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BioC 3.4: CHECK report for GSVA on malbec1

This page was generated on 2017-04-15 16:10:25 -0400 (Sat, 15 Apr 2017).

Package 571/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSVA 1.22.4
Justin Guinney
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GSVA
Last Changed Rev: 126405 / Revision: 128728
Last Changed Date: 2017-02-01 12:15:30 -0500 (Wed, 01 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSVA
Version: 1.22.4
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GSVA_1.22.4.tar.gz
StartedAt: 2017-04-14 23:06:35 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:07:46 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 71.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GSVA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GSVA_1.22.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GSVA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘1.22.4’
* 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 ... 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘compute.geneset.es’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compute.gene.density : <anonymous>: no visible global function
  definition for ‘ecdf’
compute.geneset.es: no visible global function definition for
  ‘txtProgressBar’
compute.geneset.es: no visible global function definition for
  ‘setTxtProgressBar’
ks_test_Rcode: no visible global function definition for ‘plot’
ks_test_m: no visible global function definition for
  ‘setTxtProgressBar’
plage: no visible global function definition for ‘txtProgressBar’
plage : <anonymous>: no visible global function definition for ‘sd’
plage : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
plage: no visible global function definition for ‘setTxtProgressBar’
ssgsea: no visible global function definition for ‘txtProgressBar’
ssgsea : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
ssgsea: no visible global function definition for ‘setTxtProgressBar’
zscore: no visible global function definition for ‘txtProgressBar’
zscore : <anonymous>: no visible global function definition for ‘sd’
zscore : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
zscore: no visible global function definition for ‘setTxtProgressBar’
computeGeneSetsOverlap,GeneSetCollection-ExpressionSet: no visible
  global function definition for ‘incidence’
computeGeneSetsOverlap,GeneSetCollection-character: no visible global
  function definition for ‘incidence’
computeGeneSetsOverlap,list-ExpressionSet : <anonymous>: no visible
  global function definition for ‘na.omit’
computeGeneSetsOverlap,list-character : <anonymous>: no visible global
  function definition for ‘na.omit’
filterGeneSets,GeneSetCollection: no visible global function definition
  for ‘geneIds’
gsva,ExpressionSet-GeneSetCollection: no visible binding for global
  variable ‘sd’
gsva,ExpressionSet-GeneSetCollection: no visible global function
  definition for ‘geneIds’
gsva,ExpressionSet-GeneSetCollection : <anonymous>: no visible global
  function definition for ‘na.omit’
gsva,ExpressionSet-GeneSetCollection: no visible global function
  definition for ‘featureNames’
gsva,ExpressionSet-GeneSetCollection: no visible global function
  definition for ‘phenoData’
gsva,ExpressionSet-GeneSetCollection: no visible global function
  definition for ‘experimentData’
gsva,ExpressionSet-list: no visible binding for global variable ‘sd’
gsva,ExpressionSet-list : <anonymous>: no visible global function
  definition for ‘na.omit’
gsva,ExpressionSet-list: no visible global function definition for
  ‘featureNames’
gsva,ExpressionSet-list: no visible global function definition for
  ‘phenoData’
gsva,ExpressionSet-list: no visible global function definition for
  ‘experimentData’
gsva,matrix-GeneSetCollection: no visible binding for global variable
  ‘sd’
gsva,matrix-GeneSetCollection: no visible global function definition
  for ‘geneIds’
gsva,matrix-GeneSetCollection : <anonymous>: no visible global function
  definition for ‘na.omit’
gsva,matrix-list: no visible binding for global variable ‘sd’
gsva,matrix-list : <anonymous>: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  ecdf experimentData featureNames geneIds incidence na.omit phenoData
  plot sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "na.omit", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/GSVA.Rcheck/00check.log’
for details.


GSVA.Rcheck/00install.out:

* installing *source* package ‘GSVA’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c kernel_estimation.c -o kernel_estimation.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ks_test.c -o ks_test.o
ks_test.c: In function ‘ks_sample’:
ks_test.c:22:9: warning: unused variable ‘mx_value’ [-Wunused-variable]
  double mx_value = 0.0;
         ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/GSVA.Rcheck/GSVA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSVA)

GSVA.Rcheck/GSVA-Ex.timings:

nameusersystemelapsed
computeGeneSetsOverlap0.0040.0000.004
filterGeneSets0.0000.0000.001
gsva0.1880.0200.218