qrqc 1.12.0
Vince Buffalo
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/qrqc | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/qrqc.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.12.0’
* 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 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 14.901 1.164 18.671
getMCQual-methods 6.212 0.112 7.817
basePlot-methods 4.209 0.908 7.693
kmerEntropyPlot 4.541 0.152 5.143
list2df 1.152 1.348 5.212
getQual-methods 1.444 0.180 5.263
getKmer-methods 1.364 0.164 7.380
* 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-2.11-bioc/meat/qrqc.Rcheck/00check.log’
for details.
* installing *source* package ‘qrqc’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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-2.11-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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)