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chore: revdepcheck

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revdep/README.md
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# Revdeps
## Failed to check (29)
## Failed to check (20)
|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 |? | | | |
|package |version |error |warning |note |
|:------------------|:-------|:-----|:-------|:----|
|animalEKF |1.2 |1 | | |
|AovBay |0.1.0 |1 | | |
|Certara.VPCResults |3.0.2 |1 | | |
|chipPCR |1.0-2 |1 | | |
|ctsem |3.10.1 |1 | | |
|dartR.sim |? | | | |
|diveR |? | | | |
|gap |? | | | |
|jsmodule |? | | | |
|loon.shiny |? | | | |
|robmedExtra |0.1.1 |1 | | |
|rstanarm |2.32.1 |1 | | |
|SensMap |0.7 |1 | | |
|Seurat |5.1.0 |1 | |1 |
|shinyTempSignal |0.0.8 |1 | | |
|Signac |1.14.0 |1 | | |
|statsr |0.3.0 |1 | | |
|TestAnaAPP |1.1.2 |1 | | |
|tidyvpc |1.5.2 |1 | | |
|visR |? | | | |
## New problems (2)
|package |version |error |warning |note |
|:-------|:-------|:--------|:-------|:------|
|[EgoCor](problems.md#egocor)|1.2.0 |1 __+1__ | |-1 |
|[mxfda](problems.md#mxfda)|0.2.1 | | |__+1__ |
|package |version |error |warning |note |
|:-------|:-------|:-----|:-------|:------|
|[HH](problems.md#hh)|3.1-52 | | |__+1__ |
|[PopED](problems.md#poped)|0.7.0 | | |__+1__ |

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revdep/cran.md
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## revdepcheck results
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 checked 1278 reverse dependencies (1277 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 2 new problems
* We failed to check 16 packages
* We failed to check 19 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
* EgoCor
checking running R code from vignettes ... ERROR
* HH
checking installed package size ... NOTE
* mxfda
* PopED
checking installed package size ... NOTE
### Failed to check
* animalEKF (NA)
* AovBay (NA)
* chipPCR (NA)
* ctsem (NA)
* diveR (NA)
* DynNom (NA)
* loon.shiny (NA)
* robmedExtra (NA)
* RQuantLib (NA)
* rstanarm (NA)
* SensMap (NA)
* Seurat (NA)
* shinyTempSignal (NA)
* Signac (NA)
* statsr (NA)
* tidyvpc (NA)
* animalEKF (NA)
* AovBay (NA)
* Certara.VPCResults (NA)
* chipPCR (NA)
* ctsem (NA)
* dartR.sim (NA)
* diveR (NA)
* gap (NA)
* jsmodule (NA)
* loon.shiny (NA)
* robmedExtra (NA)
* rstanarm (NA)
* SensMap (NA)
* Seurat (NA)
* shinyTempSignal (NA)
* Signac (NA)
* statsr (NA)
* TestAnaAPP (NA)
* tidyvpc (NA)

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revdep/problems.md
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# EgoCor
# HH
<details>
* 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
* Version: 3.1-52
* GitHub: NA
* Source code: https://github.com/cran/HH
* Date/Publication: 2024-02-11 00:00:02 UTC
* Number of recursive dependencies: 165
Run `revdepcheck::cloud_details(, "EgoCor")` for more info
</details>
## Newly broken
* checking running R code from vignettes ... ERROR
```
Errors in running code in vignettes:
when running code in ‘Intro_to_EgoCor.Rmd’
...
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 ‘Intro_to_EgoCor.R’:
Error: missing value where TRUE/FALSE needed
Execution halted
‘Intro_to_EgoCor.Rmd’ using ‘UTF-8’... failed
```
## 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: 0.2.1
* 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(, "mxfda")` for more info
Run `revdepcheck::cloud_details(, "HH")` for more info
</details>
@@ -86,8 +16,34 @@ Run `revdepcheck::cloud_details(, "mxfda")` for more info
* checking installed package size ... NOTE
```
installed size is 5.6Mb
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 4.0Mb
R 1.5Mb
help 1.5Mb
```
# PopED
<details>
* Version: 0.7.0
* GitHub: https://github.com/andrewhooker/PopED
* Source code: https://github.com/cran/PopED
* Date/Publication: 2024-10-07 19:30:02 UTC
* Number of recursive dependencies: 140
Run `revdepcheck::cloud_details(, "PopED")` for more info
</details>
## Newly broken
* checking installed package size ... NOTE
```
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.5Mb
doc 1.4Mb
test 1.1Mb
```