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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSVA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSVA_2.1.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GSVA.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘2.1.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSVA’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
GsvaExprData-class.Rd: dgCMatrix-class, ExpressionSet-class,
SummarizedExperiment-class, SingleCellExperiment-class,
SpatialExperiment-class
GsvaGeneSets-class.Rd: GeneSetCollection
GsvaMethodParam-class.Rd: GeneIdentifierType-class,
GeneIdentifierType
geneIdsToGeneSetCollection.Rd: GeneIdentifierType, CollectionType,
GeneSetCollection, GeneSet, geneIds
gsva.Rd: BiocParallelParam, dgCMatrix-class, ExpressionSet,
SingleCellExperiment
gsvaAnnotation.Rd: ExpressionSet-class, SummarizedExperiment-class,
GeneIdentifierType
gsvaParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType,
ExpressionSet, SummarizedExperiment, SingleCellExperiment
gsvaRanks.Rd: BiocParallelParam, dgCMatrix-class, ExpressionSet,
SingleCellExperiment
guessGeneIdType.Rd: GeneIdentifierType
plageParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType
readGMT.Rd: GeneIdentifierType, getGmt, GeneSetCollection, GSEABase
spatCor.Rd: BiocParallelParam
ssgseaParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType,
ExpressionSet, SummarizedExperiment, SingleCellExperiment
zscoreParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readGMT 5.512 0.114 5.645
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘test_gsva_newapi.R’
Comparing ‘test_gsva_newapi.Rout’ to ‘test_gsva_newapi.Rout.save’ ...124c124
< KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22812891 -0.263355222 -0.37470050 0.290732334 0.17079093 -0.45765232 0.50012601 -0.09532256 -0.47875047 0.2005760985 0.092621366 0.393690568 -0.10337215 0.25814796 -0.007047109 -0.32196546 0.54100312 0.36730644 -0.229340073 -0.21569337 -0.39089158 -0.10367966 -0.0265281455 0.206218417 -0.38405692 -0.26149665 0.11109491 -0.305540564 -0.23084358 0.119516674 0.40469862 -0.359303191 -0.2285660734 0.0670553834 -0.193418010 0.406591786
---
> KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22812891 -0.263355222 -0.37470050 0.290732334 0.17079093 -0.45765232 0.50012601 -0.09532256 -0.47875336 0.2005760985 0.092621366 0.393690568 -0.10337215 0.25814796 -0.007047109 -0.32196546 0.54100312 0.36730644 -0.229340073 -0.21569337 -0.39089158 -0.10367966 -0.0265281455 0.206218417 -0.38405692 -0.26149665 0.11109491 -0.305540564 -0.23084358 0.119516674 0.40469862 -0.359303191 -0.2285660734 0.0670553834 -0.193418010 0.406591786
126c126
< KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39550501 -0.351321414 -0.14110425 0.358243057 0.16435766 -0.26645789 0.66763824 0.18030231 -0.55042292 0.0557952309 0.021388295 0.576276913 0.11071439 0.29896526 0.104972515 -0.50323751 0.57733745 0.46874390 -0.256221334 -0.36544895 -0.33575684 -0.39328574 0.1106353940 0.023796472 -0.34202930 -0.25875177 0.28102418 -0.433601675 -0.31440655 -0.006812749 0.26563946 -0.454982215 -0.4530852168 0.2943696221 -0.265834459 0.464109149
---
> KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39550501 -0.351321414 -0.14110425 0.358243057 0.16435766 -0.26645789 0.66763824 0.18030231 -0.55044204 0.0557952309 0.021388295 0.576276913 0.11071439 0.29896526 0.104972515 -0.50323751 0.57733745 0.46874390 -0.256221334 -0.36544895 -0.33575684 -0.39328574 0.1106353940 0.023796472 -0.34202930 -0.25875177 0.28102418 -0.433601675 -0.31440655 -0.006812749 0.26563946 -0.454982215 -0.4530852168 0.2943696221 -0.265834459 0.464109149
129c129
< KEGG_GALACTOSE_METABOLISM 0.05968213 -0.423880642 -0.04004200 0.349477244 -0.12227027 -0.46339930 0.51695869 -0.01678146 -0.35305823 0.2445369055 0.472971320 0.344522701 0.33867856 0.24989655 0.250426294 -0.45236845 0.57775802 0.21524751 -0.336019746 -0.08788026 -0.42317686 -0.04080587 -0.2214574734 0.056153250 -0.07821159 0.07863864 0.27266698 -0.411791653 -0.36014334 -0.190298991 0.39452862 -0.533045360 -0.4125257996 0.3437504852 -0.176878763 0.513759918
---
> KEGG_GALACTOSE_METABOLISM 0.05968213 -0.423880642 -0.04004200 0.349477244 -0.12227027 -0.46339930 0.51695869 -0.01678146 -0.35296517 0.2445369055 0.472971320 0.344522701 0.33867856 0.24989655 0.250426294 -0.45236845 0.57775802 0.21524751 -0.336019746 -0.08788026 -0.42317686 -0.04080587 -0.2214574734 0.056153250 -0.07821159 0.07863864 0.27266698 -0.411791653 -0.36014334 -0.190298991 0.39452862 -0.533045360 -0.4125257996 0.3437504852 -0.176878763 0.513759918
136c136
< KEGG_PURINE_METABOLISM 0.20023659 -0.107367072 -0.10728443 0.291663773 -0.05283553 -0.02859522 0.36157660 0.19316332 -0.19143196 -0.1572998000 0.049080483 0.109067828 -0.11833371 0.10564365 0.139338503 -0.10233547 0.24853991 0.18038953 0.046367008 -0.21468925 -0.19907099 -0.17785664 -0.1297500619 -0.149496262 -0.20375506 -0.18721379 0.14549532 -0.025164874 0.03659184 0.032750693 -0.01289068 0.002391921 -0.1715995805 0.1037162394 -0.157361053 -0.016062020
---
> KEGG_PURINE_METABOLISM 0.20023659 -0.107367072 -0.10728443 0.291663773 -0.05283553 -0.02859522 0.36157660 0.19316332 -0.19143021 -0.1572998000 0.049080483 0.109067828 -0.11833371 0.10564365 0.139338503 -0.10233547 0.24853991 0.18038953 0.046367008 -0.21468925 -0.19907099 -0.17785664 -0.1297500619 -0.149496262 -0.20375506 -0.18721379 0.14549532 -0.025164874 0.03659184 0.032750693 -0.01289068 0.002391921 -0.1715995805 0.1037162394 -0.157361053 -0.016062020
Running ‘test_plage_newapi.R’
Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ... OK
Running ‘test_ssgsea_newapi.R’
Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ... OK
Running ‘test_zscore_newapi.R’
Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ... OK
NOTE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/GSVA.Rcheck/00check.log’
for details.