BioC 3.4: CHECK report for mosaics on malbec1

Package: mosaics

Version: 2.12.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mosaics_2.12.0.tar.gz

StartedAt: 2017-04-14 23:57:55 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:00:37 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 161.5 seconds

RetCode: 0

Status:  OK

CheckDir: mosaics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mosaics_2.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mosaics.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘2.12.0’
* 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 ... 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 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: OK

* installing *source* package ‘mosaics’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c convolution_1S.cpp -o convolution_1S.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c convolution_2S.cpp -o convolution_2S.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c emHMM.cpp -o emHMM.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c stack.cpp -o stack.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updatePiMat.cpp -o updatePiMat.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c viterbi.cpp -o viterbi.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o mosaics.so convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/mosaics.Rcheck/mosaics/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 (mosaics)

name	user	system	elapsed
BinData-class	0.004	0.000	0.002
MosaicsFit-class	0.000	0.000	0.001
MosaicsFitEst-class	0.000	0.004	0.000
MosaicsFitParam-class	0.000	0.000	0.001
MosaicsHMM-class	0.004	0.000	0.002
MosaicsPeak-class	0.000	0.004	0.003
MosaicsPeakParam-class	0	0	0
TagData-class	0.000	0.000	0.001
adjustBoundary	0.004	0.000	0.000
constructBins	0.000	0.000	0.001
estimates	0	0	0
export	0.004	0.000	0.001
extractReads	0	0	0
findSummit	0.004	0.000	0.001
fllterPeak	0.000	0.000	0.001
generateWig	0.000	0.000	0.001
mosaics-package	0.004	0.000	0.002
mosaicsFit	0	0	0
mosaicsFitHMM	0.004	0.000	0.001
mosaicsPeak	0	0	0
mosaicsPeakHMM	0.000	0.004	0.001
mosaicsRunAll	0.000	0.000	0.001
readBins	0	0	0