Package: qrqc

Version: 1.13.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.13.1.tar.gz

StartedAt: 2013-01-16 05:31:19 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:36:41 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 322.0 seconds

RetCode: 0

Status:  OK

CheckDir: qrqc.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/qrqc.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 ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.13.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qrqc’ can be installed ... OK
* checking installed package size ... OK
* 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
basePlot,SequenceSummary: no visible binding for global variable ‘base’
basePlot,list: no visible binding for global variable ‘base’
gcPlot,SequenceSummary: no visible binding for global variable
  ‘position’
gcPlot,list: no visible binding for global variable ‘position’
getBase,SequenceSummary: no visible binding for global variable ‘base’
getBaseProp,SequenceSummary: no visible binding for global variable
  ‘base’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  ‘position’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  ‘entropy’
kmerEntropyPlot,list: no visible binding for global variable ‘position’
kmerEntropyPlot,list: no visible binding for global variable ‘entropy’
kmerKLPlot,SequenceSummary: no visible binding for global variable
  ‘kmer’
kmerKLPlot,SequenceSummary: no visible binding for global variable
  ‘position’
kmerKLPlot,SequenceSummary: no visible binding for global variable ‘kl’
kmerKLPlot,list : <anonymous>: no visible binding for global variable
  ‘kmer’
kmerKLPlot,list: no visible binding for global variable ‘position’
kmerKLPlot,list: no visible binding for global variable ‘kl’
kmerKLPlot,list: no visible binding for global variable ‘kmer’
qualPlot,FASTQSummary: no visible binding for global variable
  ‘position’
qualPlot,list: no visible binding for global variable ‘position’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
kmerKLPlot        15.885  0.088  15.980
getMCQual-methods  6.513  0.036   6.567
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-functions.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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck/00check.log’
for details.

* installing *source* package ‘qrqc’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c R_init_io.c -o R_init_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c io.c -o io.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o qrqc.so R_init_io.o io.o -lz /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck/qrqc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘qrqc.Rnw’ 
** testing if installed package can be loaded

* DONE (qrqc)

name	user	system	elapsed
FASTASummary-class	0.008	0.000	0.010
FASTQSummary-class	0.012	0.000	0.014
SequenceSummary-class	0.008	0.004	0.012
basePlot-methods	3.949	0.044	3.993
calcKL	2.056	0.028	2.083
gcPlot-methods	1.388	0.040	1.430
getBase-methods	1.408	0.024	1.438
getBaseProp-methods	0.924	0.016	0.941
getGC-methods	0.696	0.024	0.719
getKmer-methods	1.436	0.008	1.444
getMCQual-methods	6.513	0.036	6.567
getQual-methods	0.924	0.028	0.952
getSeqlen-methods	0.728	0.020	0.748
kmerEntropyPlot	4.480	0.100	4.612
kmerKLPlot	15.885	0.088	15.980
list2df	1.152	0.044	1.193
makeReport	1.944	0.052	1.997
plotBases	0.02	0.00	0.02
plotGC	0.004	0.000	0.005
plotQuals	0.016	0.000	0.017
plotSeqLengths	0.004	0.000	0.004
qualPlot-methods	3.464	0.032	3.501
readSeqFile	0.400	0.020	0.419
scale_color_dna	0.664	0.020	0.682
scale_color_iupac	0.660	0.024	0.683
seqlenPlot-methods	1.285	0.032	1.318