Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P [Q] R  S  T  U  V  W  X  Y  Z 

Package 500/658HostnameOS / ArchBUILDCHECKBUILD BIN
qrqc 1.13.1
Vince Buffalo
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qrqc
Last Changed Rev: 72298 / Revision: 74774
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: qrqc
Version: 1.13.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.13.1.tar.gz
StartedAt: 2013-03-25 03:58:20 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:06:19 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 478.4 seconds
RetCode: 0
Status:  OK 
CheckDir: qrqc.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.13.1’
* 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 ... [42s/48s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [89s/91s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
kmerKLPlot        23.617  0.172  24.404
getMCQual-methods  9.828  0.072  10.054
kmerEntropyPlot    7.637  0.160   7.828
basePlot-methods   5.060  0.072   5.143
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-functions.R’ [20s/20s]
 [20s/20s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/qrqc.Rcheck/00check.log’
for details.

qrqc.Rcheck/00install.out:

* installing *source* package ‘qrqc’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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
   ‘qrqc.Rnw’ 
** testing if installed package can be loaded
* DONE (qrqc)

qrqc.Rcheck/qrqc-Ex.timings:

nameusersystemelapsed
FASTASummary-class0.0120.0000.012
FASTQSummary-class0.0160.0000.017
SequenceSummary-class0.0120.0000.012
basePlot-methods5.0600.0725.143
calcKL2.8400.0202.862
gcPlot-methods2.6320.0682.701
getBase-methods1.2000.0321.233
getBaseProp-methods1.1720.0241.249
getGC-methods0.8920.0120.939
getKmer-methods2.0050.0322.537
getMCQual-methods 9.828 0.07210.054
getQual-methods1.3240.0641.387
getSeqlen-methods0.8920.0480.937
kmerEntropyPlot7.6370.1607.828
kmerKLPlot23.617 0.17224.404
list2df1.3960.0641.574
makeReport2.5480.0282.647
plotBases0.0080.0000.007
plotGC0.0320.0000.033
plotQuals0.0240.0000.030
plotSeqLengths0.0200.0000.023
qualPlot-methods3.9530.0604.016
readSeqFile0.4960.0200.524
scale_color_dna0.8160.0240.843
scale_color_iupac0.8960.0240.939
seqlenPlot-methods1.8080.0481.865