stminsights

Run revdep_details(,"stminsights") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.

STMotif

Run revdep_details(,"STMotif") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.

strand

Run revdep_details(,"strand") for more info

In both

  • checking package dependencies ... NOTE 
    Package suggested but not available for checking: ‘Rsymphony’

subscreen

Run revdep_details(,"subscreen") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  All declared Imports should be used.

tableHTML

Run revdep_details(,"tableHTML") for more info

In both

  • checking installed package size ... NOTE

      installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.

tablerDash

Run revdep_details(,"tablerDash") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.

TAShiny

Run revdep_details(,"TAShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.

TBSignatureProfiler

Run revdep_details(,"TBSignatureProfiler") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    1.8Mb

TCGAbiolinksGUI

Run revdep_details(,"TCGAbiolinksGUI") for more info

In both

  • checking installed package size ... NOTE

      installed size is 33.7Mb
  sub-directories of 1Mb or more:
    app   1.1Mb
    doc  32.4Mb

  • checking DESCRIPTION meta-information ... NOTE

    Malformed Description field: should contain one or more complete sentences.

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
Package in Depends field not imported from: 'TCGAbiolinksGUI.data'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

TeachBayes

Run revdep_details(,"TeachBayes") for more info

In both

  • checking Rd \usage sections ... WARNING 
    Documented arguments not in \usage in documentation object 'beta_draw':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

tenXplore

Run revdep_details(,"tenXplore") for more info

In both

  • checking R code for possible problems ... NOTE 
    apd: warning in dir(system.file("app", package = "tenXplore"), full =
  TRUE): partial argument match of 'full' to 'full.names'

TestDesign

Run revdep_details(,"TestDesign") for more info

In both

  • checking package dependencies ... NOTE 
    Packages suggested but not available for checking: 'Rsymphony', 'gurobi'

testextra

Run revdep_details(,"testextra") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.

texPreview

Run revdep_details(,"texPreview") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.

TFutils

Run revdep_details(,"TFutils") for more info

In both

  • checking examples ... ERROR

    Running examples in ‘TFutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: tffamCirc.plot
> ### Title: use a radial plot (by default) for motif stack
> ### Aliases: tffamCirc.plot
> 
> ### ** Examples
> 
> p1 = tffamCirc.prep( )
Loading required namespace: motifStack
Failed with error:  'there is no package called 'MotIV''
Error in FUN(X[[i]], ...) : 
  please install package motifStack to use this function.
Calls: tffamCirc.prep -> sapply -> lapply -> FUN
Execution halted

  • checking dependencies in R code ... WARNING

    '::' or ':::' imports not declared from:
  'BiocFileCache' 'DT' 'httr' 'readxl' 'rjson'

  • checking installed package size ... NOTE

      installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data      4.0Mb
    doc       2.2Mb
    lambert   1.4Mb

  • checking DESCRIPTION meta-information ... NOTE

    Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rsamtools’
A package should be listed in only one of these fields.

  • checking R code for possible problems ... NOTE

    ...
fimo_granges : <anonymous>: no visible global function definition for
  ‘seqinfo<-’
retrieve_lambert_main: no visible global function definition for
  ‘bfcadd’
setupHIZE: no visible global function definition for ‘read.delim’
tffamCirc.prep: no visible binding for global variable ‘TF family’
tffamCirc.prep: no visible binding for global variable ‘TFfamily’
tffamCirc.prep: no visible binding for global variable ‘Transcription
  factor’
topTraitsOfTargets: no visible global function definition for ‘mcols’
topTraitsOfTargets: no visible binding for global variable
  ‘DISEASE.TRAIT’
Undefined global functions or variables:
  DISEASE.TRAIT Family_Name HGNC MAPPED_GENE TF family TFfamily
  Transcription factor bfcadd cisbpTFcat mcols read.csv read.delim
  reduceByRange rowRanges<- seqinfo<-
Consider adding
  importFrom("base", "factor")
  importFrom("stats", "family")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.

  • checking data for non-ASCII characters ... NOTE

      Note: found 62 marked UTF-8 strings

tidycells

Run revdep_details(,"tidycells") for more info

In both

  • checking examples ... ERROR

    ...
> cd <- as_cell_df(d) %>% numeric_values_classifier()
Error: `x` must be a vector, not a `tbl_df/tbl/data.frame/unpivotr` object.
Backtrace:
     █
  1. ├─as_cell_df(d) %>% numeric_values_classifier()
  2. │ └─base::eval(lhs, parent, parent)
  3. │   └─base::eval(lhs, parent, parent)
  4. ├─tidycells::as_cell_df(d)
  5. └─tidycells:::as_cell_df.data.frame(d)
  6.   └─d %>% attach_intermediate_class() %>% as_cell_df_internal(...)
  7.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  8.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  9.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
 10.         └─tidycells:::`_fseq`(`_lhs`)
 11.           └─magrittr::freduce(value, `_function_list`)
 12.             ├─base::withVisible(function_list[[k]](value))
 13.             └─function_list[[k]](value)
 14.               ├─tidycells:::as_cell_df_internal(., ...)
 15.               └─tidycells:::as_cell_df_internal.default(., ...)
 16.                 └─`%
Execution halted

  • checking tests ...

     ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 2 | WARNINGS: 8 | FAILED: 29 ]
  1. Error: numeric_values_classifier works (@test-VA_classifier.R#5) 
  2. Error: sample_based_classifier works (@test-VA_classifier.R#45) 
  3. Error: sample_based_classifier works (@test-VA_classifier.R#41) 
  4. Error: (unknown) (@test-VA_classifier.R#41) 
  5. Error: analyze_cell works: base 
  6. Error: analyze_cell works: tidyxl (@test-analyze_cells.R#28) 
  7. Error: analyze_cell works: tidyxl (@test-analyze_cells.R#25) 
  8. Error: (unknown) (@test-analyze_cells.R#25) 
  9. Error: as_cell_df() works on tidyxl::xlsx_cells on single sheet (@test-as_cell_df.R#6) 
  1. ...

  Error: testthat unit tests failed
  Execution halted

timeline

Run revdep_details(,"timeline") for more info

In both

  • checking dependencies in R code ... NOTE

    'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

  • checking R code for possible problems ... NOTE

    timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab

TimerQuant

Run revdep_details(,"TimerQuant") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
genTimeSteadyStateHeatmap: no visible global function definition for
  ‘rainbow’
plotPrimordiumProfile: no visible binding for global variable ‘median’
plotPrimordiumProfile: no visible binding for global variable ‘mad’
plotPrimordiumProfile: no visible global function definition for ‘par’
plotPrimordiumProfile: no visible global function definition for ‘axis’
plotPrimordiumProfile: no visible global function definition for
  ‘points’
plotPrimordiumProfile: no visible global function definition for
  ‘polygon’
plotPrimordiumProfile: no visible global function definition for ‘rgb’
simulatedRatio: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approxfun axis mad median optimize par points polygon predict rainbow
  rgb rnorm
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "par", "points", "polygon")
  importFrom("stats", "approxfun", "mad", "median", "optimize",
             "predict", "rnorm")
to your NAMESPACE file.

timeseriesdb

Run revdep_details(,"timeseriesdb") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.

timevis

Run revdep_details(,"timevis") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.

tmaptools

Run revdep_details(,"tmaptools") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘KernSmooth’
  All declared Imports should be used.

TR8

Run revdep_details(,"TR8") for more info

In both

  • checking data for non-ASCII characters ... NOTE 
      Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings

trackeRapp

Run revdep_details(,"trackeRapp") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.

treespace

Run revdep_details(,"treespace") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb

TSCAN

Run revdep_details(,"TSCAN") for more info

In both

  • checking R code for possible problems ... NOTE 
    ...
  ‘lm’
exprmclust: no visible global function definition for ‘dist’
plotmclust: no visible binding for global variable ‘pca_dim_1’
plotmclust: no visible binding for global variable ‘pca_dim_2’
plotmclust: no visible binding for global variable ‘sample_name’
preprocess: no visible binding for global variable ‘sd’
preprocess: no visible global function definition for ‘hclust’
preprocess: no visible global function definition for ‘dist’
preprocess: no visible global function definition for ‘cutree’
preprocess: no visible global function definition for ‘aggregate’
singlegeneplot: no visible global function definition for
  ‘fitted.values’
singlegeneplot: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  aggregate cutree dist fitted.values hclust lm p.adjust pca_dim_1
  pca_dim_2 pchisq prcomp predict sample_name sd
Consider adding
  importFrom("stats", "aggregate", "cutree", "dist", "fitted.values",
             "hclust", "lm", "p.adjust", "pchisq", "prcomp", "predict",
             "sd")
to your NAMESPACE file.

ttestshiny

Run revdep_details(,"ttestshiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.

TVTB

Run revdep_details(,"TVTB") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.7Mb

twoddpcr

Run revdep_details(,"twoddpcr") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    4.1Mb

TxRegInfra

Run revdep_details(,"TxRegInfra") for more info

In both

  • checking DESCRIPTION meta-information ... NOTE

    Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rjson’
A package should be listed in only one of these fields.

  • checking dependencies in R code ... NOTE

    'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

  • checking R code for possible problems ... NOTE

    ...
dnmetaApp: no visible global function definition for ‘fluidPage’
dnmetaApp: no visible global function definition for ‘sidebarLayout’
dnmetaApp: no visible global function definition for ‘sidebarPanel’
dnmetaApp: no visible global function definition for ‘helpText’
dnmetaApp: no visible global function definition for ‘radioButtons’
dnmetaApp: no visible global function definition for
  ‘checkboxGroupInput’
dnmetaApp: no visible global function definition for ‘uiOutput’
dnmetaApp: no visible global function definition for ‘mainPanel’
dnmetaApp: no visible global function definition for ‘dataTableOutput’
dnmetaApp : server: no visible global function definition for
  ‘renderUI’
dnmetaApp : server: no visible global function definition for
  ‘selectInput’
dnmetaApp : server: no visible global function definition for
  ‘renderDataTable’
dnmetaApp: no visible global function definition for ‘runApp’
Undefined global functions or variables:
  checkboxGroupInput dataTableOutput fluidPage genes helpText mainPanel
  radioButtons renderDataTable renderUI runApp selectInput
  sidebarLayout sidebarPanel uiOutput

  • checking Rd files ... NOTE

    prepare_Rd: addsyms.Rd:23-25: Dropping empty section \examples

  • checking data for non-ASCII characters ... NOTE

      Note: found 14 marked UTF-8 strings

ubiquity

Run revdep_details(,"ubiquity") for more info

In both

  • checking installed package size ... NOTE 
      installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb

UCSCXenaShiny

Run revdep_details(,"UCSCXenaShiny") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.

  • checking data for non-ASCII characters ... NOTE

      Note: found 162 marked UTF-8 strings

Ularcirc

Run revdep_details(,"Ularcirc") for more info

In both

  • checking package dependencies ... ERROR 
    Package required but not available: ‘mirbase.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ursa

Run revdep_details(,"ursa") for more info

In both

  • checking Rd cross-references ... NOTE 
    Package unavailable to check Rd xrefs: ‘rje’

VariantFiltering

Run revdep_details(,"VariantFiltering") for more info

In both

  • checking running R code from vignettes ...

      ‘usingVariantFiltering.Rnw’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘usingVariantFiltering.Rnw’
  ...
> vfpar <- VariantFilteringParam(CEUvcf)
Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Loading SNPlocs annotation package SNPlocs.Hsapiens.dbSNP144.GRCh37
Loading annotation package MafDb.1Kgenomes.phase1.hs37d5

  When sourcing 'usingVariantFiltering.R':
Error: please install the Bioconductor package PolyPhen.Hsapiens.dbSNP131.
Execution halted

  • checking package dependencies ... NOTE

    Packages suggested but not available for checking:
  'PolyPhen.Hsapiens.dbSNP131', 'SIFT.Hsapiens.dbSNP137'

  • checking installed package size ... NOTE

      installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   3.6Mb

  • checking dependencies in R code ... NOTE

    Unexported objects imported by ':::' calls:
  'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs'
  'VariantAnnotation:::.consolidateHits'
  'VariantAnnotation:::.returnEmpty'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.adjustForStrandSense' '.ancestorsSO' '.findSOIDs'

VarSelLCM

Run revdep_details(,"VarSelLCM") for more info

In both

  • checking line endings in C/C++/Fortran sources/headers ... NOTE 
    ...
  inst/include/AlgorithmCategorical.h
  inst/include/AlgorithmContinuous.h
  inst/include/AlgorithmInteger.h
  inst/include/AlgorithmMixed.h
  inst/include/Data.h
  inst/include/DataCategorical.h
  inst/include/DataContinuous.h
  inst/include/DataInteger.h
  inst/include/DataMixed.h
  inst/include/Param.h
  inst/include/ParamCategorical.h
  inst/include/ParamContinuous.h
  inst/include/ParamInteger.h
  inst/include/ParamMixed.h
  inst/include/XEM.h
  inst/include/XEMCategorical.h
  inst/include/XEMContinuous.h
  inst/include/XEMInteger.h
  inst/include/XEMMixed.h
  inst/include/XEMPen.h
Some compilers warn on such files.

vdiffr

Run revdep_details(,"vdiffr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.

viromeBrowser

Run revdep_details(,"viromeBrowser") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘plyr’ ‘reshape’
  All declared Imports should be used.

visit

Run revdep_details(,"visit") for more info

In both

  • checking dependencies in R code ... NOTE

    Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.

  • checking for GNU extensions in Makefiles ... NOTE

    GNU make is a SystemRequirements.

visNetwork

Run revdep_details(,"visNetwork") for more info

In both

  • checking installed package size ... NOTE 
      installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb

VTShiny

Run revdep_details(,"VTShiny") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.

waiter

Run revdep_details(,"waiter") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.

wallace

Run revdep_details(,"wallace") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘testthat’ ‘zip’
  All declared Imports should be used.

webr

Run revdep_details(,"webr") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.

wiseR

Run revdep_details(,"wiseR") for more info

In both

  • checking installed package size ... NOTE

      installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb

  • checking dependencies in R code ... NOTE

    Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.

wTO

  • Version: 1.6.3
  • Source code: https://github.com/cran/wTO
  • Date/Publication: 2018-11-17 11:50:03 UTC
  • Number of recursive dependencies: 39

Run revdep_details(,"wTO") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.

xROI

Run revdep_details(,"xROI") for more info

In both

  • checking whether package ‘xROI’ can be installed ... WARNING 
    Found the following significant warnings:
  Warning: replacing previous import ‘lubridate::intersect’ by ‘raster::intersect’ when loading ‘xROI’
  Warning: replacing previous import ‘lubridate::union’ by ‘raster::union’ when loading ‘xROI’
See ‘/Users/barret/Documents/git/rstudio/shiny/shiny/revdep/checks.noindex.nosync/xROI/new/xROI.Rcheck/00install.out’ for details.

ymlthis

Run revdep_details(,"ymlthis") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.

yuimaGUI

Run revdep_details(,"yuimaGUI") for more info

In both

  • checking dependencies in R code ... NOTE 
    Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
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