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BioC 3.3: CHECK report for qrqc on windows2.bioconductor.org

This page was generated on 2015-10-27 12:14:47 -0400 (Tue, 27 Oct 2015).

Package 823/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.25.0
Vince Buffalo
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qrqc
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qrqc
Version: 1.25.0
Command: rm -rf qrqc.buildbin-libdir qrqc.Rcheck && mkdir qrqc.buildbin-libdir qrqc.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qrqc.buildbin-libdir qrqc_1.25.0.tar.gz >qrqc.Rcheck\00install.out 2>&1 && cp qrqc.Rcheck\00install.out qrqc-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=qrqc.buildbin-libdir --install="check:qrqc-install.out" --force-multiarch --no-vignettes --timings qrqc_1.25.0.tar.gz
StartedAt: 2015-10-27 05:14:17 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:19:28 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 311.2 seconds
RetCode: 0
Status:  OK  
CheckDir: qrqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf qrqc.buildbin-libdir qrqc.Rcheck && mkdir qrqc.buildbin-libdir qrqc.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qrqc.buildbin-libdir qrqc_1.25.0.tar.gz >qrqc.Rcheck\00install.out 2>&1 && cp qrqc.Rcheck\00install.out qrqc-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=qrqc.buildbin-libdir --install="check:qrqc-install.out" --force-multiarch --no-vignettes --timings qrqc_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/qrqc.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qrqc/DESCRIPTION' ... OK
* this is package 'qrqc' version '1.25.0'
* 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 whether package 'qrqc' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'Rsamtools' 'brew' 'testthat' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 'DNAStringSet'
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'
Undefined global functions or variables:
  DNAStringSet base entropy kl kmer position write.XStringSet
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'c:/biocbld/bbs-3.3-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/i386/qrqc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'c:/biocbld/bbs-3.3-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/x64/qrqc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kmerKLPlot 6.79   0.01    6.81
** running examples for arch 'x64' ... [34s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kmerKLPlot  6.2   0.12    6.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-functions.R' [8s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'test-functions.R' [8s]
 [8s] 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
* DONE

Status: 5 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/qrqc.Rcheck/00check.log'
for details.


qrqc.Rcheck/00install.out:


install for i386

* installing *source* package 'qrqc' ...
** libs
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"c:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_io.c -o R_init_io.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"c:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c:28:1: warning: 'kseq_destroy' defined but not used [-Wunused-function]
gcc -m32 -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'qrqc' ...
** libs
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"c:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_io.c -o R_init_io.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"c:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c:28:1: warning: 'kseq_destroy' defined but not used [-Wunused-function]
gcc -m64 -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qrqc' as qrqc_1.25.0.zip
* DONE (qrqc)

qrqc.Rcheck/examples_i386/qrqc-Ex.timings:

nameusersystemelapsed
FASTASummary-class000
FASTQSummary-class000
SequenceSummary-class000
basePlot-methods1.720.061.78
calcKL0.550.020.57
gcPlot-methods0.800.030.82
getBase-methods0.750.000.75
getBaseProp-methods0.580.030.61
getGC-methods0.370.000.38
getKmer-methods0.750.060.81
getMCQual-methods2.140.042.17
getQual-methods0.520.010.53
getSeqlen-methods0.650.030.69
kmerEntropyPlot2.820.102.91
kmerKLPlot6.790.016.81
list2df0.830.080.91
makeReport1.130.021.14
plotBases000
plotGC000
plotQuals000
plotSeqLengths000
qualPlot-methods1.500.041.54
readSeqFile0.340.000.35
scale_color_dna0.410.000.40
scale_color_iupac0.400.000.41
seqlenPlot-methods0.860.030.89

qrqc.Rcheck/examples_x64/qrqc-Ex.timings:

nameusersystemelapsed
FASTASummary-class000
FASTQSummary-class000
SequenceSummary-class000
basePlot-methods1.930.011.95
calcKL0.630.000.62
gcPlot-methods0.970.020.99
getBase-methods0.630.010.64
getBaseProp-methods0.670.020.69
getGC-methods0.640.010.66
getKmer-methods1.130.081.20
getMCQual-methods2.170.022.19
getQual-methods0.540.030.58
getSeqlen-methods0.350.040.39
kmerEntropyPlot1.950.021.98
kmerKLPlot6.200.126.33
list2df0.970.111.08
makeReport1.480.041.52
plotBases000
plotGC000
plotQuals000
plotSeqLengths000
qualPlot-methods2.120.072.21
readSeqFile0.440.030.47
scale_color_dna0.500.020.51
scale_color_iupac0.440.000.44
seqlenPlot-methods0.920.030.95