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CHECK report for mosaics on malbec1

This page was generated on 2021-05-06 12:28:18 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the mosaics package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1140/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosaics 2.28.0  (landing page)
Dongjun Chung
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/mosaics
Branch: RELEASE_3_12
Last Commit: 4f6e125
Last Changed Date: 2020-10-27 10:40:07 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: mosaics
Version: 2.28.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:mosaics.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings mosaics_2.28.0.tar.gz
StartedAt: 2021-05-06 03:40:46 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:44:04 -0400 (Thu, 06 May 2021)
EllapsedTime: 197.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mosaics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:mosaics.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings mosaics_2.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/mosaics.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.28.0’
* 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 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 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


Installation output

mosaics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL mosaics
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘mosaics’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c convolution_1S.cpp -o convolution_1S.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c convolution_2S.cpp -o convolution_2S.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c emHMM.cpp -o emHMM.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stack.cpp -o stack.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updatePiMat.cpp -o updatePiMat.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c viterbi.cpp -o viterbi.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-mosaics/00new/mosaics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mosaics)

Tests output


Example timings

mosaics.Rcheck/mosaics-Ex.timings

nameusersystemelapsed
BinData-class0.0040.0000.001
MosaicsFit-class000
MosaicsFitEst-class000
MosaicsFitParam-class000
MosaicsHMM-class0.0040.0000.001
MosaicsPeak-class0.0000.0000.001
MosaicsPeakParam-class0.0000.0000.001
TagData-class0.0040.0000.001
adjustBoundary000
constructBins000
estimates000
export0.0000.0000.001
extractReads000
findSummit000
fllterPeak000
generateWig000
mosaics-package000
mosaicsFit000
mosaicsFitHMM0.0000.0040.001
mosaicsPeak000
mosaicsPeakHMM000
mosaicsRunAll0.0000.0000.001
readBins000