Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 698/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fgsea 1.26.0  (landing page)
Alexey Sergushichev
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/fgsea
git_branch: RELEASE_3_17
git_last_commit: 102b439
git_last_commit_date: 2023-04-25 10:47:56 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for fgsea on kjohnson2


To the developers/maintainers of the fgsea package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: fgsea
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fgsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fgsea_1.26.0.tar.gz
StartedAt: 2023-10-17 19:31:33 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 19:37:34 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 361.0 seconds
RetCode: 0
Status:   OK  
CheckDir: fgsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fgsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fgsea_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/fgsea.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.26.0’
* 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 ‘fgsea’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.9Mb
* 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 R 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 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 ... NOTE
setUpBPPARAM: warning in MulticoreParam(workers = nproc, progress =
  TRUE): partial argument match of 'progress' to 'progressbar'
addGesecaScores: no visible global function definition for
  ‘DefaultAssay’
addGesecaScores: no visible global function definition for ‘GetAssay’
collapsePathways: no visible binding for global variable ‘pathway’
collapsePathways: no visible binding for global variable ‘ES’
collapsePathwaysGeseca: no visible binding for global variable
  ‘pvalCond’
collapsePathwaysGeseca: no visible binding for global variable
  ‘pathway’
collapsePathwaysGeseca: no visible binding for global variable
  ‘reciprocalPvalCond’
collapsePathwaysGeseca: no visible binding for global variable ‘pScore’
collapsePathwaysGeseca: no visible binding for global variable ‘pval’
fgseaMultilevel: no visible binding for global variable ‘modeFraction’
fgseaMultilevel: no visible binding for global variable ‘denomProb’
fora: no visible binding for global variable ‘pval’
geseca: no visible binding for global variable ‘gsScore’
geseca: no visible binding for global variable ‘log2err’
geseca: no visible binding for global variable ‘nGeScore’
geseca: no visible binding for global variable ‘pctVar’
geseca: no visible binding for global variable ‘size’
geseca: no visible binding for global variable ‘pathway’
geseca: no visible global function definition for ‘.’
geseca: no visible binding for global variable ‘pval’
geseca: no visible binding for global variable ‘padj’
gesecaSimple: no visible binding for global variable ‘pctVar’
gesecaSimple: no visible binding for global variable ‘size’
gesecaSimple: no visible binding for global variable ‘pval’
gesecaSimpleImpl: no visible binding for global variable ‘pval’
gesecaSimpleImpl: no visible binding for global variable ‘nGeScore’
gesecaSimpleImpl: no visible binding for global variable ‘padj’
gesecaSimpleImpl: no visible binding for global variable ‘size’
plotCoregulationProfile: no visible binding for global variable ‘id’
plotCoregulationProfile: no visible binding for global variable ‘gene’
plotCoregulationProfile: no visible binding for global variable
  ‘expressionValue’
plotCoregulationProfile: no visible binding for global variable ‘x’
plotCoregulationProfile: no visible binding for global variable ‘y’
plotCoregulationProfile: no visible binding for global variable
  ‘condition’
plotCoregulationProfileReduction: no visible global function definition
  for ‘DefaultAssay’
plotCoregulationProfileSpatial: no visible global function definition
  for ‘DefaultAssay’
plotGesecaTable: no visible global function definition for ‘modifyList’
plotGesecaTable: no visible binding for global variable ‘pathway’
plotGesecaTable: no visible binding for global variable ‘value’
plotGesecaTable : <anonymous>: no visible binding for global variable
  ‘pathway’
plotGesecaTable : <anonymous>: no visible binding for global variable
  ‘value’
plotGseaTable: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  . DefaultAssay ES GetAssay condition denomProb expressionValue gene
  gsScore id log2err modeFraction modifyList nGeScore pScore padj
  pathway pctVar pval pvalCond reciprocalPvalCond size value x y
Consider adding
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
plotGseaTable    17.237  0.468  22.610
collapsePathways 11.686  0.440  13.506
mapIdsList        9.306  0.468  11.790
fgseaSimple       8.069  1.064   6.180
fgsea             8.276  0.279   7.889
fgseaMultilevel   7.971  0.245   7.385
geseca            5.609  0.488   5.884
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/fgsea.Rcheck/00check.log’
for details.



Installation output

fgsea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fgsea
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ScoreCalculation.cpp -o ScoreCalculation.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ScoreRuler.cpp -o ScoreRuler.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c esCalculation.cpp -o esCalculation.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fastGSEA.cpp -o fastGSEA.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fgseaMultilevel.cpp -o fgseaMultilevel.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp:77:16: warning: unused variable 'currentES' [-Wunused-variable]
        double currentES = calcES(ranks, currentSamples[sampleId]);
               ^
fgseaMultilevelSupplement.cpp:260:14: warning: unused variable 'fl' [-Wunused-variable]
        bool fl = false;
             ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c geseca.cpp -o geseca.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c util.cpp -o util.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-fgsea/00new/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fgsea)

Tests output

fgsea.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(fgsea)
> 
> test_check("fgsea")

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2023-10-17 19:37:08.168 R[55172:42542775] XType: com.apple.fonts is not accessible.
2023-10-17 19:37:08.174 R[55172:42542775] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 127 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_gsea_analysis.R:80:5'
• On Mac (1): 'test_gsea_stat.R:84:5'

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
112.421  12.024 157.541 

Example timings

fgsea.Rcheck/fgsea-Ex.timings

nameusersystemelapsed
calcGseaStat0.0420.0060.068
collapsePathways11.686 0.44013.506
collapsePathwaysORA0.1470.0060.234
fgsea8.2760.2797.889
fgseaLabel0.0000.0010.000
fgseaMultilevel7.9710.2457.385
fgseaSimple8.0691.0646.180
fora0.0890.0210.167
geseca5.6090.4885.884
gesecaSimple0.8890.1771.599
gmtPathways0.1040.0130.185
mapIdsList 9.306 0.46811.790
multilevelError0.0010.0000.000
plotEnrichment0.0020.0020.007
plotEnrichmentData0.4980.0400.823
plotGseaTable17.237 0.46822.610
reactomePathways2.4810.1544.023
writeGmtPathways0.0600.0030.097