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BioC 3.2: CHECK report for BicARE on zin1

This page was generated on 2016-04-23 10:11:04 -0700 (Sat, 23 Apr 2016).

Package 89/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BicARE 1.28.0
Pierre Gestraud
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BicARE
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BicARE
Version: 1.28.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BicARE_1.28.0.tar.gz
StartedAt: 2016-04-22 22:25:49 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:34:56 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 547.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BicARE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BicARE_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BicARE.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BicARE/DESCRIPTION’ ... OK
* this is package ‘BicARE’ version ‘1.28.0’
* 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 ‘BicARE’ can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSEABase’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FLOC: no visible global function definition for ‘exprs’
bicluster: no visible global function definition for ‘exprs’
bicluster: no visible global function definition for ‘featureNames’
bicluster: no visible global function definition for ‘sampleNames’
makeReport: no visible global function definition for ‘annotation’
makeReport: no visible global function definition for ‘getSYMBOL’
makeReport: no visible global function definition for ‘setName’
residue: no visible global function definition for ‘exprs’
testAnnot: no visible global function definition for ‘pData’
testAnnot: no visible global function definition for ‘phenoData’
testAnnot: no visible global function definition for ‘mt.rawp2adjp’
testSet: no visible global function definition for ‘exprs’
testSet: no visible global function definition for ‘GeneSet’
testSet: no visible global function definition for ‘geneIdType’
testSet: no visible global function definition for ‘geneIds’
testSet: no visible global function definition for ‘mapIdentifiers’
testSet: no visible global function definition for ‘mt.rawp2adjp’
* 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 data for ASCII and uncompressed saves ... 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 ... [460s/462s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
testSet 424.362  0.251 426.963
FLOC     27.139  0.020  27.161
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/BicARE.Rcheck/00check.log’
for details.


BicARE.Rcheck/00install.out:

* installing *source* package ‘BicARE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BicARE.c -o BicARE.o
BicARE.c: In function ‘floc’:
BicARE.c:439:12: warning: unused variable ‘invk’ [-Wunused-variable]
     double invk = 1/(double)*k;
            ^
BicARE.c: In function ‘action’:
BicARE.c:391:29: warning: ‘j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
        bicCol2[ncolData * z + j] = bicCol[ncolData * z +j];
                             ^
BicARE.c:380:29: warning: ‘i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
        bicRow2[nrowData * z + i] = bicRow[nrowData * z + i];
                             ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o BicARE.so BicARE.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/BicARE.Rcheck/BicARE/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BicARE)

BicARE.Rcheck/BicARE-Ex.timings:

nameusersystemelapsed
FLOC27.139 0.02027.161
bicluster0.2920.0000.291
makeReport2.8680.0162.886
residue0.0040.0000.004
testAnnot0.0180.0000.018
testSet424.362 0.251426.963