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BioC 3.4: CHECK report for mosaics on moscato1

This page was generated on 2016-09-21 03:43:19 -0700 (Wed, 21 Sep 2016).

Package 773/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosaics 2.11.1
Dongjun Chung
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mosaics
Last Changed Rev: 120052 / Revision: 121152
Last Changed Date: 2016-08-11 01:54:04 -0700 (Thu, 11 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mosaics
Version: 2.11.1
Command: rm -rf mosaics.buildbin-libdir mosaics.Rcheck && mkdir mosaics.buildbin-libdir mosaics.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mosaics.buildbin-libdir mosaics_2.11.1.tar.gz >mosaics.Rcheck\00install.out 2>&1 && cp mosaics.Rcheck\00install.out mosaics-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=mosaics.buildbin-libdir --install="check:mosaics-install.out" --force-multiarch --no-vignettes --timings mosaics_2.11.1.tar.gz
StartedAt: 2016-09-20 12:30:20 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:35:01 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 280.4 seconds
RetCode: 0
Status:  OK  
CheckDir: mosaics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mosaics.buildbin-libdir mosaics.Rcheck && mkdir mosaics.buildbin-libdir mosaics.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mosaics.buildbin-libdir mosaics_2.11.1.tar.gz >mosaics.Rcheck\00install.out 2>&1 && cp mosaics.Rcheck\00install.out mosaics-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=mosaics.buildbin-libdir --install="check:mosaics-install.out" --force-multiarch --no-vignettes --timings mosaics_2.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/mosaics.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mosaics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mosaics' version '2.11.1'
* 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 whether package 'mosaics' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 ... 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/mosaics.buildbin-libdir/mosaics/libs/i386/mosaics.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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' ... OK
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/mosaics.Rcheck/00check.log'
for details.


mosaics.Rcheck/00install.out:


install for i386

* installing *source* package 'mosaics' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c convolution_1S.cpp -o convolution_1S.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c convolution_2S.cpp -o convolution_2S.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c emHMM.cpp -o emHMM.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c stack.cpp -o stack.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updatePiMat.cpp -o updatePiMat.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c viterbi.cpp -o viterbi.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o mosaics.dll tmp.def convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/mosaics.buildbin-libdir/mosaics/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'mosaics'
Creating a generic function for 'plot' from package 'graphics' in package 'mosaics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'mosaics' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c convolution_1S.cpp -o convolution_1S.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c convolution_2S.cpp -o convolution_2S.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c emHMM.cpp -o emHMM.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c stack.cpp -o stack.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c updatePiMat.cpp -o updatePiMat.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c viterbi.cpp -o viterbi.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o mosaics.dll tmp.def convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/mosaics.buildbin-libdir/mosaics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mosaics' as mosaics_2.11.1.zip
* DONE (mosaics)

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

nameusersystemelapsed
BinData-class000
MosaicsFit-class0.020.000.02
MosaicsFitEst-class000
MosaicsFitParam-class000
MosaicsHMM-class000
MosaicsPeak-class000
MosaicsPeakParam-class0.010.000.02
TagData-class000
adjustBoundary000
constructBins000
estimates000
export000
extractReads000
findSummit0.000.010.01
fllterPeak000
generateWig000
mosaics-package000
mosaicsFit000
mosaicsFitHMM000
mosaicsPeak0.000.000.02
mosaicsPeakHMM000
mosaicsRunAll000
readBins000

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

nameusersystemelapsed
BinData-class0.020.000.01
MosaicsFit-class000
MosaicsFitEst-class000
MosaicsFitParam-class000
MosaicsHMM-class000
MosaicsPeak-class0.010.000.02
MosaicsPeakParam-class000
TagData-class000
adjustBoundary000
constructBins000
estimates000
export000
extractReads000
findSummit000
fllterPeak000
generateWig000
mosaics-package000
mosaicsFit000
mosaicsFitHMM000
mosaicsPeak000
mosaicsPeakHMM000
mosaicsRunAll000
readBins000