Package: qrqc

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qrqc_1.13.1.tar.gz

StartedAt: 2013-03-25 04:11:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:17:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 355.3 seconds

RetCode: 0

Status:  OK

CheckDir: qrqc.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... [32s/32s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [77s/77s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
kmerKLPlot        14.261  1.194  15.471
getMCQual-methods  7.190  0.279   7.475
basePlot-methods   5.941  0.189   6.133
kmerEntropyPlot    4.713  0.377   5.094
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-functions.R' [16s/16s]
 [16s/16s] 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck/00check.log'
for details.

* installing *source* package 'qrqc' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_io.c -o R_init_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c io.c -o io.o
io.c:34: warning: 'kseq_destroy' defined but not used
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/i386/libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/i386/libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck/qrqc/libs/i386
** 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	0.006	0.014
FASTQSummary-class	0.008	0.006	0.014
SequenceSummary-class	0.007	0.006	0.014
basePlot-methods	5.941	0.189	6.133
calcKL	2.022	0.098	2.121
gcPlot-methods	2.718	0.106	2.829
getBase-methods	1.565	0.066	1.635
getBaseProp-methods	1.541	0.051	1.593
getGC-methods	1.179	0.054	1.234
getKmer-methods	2.243	0.064	2.307
getMCQual-methods	7.190	0.279	7.475
getQual-methods	1.565	0.101	1.668
getSeqlen-methods	1.109	0.064	1.174
kmerEntropyPlot	4.713	0.377	5.094
kmerKLPlot	14.261	1.194	15.471
list2df	1.362	0.130	1.494
makeReport	2.099	0.195	2.316
plotBases	0.010	0.008	0.018
plotGC	0.021	0.011	0.033
plotQuals	0.003	0.006	0.010
plotSeqLengths	0.009	0.009	0.018
qualPlot-methods	3.036	0.436	3.475
readSeqFile	0.493	0.074	0.570
scale_color_dna	0.884	0.048	0.933
scale_color_iupac	1.093	0.051	1.145
seqlenPlot-methods	2.374	0.126	2.501