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BioC 3.5: CHECK report for RJMCMCNucleosomes on malbec2

This page was generated on 2017-08-16 13:18:07 -0400 (Wed, 16 Aug 2017).

Package 1122/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RJMCMCNucleosomes 1.0.0
Astrid DeschĂȘnes
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/RJMCMCNucleosomes
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RJMCMCNucleosomes
Version: 1.0.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_1.0.0.tar.gz
StartedAt: 2017-08-16 01:54:19 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:58:22 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 242.2 seconds
RetCode: 0
Status:  OK 
CheckDir: RJMCMCNucleosomes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK
* this is package ‘RJMCMCNucleosomes’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘RJMCMCNucleosomes’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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

RJMCMCNucleosomes.Rcheck/00install.out:

* installing *source* package ‘RJMCMCNucleosomes’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c NucleoDirichlet.cpp -o NucleoDirichlet.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Nucleosome.cpp -o Nucleosome.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SegmentSeq.cpp -o SegmentSeq.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG `gsl-config --cflags` -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o RJMCMCNucleosomes.so NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RJMCMCNucleosomes)

RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes-Ex.timings:

nameusersystemelapsed
RJMCMC_result0.9800.0040.986
mergeAllRDSFiles0.3120.0000.312
mergeAllRDSFilesFromDirectory0.0600.0000.061
mergeRDSFiles0.0440.0000.046
plotNucleosomes0.5880.0000.639
postMerge0.5760.0040.579
postTreatment0.40.00.4
print.rjmcmcNucleosomes0.0040.0000.004
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.1960.0040.200
print.rjmcmcNucleosomesMerge0.0480.0000.051
reads_demo_010.0320.0000.034
reads_demo_020.0440.0000.044
rjmcmc0.1080.0000.109
rjmcmcCHR0.6680.0000.666
rjmcmcNucleo0.0920.0000.092
runCHR0.0640.0080.071
segmentation0.0800.0080.087
validateDirectoryParameters0.0000.0000.002
validatePlotNucleosomesParameters0.0280.0000.031
validatePrepMergeParameters0.0040.0000.004
validateRDSFilesParameters0.0040.0000.006
validateRJMCMCParameters0.0040.0040.007
validateSegmentationParameters0.0160.0000.014