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Package 538/631HostnameOS / ArchBUILDCHECKBUILD BIN
Rsubread 1.9.1
Wei Shi
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread
Last Changed Rev: 70675 / Revision: 72575
Last Changed Date: 2012-10-18 17:00:05 -0700 (Thu, 18 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Leopard (10.5.8) / i386 N O T   S U P P O R T E D

Summary

Package: Rsubread
Version: 1.9.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Rsubread_1.9.1.tar.gz
StartedAt: 2013-01-16 06:08:31 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 06:09:06 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 34.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rsubread.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsubread’ version ‘1.9.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 90.6Mb
  sub-directories of 1Mb or more:
    annot  89.0Mb
* checking package 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 for unstated 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
createAnnotationFile: no visible global function definition for
  ‘values’
createAnnotationFile: no visible global function definition for
  ‘values<-’
createAnnotationFile: no visible global function definition for
  ‘seqnames’
write.Rsubread: no visible global function definition for ‘values’
write.Rsubread: no visible global function definition for ‘values<-’
write.Rsubread: no visible global function definition for ‘seqnames’
* 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 line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/Rsubread/libs/Rsubread.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘gene-algorithms.o’, ‘propmapped.o’, ‘readSummary.o’,
      ‘sam2bed.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘SNPCalling.o’, ‘aligner.o’, ‘detectionCallAnnotation.o’,
      ‘exon-align.o’, ‘fullscan.o’, ‘gene-algorithms.o’,
      ‘index-builder.o’, ‘input-files.o’, ‘processExons.o’,
      ‘propmapped.o’, ‘readSummary.o’, ‘removeDupReads.o’,
      ‘sorted-hashtable.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Objects: ‘aligner.o’, ‘exon-align.o’, ‘gene-algorithms.o’,
      ‘index-builder.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘SNPCalling.o’, ‘aligner.o’, ‘detectionCallAnnotation.o’,
      ‘exon-align.o’, ‘fullscan.o’, ‘gene-algorithms.o’,
      ‘gene-value-index.o’, ‘index-builder.o’, ‘input-files.o’,
      ‘processExons.o’, ‘propmapped.o’, ‘readSummary.o’,
      ‘removeDupReads.o’, ‘sam2bed.o’, ‘sorted-hashtable.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Objects: ‘SNPCalling.o’, ‘aligner.o’, ‘exon-align.o’,
      ‘gene-algorithms.o’, ‘index-builder.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

Rsubread.Rcheck/00install.out:

* installing *source* package ‘Rsubread’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c SNPCalling.c -o SNPCalling.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c aligner.c -o aligner.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c atgcContent.c -o atgcContent.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c detectionCall.c -o detectionCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c exon-algorithms.c -o exon-algorithms.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c exon-align.c -o exon-align.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c fullscan.c -o fullscan.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c gene-algorithms.c -o gene-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c gene-value-index.c -o gene-value-index.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c index-builder.c -o index-builder.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c input-files.c -o input-files.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c processExons.c -o processExons.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c propmapped.c -o propmapped.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c qualityScores.c -o qualityScores.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c readSummary.c -o readSummary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c removeDupReads.c -o removeDupReads.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c sam2bed.c -o sam2bed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -fpic  -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsubread.so R_wrapper.o SNPCalling.o aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sorted-hashtable.o -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Rsubread.Rnw’ 
** testing if installed package can be loaded

* DONE (Rsubread)

Rsubread.Rcheck/Rsubread-Ex.timings:

nameusersystemelapsed
align0.3081.5041.816
atgcContent0.0200.0040.023
buildindex0.2121.4681.681
createAnnotationFile0.0240.0000.022
propmapped0.3321.4561.804
qualityScores0.4320.0040.437