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This page was generated on 2024-03-27 11:37:40 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 919/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSVA 1.50.1  (landing page)
Robert Castelo
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/GSVA
git_branch: RELEASE_3_18
git_last_commit: e15f1c0
git_last_commit_date: 2024-03-05 06:24:37 -0400 (Tue, 05 Mar 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GSVA on merida1


To the developers/maintainers of the GSVA package:
- 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 Troubleshooting Build Report for more information.
- 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: GSVA
Version: 1.50.1
Command: /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_1.50.1.tar.gz
StartedAt: 2024-03-26 03:34:03 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 03:44:25 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 622.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GSVA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.50.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GSVA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘1.50.1’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 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 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/GSVA.Rcheck/00check.log’
for details.



Installation output

GSVA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘GSVA’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c kernel_estimation.c -o kernel_estimation.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ks_test.c -o ks_test.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c register_cmethods.c -o register_cmethods.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-GSVA/00new/GSVA/libs
** R
** 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 (GSVA)

Tests output

GSVA.Rcheck/tests/runTests.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

> 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 combined z-scores for 2 gene sets.

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Estimating ssGSEA scores for 2 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
Estimating ssGSEA scores for 2 gene sets.

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Estimating GSVA scores for 5 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 5 gene sets.
Estimating ECDFs with Poisson kernels

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Estimating GSVA scores for 5 gene sets.
Estimating ECDFs directly

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Estimating GSVA scores for 5 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 5 gene sets.
Estimating ECDFs with Poisson kernels

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Estimating GSVA scores for 5 gene sets.
Estimating ECDFs directly

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Estimating PLAGE scores for 5 gene sets.

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Estimating combined z-scores for 5 gene sets.

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Estimating ssGSEA scores for 5 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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Estimating GSVA scores for 2 gene sets.
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Estimating PLAGE scores for 2 gene sets.
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    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.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
Estimating ssGSEA scores for 2 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."


RUNIT TEST PROTOCOL -- Tue Mar 26 03:44:12 2024 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSVA RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
There were 30 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 48.533   3.843  56.014 

Example timings

GSVA.Rcheck/GSVA-Ex.timings

nameusersystemelapsed
computeGeneSetsOverlap0.1540.0050.160
filterGeneSets0.0000.0010.002
gsva0.7030.0500.759
gsvaParam-class3.4860.1553.717
igsva000
plageParam-class3.5190.0583.643
ssgseaParam-class2.6040.0632.758
zscoreParam-class2.5790.0722.745