From 142ba3a48dd93f1b5c35c5ea6fe95a3e9ce41e04 Mon Sep 17 00:00:00 2001 From: Thomas Lin Pedersen Date: Fri, 25 Oct 2024 14:23:00 +0200 Subject: [PATCH] run revdepcheck --- revdep/README.md | 13 +- revdep/cran.md | 11 +- revdep/failures.md | 302 ++++++++++++++++++++++++++++----------------- 3 files changed, 202 insertions(+), 124 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index cce0984..c01d542 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,10 +1,11 @@ # Revdeps -## Failed to check (3) +## Failed to check (4) -|package |version |error |warning |note | -|:-----------|:-------|:-----|:-------|:----| -|ggPMX |? | | | | -|loon.ggplot |? | | | | -|tidySEM |? | | | | +|package |version |error |warning |note | +|:------------|:-------|:-----|:-------|:----| +|dartR.base |? | | | | +|Hmisc |? | | | | +|snplinkage |? | | | | +|spikeSlabGAM |1.1-20 |1 | | | diff --git a/revdep/cran.md b/revdep/cran.md index 1d05b50..12c5d70 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,14 +1,15 @@ ## revdepcheck results -We checked 91 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 98 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems - * We failed to check 3 packages + * We failed to check 4 packages Issues with CRAN packages are summarised below. ### Failed to check -* ggPMX (NA) -* loon.ggplot (NA) -* tidySEM (NA) +* dartR.base (NA) +* Hmisc (NA) +* snplinkage (NA) +* spikeSlabGAM (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 2e21562..8b6bf95 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,14 +1,14 @@ -# ggPMX +# dartR.base
-* Version: 1.2.8 -* GitHub: https://github.com/ggPMXdevelopment/ggPMX -* Source code: https://github.com/cran/ggPMX -* Date/Publication: 2022-06-17 23:10:02 UTC -* Number of recursive dependencies: 174 +* Version: 0.98 +* GitHub: NA +* Source code: https://github.com/cran/dartR.base +* Date/Publication: 2024-09-19 13:20:02 UTC +* Number of recursive dependencies: 286 -Run `cloud_details(, "ggPMX")` for more info +Run `revdepcheck::cloud_details(, "dartR.base")` for more info
@@ -17,27 +17,27 @@ Run `cloud_details(, "ggPMX")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/ggPMX/new/ggPMX.Rcheck’ -* using R version 4.1.1 (2021-08-10) +* using log directory ‘/tmp/workdir/dartR.base/new/dartR.base.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘ggPMX/DESCRIPTION’ ... OK -* this is package ‘ggPMX’ version ‘1.2.8’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE +* checking for file ‘dartR.base/DESCRIPTION’ ... OK ... - [ FAIL 1 | WARN 14 | SKIP 8 | PASS 327 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘ggPMX-guide.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘dartR.base’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/dartR.base/new/dartR.base.Rcheck/00install.out’ for details. * DONE -Status: 1 ERROR, 2 NOTEs +Status: 1 ERROR @@ -47,44 +47,44 @@ Status: 1 ERROR, 2 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/ggPMX/old/ggPMX.Rcheck’ -* using R version 4.1.1 (2021-08-10) +* using log directory ‘/tmp/workdir/dartR.base/old/dartR.base.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘ggPMX/DESCRIPTION’ ... OK -* this is package ‘ggPMX’ version ‘1.2.8’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE +* checking for file ‘dartR.base/DESCRIPTION’ ... OK ... - [ FAIL 1 | WARN 14 | SKIP 8 | PASS 327 ] - Error: Test failures - Execution halted -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘ggPMX-guide.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘dartR.base’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/dartR.base/old/dartR.base.Rcheck/00install.out’ for details. * DONE -Status: 1 ERROR, 2 NOTEs +Status: 1 ERROR ``` -# loon.ggplot +# Hmisc
-* Version: 1.3.3 -* GitHub: https://github.com/great-northern-diver/loon.ggplot -* Source code: https://github.com/cran/loon.ggplot -* Date/Publication: 2022-11-12 22:30:02 UTC -* Number of recursive dependencies: 104 +* Version: 5.1-3 +* GitHub: NA +* Source code: https://github.com/cran/Hmisc +* Date/Publication: 2024-05-28 07:10:02 UTC +* Number of recursive dependencies: 170 -Run `cloud_details(, "loon.ggplot")` for more info +Run `revdepcheck::cloud_details(, "Hmisc")` for more info
@@ -93,25 +93,27 @@ Run `cloud_details(, "loon.ggplot")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/loon.ggplot/new/loon.ggplot.Rcheck’ -* using R version 4.1.1 (2021-08-10) +* using log directory ‘/tmp/workdir/Hmisc/new/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘loon.ggplot/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘loon.ggplot’ version ‘1.3.3’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘loon’ - -Package suggested but not available for checking: ‘zenplots’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK * DONE -Status: 1 ERROR +Status: 4 NOTEs @@ -121,42 +123,44 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/loon.ggplot/old/loon.ggplot.Rcheck’ -* using R version 4.1.1 (2021-08-10) +* using log directory ‘/tmp/workdir/Hmisc/old/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘loon.ggplot/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘loon.ggplot’ version ‘1.3.3’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘loon’ - -Package suggested but not available for checking: ‘zenplots’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK * DONE -Status: 1 ERROR +Status: 4 NOTEs ``` -# tidySEM +# snplinkage
-* Version: 0.2.3 -* GitHub: https://github.com/cjvanlissa/tidySEM -* Source code: https://github.com/cran/tidySEM -* Date/Publication: 2022-04-14 17:50:02 UTC -* Number of recursive dependencies: 171 +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/snplinkage +* Date/Publication: 2024-09-09 19:10:02 UTC +* Number of recursive dependencies: 153 -Run `cloud_details(, "tidySEM")` for more info +Run `revdepcheck::cloud_details(, "snplinkage")` for more info
@@ -165,27 +169,27 @@ Run `cloud_details(, "tidySEM")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’ -* using R version 4.1.1 (2021-08-10) +* using log directory ‘/tmp/workdir/snplinkage/new/snplinkage.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘tidySEM/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘tidySEM’ version ‘0.2.3’ +* checking for file ‘snplinkage/DESCRIPTION’ ... OK +... +* this is package ‘snplinkage’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK -... -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK - ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK - ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK - ‘sem_graph.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘GWASTools’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 1 NOTE +Status: 1 ERROR @@ -195,30 +199,102 @@ Status: 1 NOTE ### CRAN ``` -* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’ -* using R version 4.1.1 (2021-08-10) +* using log directory ‘/tmp/workdir/snplinkage/old/snplinkage.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 + GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 +* running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘tidySEM/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘tidySEM’ version ‘0.2.3’ +* checking for file ‘snplinkage/DESCRIPTION’ ... OK +... +* this is package ‘snplinkage’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK -... -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK - ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK - ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK - ‘sem_graph.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘GWASTools’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 1 NOTE +Status: 1 ERROR + + + + + +``` +# spikeSlabGAM + +
+ +* Version: 1.1-20 +* GitHub: https://github.com/fabian-s/spikeSlabGAM +* Source code: https://github.com/cran/spikeSlabGAM +* Date/Publication: 2024-10-22 17:30:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "spikeSlabGAM")` for more info + +
+ +## In both +* checking whether package ‘spikeSlabGAM’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/spikeSlabGAM/new/spikeSlabGAM.Rcheck/00install.out’ for details. + ``` +## Installation + +### Devel +``` +* installing *source* package ‘spikeSlabGAM’ ... +** package ‘spikeSlabGAM’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sampler.c -o sampler.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spikeSlabGAM_init.c -o spikeSlabGAM_init.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o spikeSlabGAM.so sampler.o spikeSlabGAM_init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/spikeSlabGAM/new/spikeSlabGAM.Rcheck/00LOCK-spikeSlabGAM/00new/spikeSlabGAM/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘spikeSlabGAM’ +* removing ‘/tmp/workdir/spikeSlabGAM/new/spikeSlabGAM.Rcheck/spikeSlabGAM’ + + +``` +### CRAN + +``` +* installing *source* package ‘spikeSlabGAM’ ... +** package ‘spikeSlabGAM’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sampler.c -o sampler.o +gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spikeSlabGAM_init.c -o spikeSlabGAM_init.o +gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o spikeSlabGAM.so sampler.o spikeSlabGAM_init.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/spikeSlabGAM/old/spikeSlabGAM.Rcheck/00LOCK-spikeSlabGAM/00new/spikeSlabGAM/libs +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘spikeSlabGAM’ +* removing ‘/tmp/workdir/spikeSlabGAM/old/spikeSlabGAM.Rcheck/spikeSlabGAM’ ```