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BioC 3.1: CHECK report for GSVA on petty

This page was generated on 2015-10-09 09:34:31 -0700 (Fri, 09 Oct 2015).

Package 448/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSVA 1.16.0
Justin Guinney
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GSVA
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSVA
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSVA_1.16.0.tar.gz
StartedAt: 2015-10-08 23:35:47 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:38:16 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 149.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GSVA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSVA_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GSVA.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GSVA’ can be installed ... [14s/14s] 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
* 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 loading without being on the library search path ... 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
computeGeneSetsOverlap,GeneSetCollection-character : .local: no visible
  global function definition for ‘incidence’
computeGeneSetsOverlap,GeneSetCollection-ExpressionSet : .local: no
  visible global function definition for ‘incidence’
filterGeneSets,GeneSetCollection : .local: no visible global function
  definition for ‘geneIds’
gsva,ExpressionSet-GeneSetCollection : .local: no visible global
  function definition for ‘geneIds’
gsva,ExpressionSet-GeneSetCollection : .local: no visible global
  function definition for ‘featureNames’
gsva,ExpressionSet-GeneSetCollection : .local: no visible global
  function definition for ‘phenoData’
gsva,ExpressionSet-GeneSetCollection : .local: no visible global
  function definition for ‘experimentData’
gsva,ExpressionSet-list : .local: no visible global function definition
  for ‘featureNames’
gsva,ExpressionSet-list : .local: no visible global function definition
  for ‘phenoData’
gsva,ExpressionSet-list : .local: no visible global function definition
  for ‘experimentData’
gsva,matrix-GeneSetCollection : .local: no visible global function
  definition for ‘geneIds’
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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-3.1-bioc/meat/GSVA.Rcheck/00check.log’
for details.


GSVA.Rcheck/00install.out:

* installing *source* package ‘GSVA’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c kernel_estimation.c -o kernel_estimation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ks_test.c -o ks_test.o
ks_test.c: In function ‘ks_sample’:
ks_test.c:22: warning: unused variable ‘mx_value’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c register_cmethods.c -o register_cmethods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/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 /Users/biocbuild/bbs-3.1-bioc/meat/GSVA.Rcheck/GSVA/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GSVA)

GSVA.Rcheck/GSVA-Ex.timings:

nameusersystemelapsed
computeGeneSetsOverlap0.0110.0000.011
filterGeneSets0.0020.0010.002
gsva0.5740.0810.648