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BioC 3.5: CHECK report for RJMCMCNucleosomes on toluca2

This page was generated on 2017-04-23 14:42:32 -0400 (Sun, 23 Apr 2017).

Package 1117/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RJMCMCNucleosomes 0.99.15
Astrid DeschĂȘnes
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RJMCMCNucleosomes
Last Changed Rev: 128344 / Revision: 129046
Last Changed Date: 2017-04-07 15:41:19 -0400 (Fri, 07 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
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: 0.99.15
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_0.99.15.tar.gz
StartedAt: 2017-04-23 09:08:39 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 09:13:59 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 319.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RJMCMCNucleosomes.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_0.99.15.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK
* this is package ‘RJMCMCNucleosomes’ version ‘0.99.15’
* 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
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c NucleoDirichlet.cpp -o NucleoDirichlet.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Nucleosome.cpp -o Nucleosome.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c SegmentSeq.cpp -o SegmentSeq.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c rjmcmcNucleo.cpp -o rjmcmcNucleo.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 RJMCMCNucleosomes.so NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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_result1.4930.0341.531
mergeAllRDSFiles0.5070.0010.510
mergeAllRDSFilesFromDirectory0.0910.0000.092
mergeRDSFiles0.0730.0010.074
plotNucleosomes0.4080.0040.413
postMerge0.8900.0060.915
postTreatment0.4900.0040.496
print.rjmcmcNucleosomes0.0050.0010.006
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.3110.0040.316
print.rjmcmcNucleosomesMerge0.0760.0010.078
reads_demo_010.0410.0030.044
reads_demo_020.0510.0020.053
rjmcmc0.1050.0020.108
rjmcmcCHR0.8550.0040.861
rjmcmcNucleo0.0900.0030.093
runCHR0.1020.0120.116
segmentation0.1400.0110.152
validateDirectoryParameters0.0020.0000.001
validatePlotNucleosomesParameters0.0590.0090.068
validatePrepMergeParameters0.0040.0080.013
validateRDSFilesParameters0.0120.0000.012
validateRJMCMCParameters0.010.000.01
validateSegmentationParameters0.0180.0020.019