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ran revdepcheck on cloud. 2 errors reported. Both seem like false positives

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Barret Schloerke
2024-07-26 16:01:27 -04:00
parent 2f84c238ad
commit f5fdfac0d6
3 changed files with 105 additions and 107 deletions
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73
revdep/README.md
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@@ -1,42 +1,43 @@
# Revdeps
## Failed to check (27)
## Failed to check (29)
|package |version |error |warning |note |
|:------------------|:-------|:-----|:-------|:----|
|animalEKF |1.2 |1 | | |
|antaresViz |? | | | |
|AovBay |0.1.0 |1 | | |
|bigPint |? | | | |
|bioCancer |? | | | |
|chipPCR |1.0-2 |1 | | |
|ctsem |3.10.0 |1 | | |
|DynNom |5.1 |1 | | |
|EBImage |? | | | |
|g3viz |? | | | |
|GeneNetworkBuilder |? | | | |
|InterCellar |? | | | |
|LACE |? | | | |
|loon.shiny |? | | | |
|MatrixQCvis |? | | | |
|metricsgraphics |? | | | |
|modchart |? | | | |
|omicsViewer |? | | | |
|robmedExtra |0.1.0 |1 | | |
|RQuantLib |0.4.23 |1 | | |
|rstanarm |2.32.1 |1 | | |
|SensMap |0.7 |1 | | |
|Seurat |5.1.0 |1 | | |
|shinyTempSignal |0.0.8 |1 | | |
|Signac |1.13.0 |1 | | |
|statsr |0.3.0 |1 | | |
|tidyvpc |1.5.1 |1 | | |
|package |version |error |warning |note |
|:---------------|:-------|:-----|:-------|:----|
|alevinQC |? | | | |
|animalEKF |1.2 |1 | | |
|animaltracker |? | | | |
|antaresViz |? | | | |
|AovBay |0.1.0 |1 | | |
|bdclean |? | | | |
|chipPCR |1.0-2 |1 | | |
|ctsem |3.10.0 |1 | | |
|diveR |? | | | |
|DynNom |5.1 |1 | | |
|hydflood |? | | | |
|loon.shiny |? | | | |
|modchart |? | | | |
|MODIStsp |? | | | |
|protGear |? | | | |
|robmedExtra |0.1.0 |1 | | |
|RQuantLib |0.4.23 |1 | | |
|rstanarm |2.32.1 |1 | | |
|scPipe |? | | | |
|sen2r |? | | | |
|SensMap |0.7 |1 | | |
|Seurat |5.1.0 |1 | | |
|shinyTempSignal |0.0.8 |1 | | |
|Signac |1.13.0 |1 | | |
|simplevis |? | | | |
|statsr |0.3.0 |1 | | |
|teachingApps |? | | | |
|tidyvpc |1.5.1 |1 | | |
|TVTB |? | | | |
## New problems (3)
## New problems (2)
|package |version |error |warning |note |
|:------------|:-------|:-----|:-------|:------|
|[idiogramFISH](problems.md#idiogramfish)|2.0.13 |1 | |__+1__ |
|[iheatmapr](problems.md#iheatmapr)|0.7.1 | | |__+1__ |
|[polmineR](problems.md#polminer)|0.8.9 | | |__+1__ |
|package |version |error |warning |note |
|:-------|:-------|:--------|:-------|:------|
|[EgoCor](problems.md#egocor)|1.2.0 |1 __+1__ | |-1 |
|[mxfda](problems.md#mxfda)|0.2.1 | | |__+1__ |

16
revdep/cran.md
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@@ -1,22 +1,19 @@
## revdepcheck results
We checked 1213 reverse dependencies (1201 from CRAN + 12 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
We checked 1221 reverse dependencies (1208 from CRAN + 13 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 3 new problems
* We failed to check 15 packages
* We saw 2 new problems
* We failed to check 16 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
* idiogramFISH
checking installed package size ... NOTE
* EgoCor
checking running R code from vignettes ... ERROR
* iheatmapr
checking installed package size ... NOTE
* polmineR
* mxfda
checking installed package size ... NOTE
### Failed to check
@@ -25,6 +22,7 @@ Issues with CRAN packages are summarised below.
* AovBay (NA)
* chipPCR (NA)
* ctsem (NA)
* diveR (NA)
* DynNom (NA)
* loon.shiny (NA)
* robmedExtra (NA)

123
revdep/problems.md
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# idiogramFISH
# EgoCor
<details>
* Version: 2.0.13
* GitHub: NA
* Source code: https://github.com/cran/idiogramFISH
* Date/Publication: 2023-08-22 16:50:02 UTC
* Number of recursive dependencies: 164
* Version: 1.2.0
* GitHub: https://github.com/julia-dyck/EgoCor
* Source code: https://github.com/cran/EgoCor
* Date/Publication: 2024-03-28 18:10:02 UTC
* Number of recursive dependencies: 74
Run `revdepcheck::cloud_details(, "idiogramFISH")` for more info
Run `revdepcheck::cloud_details(, "EgoCor")` for more info
</details>
## Newly broken
* checking installed package size ... NOTE
```
installed size is 5.1Mb
sub-directories of 1Mb or more:
R 1.5Mb
doc 2.0Mb
```
## In both
* checking running R code from vignettes ... ERROR
```
Errors in running code in vignettes:
when running code in ‘index.Rmd’
when running code in ‘Intro_to_EgoCor.Rmd’
...
> if (requireNamespace("RCurl", quietly = TRUE)) {
+ v <- sub("Version: ", "", readLines("../DESCRIPTION")[3])
+ pkg <- "idiogramFISH"
+ l .... [TRUNCATED]
Warning in file(con, "r") :
cannot open file '../DESCRIPTION': No such file or directory
Warning in gstat::fit.variogram(emp.sv, model = v, fit.sills = TRUE, fit.ranges = TRUE, :
linear model has singular covariance matrix
Warning in gstat::fit.variogram(emp.sv, model = v, fit.sills = TRUE, fit.ranges = TRUE, :
linear model has singular covariance matrix
Warning in gstat::fit.variogram(emp.sv, model = v, fit.sills = TRUE, fit.ranges = TRUE, :
No convergence after 200 iterations: try different initial values?
When sourcing ‘index.R’:
Error: cannot open the connection
When sourcing ‘Intro_to_EgoCor.R’:
Error: missing value where TRUE/FALSE needed
Execution halted
‘AVignette.Rmd’ using ‘UTF-8’... OK
‘index.Rmd’ using ‘UTF-8’... failed
‘Intro_to_EgoCor.Rmd’ using ‘UTF-8’... failed
```
# iheatmapr
## Newly fixed
* checking re-building of vignette outputs ... NOTE
```
Error(s) in re-building vignettes:
--- re-building ‘Intro_to_EgoCor.Rmd’ using rmarkdown
```
## In both
* checking examples ... ERROR
```
Running examples in ‘EgoCor-Ex.R’ failed
The error most likely occurred in:
> ### Name: vario.reg.prep
> ### Title: Adjustment for covariates before semi-variogram model fitting
> ### Aliases: vario.reg.prep
>
> ### ** Examples
>
> ## Example 1
...
+ }
Warning in check_dep_version() :
ABI version mismatch:
lme4 was built with Matrix ABI version 1
Current Matrix ABI version is 0
Please re-install lme4 from source or restore original ‘Matrix’ package
Error in initializePtr() :
function 'cholmod_factor_ldetA' not provided by package 'Matrix'
Calls: <Anonymous> ... initialize -> <Anonymous> -> initializePtr -> .Call
Execution halted
```
# mxfda
<details>
* Version: 0.7.1
* GitHub: https://github.com/ropensci/iheatmapr
* Source code: https://github.com/cran/iheatmapr
* Date/Publication: 2024-01-25 23:50:02 UTC
* Number of recursive dependencies: 92
* Version: 0.2.1
* GitHub: https://github.com/julia-wrobel/mxfda
* Source code: https://github.com/cran/mxfda
* Date/Publication: 2024-05-08 11:00:02 UTC
* Number of recursive dependencies: 220
Run `revdepcheck::cloud_details(, "iheatmapr")` for more info
Run `revdepcheck::cloud_details(, "mxfda")` for more info
</details>
@@ -62,33 +86,8 @@ Run `revdepcheck::cloud_details(, "iheatmapr")` for more info
* checking installed package size ... NOTE
```
installed size is 5.3Mb
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.5Mb
htmlwidgets 3.5Mb
```
# polmineR
<details>
* Version: 0.8.9
* GitHub: https://github.com/PolMine/polmineR
* Source code: https://github.com/cran/polmineR
* Date/Publication: 2023-10-29 21:50:02 UTC
* Number of recursive dependencies: 96
Run `revdepcheck::cloud_details(, "polmineR")` for more info
</details>
## Newly broken
* checking installed package size ... NOTE
```
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
extdata 1.9Mb
data 4.0Mb
```