BioC 2.13: CHECK report for qrqc on zin1

Package: qrqc

Version: 1.16.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.16.0.tar.gz

StartedAt: 2014-04-05 03:17:45 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:21:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 237.7 seconds

RetCode: 0

Status:  OK

CheckDir: qrqc.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/qrqc.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.16.0’
* 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 ... [21s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rsamtools’ ‘brew’ ‘testthat’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generateReads: no visible global function definition for
  ‘write.XStringSet’
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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘qrqc.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [47s/47s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
kmerKLPlot 12.145  0.064  12.226
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-functions.R’ [10s/10s]
 [10s/10s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/qrqc.Rcheck/00check.log’
for details.

* installing *source* package ‘qrqc’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c R_init_io.c -o R_init_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c io.c -o io.o
io.c:34:1: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
gcc -std=gnu99 -shared -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.000	0.004	0.005
FASTQSummary-class	0.000	0.004	0.005
SequenceSummary-class	0.004	0.000	0.004
basePlot-methods	3.176	0.024	3.210
calcKL	1.380	0.012	1.396
gcPlot-methods	1.156	0.016	1.171
getBase-methods	0.948	0.016	0.965
getBaseProp-methods	0.725	0.012	0.735
getGC-methods	0.568	0.012	0.586
getKmer-methods	1.264	0.004	1.293
getMCQual-methods	3.584	0.028	3.628
getQual-methods	0.768	0.012	0.780
getSeqlen-methods	0.468	0.016	0.496
kmerEntropyPlot	2.872	0.048	2.953
kmerKLPlot	12.145	0.064	12.226
list2df	1.120	0.028	1.149
makeReport	2.104	0.028	2.140
plotBases	0.000	0.000	0.002
plotGC	0.020	0.000	0.018
plotQuals	0.000	0.000	0.001
plotSeqLengths	0.004	0.004	0.008
qualPlot-methods	2.148	0.032	2.183
readSeqFile	0.384	0.012	0.398
scale_color_dna	0.580	0.008	0.590
scale_color_iupac	0.564	0.004	0.570
seqlenPlot-methods	1.068	0.012	1.080