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BioC 2.14: CHECK report for qrqc on petty

This page was generated on 2014-10-08 08:59:30 -0700 (Wed, 08 Oct 2014).

Package 618/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.18.0
Vince Buffalo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/qrqc
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: qrqc
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qrqc_1.18.0.tar.gz
StartedAt: 2014-10-07 23:38:35 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:48:49 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 613.4 seconds
RetCode: 0
Status:  OK 
CheckDir: qrqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qrqc_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/qrqc.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ ‘brew’ ‘xtable’
  ‘Rsamtools’ ‘testthat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [53s/53s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘brew’ ‘Rsamtools’ ‘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,list: no visible binding for global variable ‘base’
basePlot,SequenceSummary: no visible binding for global variable ‘base’
gcPlot,list: no visible binding for global variable ‘position’
gcPlot,SequenceSummary: 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,list: no visible binding for global variable ‘position’
kmerEntropyPlot,list: no visible binding for global variable ‘entropy’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  ‘position’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  ‘entropy’
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’
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’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [94s/95s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
kmerKLPlot        20.595  0.545  21.284
getMCQual-methods  7.257  0.129   7.434
basePlot-methods   6.830  0.150   7.166
kmerEntropyPlot    5.520  0.225   5.811
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-functions.R’ [25s/25s]
 [26s/26s] 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
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/qrqc.Rcheck/00check.log’
for details.

qrqc.Rcheck/00install.out:

* 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/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c io.c -o io.o
io.c:34: warning: ‘kseq_destroy’ defined but not used
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/3.1/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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)

qrqc.Rcheck/qrqc-Ex.timings:

nameusersystemelapsed
FASTASummary-class0.0050.0010.005
FASTQSummary-class0.0030.0000.003
SequenceSummary-class0.0030.0000.003
basePlot-methods6.8300.1507.166
calcKL1.7440.0401.791
gcPlot-methods2.0950.0502.220
getBase-methods1.4230.0211.455
getBaseProp-methods1.4300.0221.459
getGC-methods1.0430.0231.068
getKmer-methods2.3100.0272.345
getMCQual-methods7.2570.1297.434
getQual-methods1.3710.0611.436
getSeqlen-methods0.9690.0461.018
kmerEntropyPlot5.5200.2255.811
kmerKLPlot20.595 0.54521.284
list2df2.7720.1402.933
makeReport3.3950.1553.591
plotBases0.0020.0000.002
plotGC0.0010.0010.001
plotQuals0.0010.0000.001
plotSeqLengths0.0010.0000.001
qualPlot-methods3.8380.2144.080
readSeqFile0.6700.0640.735
scale_color_dna1.1150.0541.172
scale_color_iupac1.1100.0221.136
seqlenPlot-methods2.0830.0412.141