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CHECK report for mosaics on tokay2

This page was generated on 2020-10-17 11:57:11 -0400 (Sat, 17 Oct 2020).

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 1122/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosaics 2.26.0
Dongjun Chung
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/mosaics
Branch: RELEASE_3_11
Last Commit: fa77ced
Last Changed Date: 2020-04-27 14:24:14 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mosaics
Version: 2.26.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mosaics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings mosaics_2.26.0.tar.gz
StartedAt: 2020-10-17 06:12:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:17:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 286.8 seconds
RetCode: 0
Status:  OK  
CheckDir: mosaics.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mosaics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings mosaics_2.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/mosaics.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.26.0'
* 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 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
* 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 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 ...
** 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: OK


Installation output

mosaics.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/mosaics_2.26.0.tar.gz && rm -rf mosaics.buildbin-libdir && mkdir mosaics.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mosaics.buildbin-libdir mosaics_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL mosaics_2.26.0.zip && rm mosaics_2.26.0.tar.gz mosaics_2.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  964k  100  964k    0     0  12.4M      0 --:--:-- --:--:-- --:--:-- 13.8M

install for i386

* installing *source* package 'mosaics' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c convolution_1S.cpp -o convolution_1S.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c convolution_2S.cpp -o convolution_2S.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c emHMM.cpp -o emHMM.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c stack.cpp -o stack.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatePiMat.cpp -o updatePiMat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c viterbi.cpp -o viterbi.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mosaics.dll tmp.def convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/mosaics.buildbin-libdir/00LOCK-mosaics/00new/mosaics/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mosaics'
    finding HTML links ... done
    BinData-class                           html  
    MosaicsFit-class                        html  
    MosaicsFitEst-class                     html  
    MosaicsFitParam-class                   html  
    MosaicsHMM-class                        html  
    MosaicsPeak-class                       html  
    MosaicsPeakParam-class                  html  
    TagData-class                           html  
    adjustBoundary                          html  
    constructBins                           html  
    estimates                               html  
    export                                  html  
    extractReads                            html  
    findSummit                              html  
    fllterPeak                              html  
    generateWig                             html  
    mosaics-internal                        html  
    mosaics-package                         html  
    mosaicsFit                              html  
    mosaicsFitHMM                           html  
    mosaicsPeak                             html  
    mosaicsPeakHMM                          html  
    mosaicsRunAll                           html  
    readBins                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'mosaics' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c convolution_1S.cpp -o convolution_1S.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c convolution_2S.cpp -o convolution_2S.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c emHMM.cpp -o emHMM.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c stack.cpp -o stack.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatePiMat.cpp -o updatePiMat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c viterbi.cpp -o viterbi.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mosaics.dll tmp.def convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/mosaics.buildbin-libdir/mosaics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mosaics' as mosaics_2.26.0.zip
* DONE (mosaics)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'mosaics' successfully unpacked and MD5 sums checked

Tests output


Example timings

mosaics.Rcheck/examples_i386/mosaics-Ex.timings

nameusersystemelapsed
BinData-class000
MosaicsFit-class000
MosaicsFitEst-class000
MosaicsFitParam-class000
MosaicsHMM-class000
MosaicsPeak-class0.010.000.01
MosaicsPeakParam-class000
TagData-class000
adjustBoundary000
constructBins000
estimates000
export000
extractReads000
findSummit000
fllterPeak000
generateWig000
mosaics-package000
mosaicsFit000
mosaicsFitHMM000
mosaicsPeak0.000.020.02
mosaicsPeakHMM000
mosaicsRunAll000
readBins000

mosaics.Rcheck/examples_x64/mosaics-Ex.timings

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