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BioC 3.2: CHECK report for mosaics on oaxaca

This page was generated on 2016-04-23 10:25:01 -0700 (Sat, 23 Apr 2016).

Package 667/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosaics 2.4.1
Dongjun Chung
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/mosaics
Last Changed Rev: 115336 / Revision: 116712
Last Changed Date: 2016-03-28 21:54:37 -0700 (Mon, 28 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mosaics
Version: 2.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mosaics_2.4.1.tar.gz
StartedAt: 2016-04-23 02:19:44 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:22:29 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 164.4 seconds
RetCode: 0
Status:  OK 
CheckDir: mosaics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mosaics_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mosaics.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mosaics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mosaics’ version ‘2.4.1’
* 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 ‘mosaics’ can be installed ... [23s/23s] 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
* 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 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
.mosaicsZ0: no visible global function definition for ‘mclapply’
.plotGOFHMM: no visible global function definition for ‘mclapply’
mosaicsRunAll: no visible global function definition for ‘mclapply’
readBins: no visible global function definition for ‘mclapply’
mosaicsFitHMM,MosaicsFit : .local: no visible global function
  definition for ‘mclapply’
mosaicsPeakHMM,MosaicsHMM : .local: no visible global function
  definition for ‘mclapply’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/6s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/mosaics.Rcheck/00check.log’
for details.


mosaics.Rcheck/00install.out:

* installing *source* package ‘mosaics’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c convolution_1S.cpp -o convolution_1S.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c convolution_2S.cpp -o convolution_2S.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c emHMM.cpp -o emHMM.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c updatePiMat.cpp -o updatePiMat.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c viterbi.cpp -o viterbi.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mosaics.so convolution_1S.o convolution_2S.o emHMM.o updatePiMat.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/mosaics.Rcheck/mosaics/libs
** 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
* DONE (mosaics)

mosaics.Rcheck/mosaics-Ex.timings:

nameusersystemelapsed
BinData-class0.0020.0000.002
MosaicsFit-class0.0020.0000.002
MosaicsFitEst-class0.0020.0000.004
MosaicsFitParam-class0.0010.0000.002
MosaicsHMM-class0.0020.0000.002
MosaicsPeak-class0.0020.0010.003
MosaicsPeakParam-class0.0010.0000.001
constructBins0.0010.0000.001
estimates0.0010.0000.001
export0.0010.0010.001
generateWig000
mosaics-package0.0010.0000.002
mosaicsFit0.0010.0010.000
mosaicsFitHMM0.0010.0000.001
mosaicsPeak0.0010.0000.000
mosaicsPeakHMM0.0010.0000.001
mosaicsRunAll0.0010.0000.008
readBins000