BioC 2.12: CHECK report for qrqc on petty

Package: qrqc

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qrqc_1.14.0.tar.gz

StartedAt: 2013-10-08 23:33:38 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:41:09 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 450.9 seconds

RetCode: 0

Status:  OK

CheckDir: qrqc.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'qrqc/DESCRIPTION' ... OK
* this is package 'qrqc' version '1.14.0'
* 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 'qrqc' can be installed ... [41s/41s] 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 ... [88s/89s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
kmerKLPlot        19.228  0.790  20.248
getMCQual-methods  7.051  0.139   7.267
basePlot-methods   5.860  0.179   6.221
kmerEntropyPlot    5.373  0.275   5.683
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-functions.R' [18s/18s]
 [19s/19s] 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -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  -mtune=core2 -g -O2  -c R_init_io.c -o R_init_io.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -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  -mtune=core2 -g -O2  -c io.c -o io.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//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
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qrqc)

name	user	system	elapsed
FASTASummary-class	0.010	0.003	0.013
FASTQSummary-class	0.009	0.003	0.012
SequenceSummary-class	0.008	0.002	0.010
basePlot-methods	5.860	0.179	6.221
calcKL	2.517	0.079	2.605
gcPlot-methods	2.228	0.103	2.336
getBase-methods	1.544	0.073	1.631
getBaseProp-methods	1.492	0.051	1.592
getGC-methods	1.104	0.051	1.202
getKmer-methods	2.679	0.078	2.767
getMCQual-methods	7.051	0.139	7.267
getQual-methods	1.437	0.085	1.530
getSeqlen-methods	0.959	0.050	1.043
kmerEntropyPlot	5.373	0.275	5.683
kmerKLPlot	19.228	0.790	20.248
list2df	1.942	0.173	2.131
makeReport	3.508	0.168	3.793
plotBases	0.004	0.006	0.009
plotGC	0.003	0.005	0.009
plotQuals	0.013	0.006	0.020
plotSeqLengths	0.004	0.005	0.011
qualPlot-methods	4.176	0.284	4.526
readSeqFile	0.685	0.065	0.755
scale_color_dna	1.135	0.056	1.198
scale_color_iupac	1.117	0.052	1.244
seqlenPlot-methods	2.196	0.109	2.342