Package: qrqc

Version: 1.10.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.10.0.tar.gz

StartedAt: 2012-04-01 02:51:06 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:53:36 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 149.9 seconds

RetCode: 0

Status:  OK

CheckDir: qrqc.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/qrqc.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qrqc/DESCRIPTION' ... OK
* this is package 'qrqc' version '1.10.0'
* 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 whether package 'qrqc' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* 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
* 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

* installing *source* package 'qrqc' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c R_init_io.c -o R_init_io.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c io.c -o io.o
gcc -std=gnu99 -shared -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-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	0.000	0.000	0.001
FASTQSummary-class	0.004	0.000	0.000
SequenceSummary-class	0	0	0
basePlot-methods	3.240	0.036	3.288
calcKL	1.064	0.016	1.084
gcPlot-methods	1.248	0.044	1.305
getBase-methods	0.768	0.024	0.795
getBaseProp-methods	0.792	0.012	0.813
getGC-methods	0.604	0.012	0.621
getKmer-methods	1.456	0.020	1.481
getMCQual-methods	3.381	0.032	3.464
getQual-methods	0.816	0.036	0.857
getSeqlen-methods	0.520	0.016	0.542
kmerEntropyPlot	2.704	0.052	2.770
kmerKLPlot	8.892	0.048	8.963
list2df	1.072	0.032	1.107
makeReport	2.113	0.020	2.200
plotBases	0	0	0
plotGC	0	0	0
plotQuals	0	0	0
plotSeqLengths	0	0	0
qualPlot-methods	2.232	0.036	2.292
readSeqFile	0.316	0.020	0.350
scale_color_dna	0.524	0.004	0.534
scale_color_iupac	0.520	0.012	0.534
seqlenPlot-methods	1.064	0.008	1.081