Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:05:17 -0500 (Fri, 03 Dec 2021).

CHECK results for GSVA on tokay2

To the developers/maintainers of the GSVA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 840/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSVA 1.42.0  (landing page)
Justin Guinney
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/GSVA
git_branch: RELEASE_3_14
git_last_commit: c99b10b
git_last_commit_date: 2021-10-26 11:59:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GSVA
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSVA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GSVA_1.42.0.tar.gz
StartedAt: 2021-12-02 21:38:20 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 21:44:58 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 398.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GSVA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSVA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GSVA_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GSVA.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSVA/DESCRIPTION' ... OK
* this is package 'GSVA' version '1.42.0'
* package encoding: latin1
* 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 whether package 'GSVA' can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/GSVA/libs/i386/GSVA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/GSVA/libs/x64/GSVA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GSVA.Rcheck/00check.log'
for details.



Installation output

GSVA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GSVA_1.42.0.tar.gz && rm -rf GSVA.buildbin-libdir && mkdir GSVA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSVA.buildbin-libdir GSVA_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GSVA_1.42.0.zip && rm GSVA_1.42.0.tar.gz GSVA_1.42.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1230k  100 1230k    0     0  2556k      0 --:--:-- --:--:-- --:--:-- 2563k

install for i386

* installing *source* package 'GSVA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c kernel_estimation.c -o kernel_estimation.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:24:9: warning: unused variable 'mx_value' [-Wunused-variable]
  double mx_value = 0.0;
         ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c register_cmethods.c -o register_cmethods.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GSVA.dll tmp.def kernel_estimation.o ks_test.o register_cmethods.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GSVA.buildbin-libdir/00LOCK-GSVA/00new/GSVA/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSVA'
    finding HTML links ... done
    computeGeneSetsOverlap                  html  
    filterGeneSets                          html  
    gsva                                    html  
    finding level-2 HTML links ... done

    igsva                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GSVA' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c kernel_estimation.c -o kernel_estimation.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:24:9: warning: unused variable 'mx_value' [-Wunused-variable]
  double mx_value = 0.0;
         ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c register_cmethods.c -o register_cmethods.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GSVA.dll tmp.def kernel_estimation.o ks_test.o register_cmethods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GSVA.buildbin-libdir/GSVA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSVA' as GSVA_1.42.0.zip
* DONE (GSVA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GSVA' successfully unpacked and MD5 sums checked

Tests output

GSVA.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> BiocGenerics:::testPackage("GSVA")
Estimating PLAGE scores for 2 gene sets.

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Estimating PLAGE scores for 2 gene sets.

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Estimating combined z-scores for 2 gene sets.

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Estimating ssGSEA scores for 2 gene sets.

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Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating ECDFs with Gaussian kernels

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Estimating PLAGE scores for 2 gene sets.
Please bear in mind that this method first scales the values of the gene
    expression data. In order to take advantage of the sparse Matrix type, the scaling
    will only be applied to the non-zero values of the data. This is a provisional 
    solution in order to give support to the dgCMatrix format.

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Estimating combined z-scores for 2 gene sets.
Please bear in mind that this method first scales the values of the gene
    expression data. In order to take advantage of the sparse Matrix type, the scaling
    will only be applied to the non-zero values of the data. This is a provisional 
    solution in order to give support to the dgCMatrix format.

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Estimating ssGSEA scores for 2 gene sets.

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Estimating ssGSEA scores for 2 gene sets.

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RUNIT TEST PROTOCOL -- Thu Dec 02 21:44:14 2021 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSVA RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  27.76    4.87   44.31 

GSVA.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> BiocGenerics:::testPackage("GSVA")
Estimating PLAGE scores for 2 gene sets.

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Estimating combined z-scores for 2 gene sets.

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Estimating ssGSEA scores for 2 gene sets.

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Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating PLAGE scores for 2 gene sets.

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Estimating PLAGE scores for 2 gene sets.
Please bear in mind that this method first scales the values of the gene
    expression data. In order to take advantage of the sparse Matrix type, the scaling
    will only be applied to the non-zero values of the data. This is a provisional 
    solution in order to give support to the dgCMatrix format.

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Estimating combined z-scores for 2 gene sets.

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Estimating combined z-scores for 2 gene sets.
Please bear in mind that this method first scales the values of the gene
    expression data. In order to take advantage of the sparse Matrix type, the scaling
    will only be applied to the non-zero values of the data. This is a provisional 
    solution in order to give support to the dgCMatrix format.

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Estimating ssGSEA scores for 2 gene sets.

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Estimating ssGSEA scores for 2 gene sets.

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RUNIT TEST PROTOCOL -- Thu Dec 02 21:44:51 2021 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSVA RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  28.48    3.07   36.04 

Example timings

GSVA.Rcheck/examples_i386/GSVA-Ex.timings

nameusersystemelapsed
computeGeneSetsOverlap0.060.000.06
filterGeneSets000
gsva0.230.110.34
igsva000

GSVA.Rcheck/examples_x64/GSVA-Ex.timings

nameusersystemelapsed
computeGeneSetsOverlap0.080.000.18
filterGeneSets0.000.000.09
gsva0.400.060.50
igsva000