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BioC 3.5: CHECK report for DNAshapeR on malbec2

This page was generated on 2017-10-18 14:17:33 -0400 (Wed, 18 Oct 2017).

Package 361/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAshapeR 1.4.0
Tsu-Pei Chiu
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/DNAshapeR
Branch: RELEASE_3_5
Last Commit: 65e94e0
Last Changed Date: 2017-04-24 15:45:44 -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: DNAshapeR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DNAshapeR_1.4.0.tar.gz
StartedAt: 2017-10-17 22:45:51 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:48:33 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 161.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAshapeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DNAshapeR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DNAshapeR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNAshapeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNAshapeR’ version ‘1.4.0’
* 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 ‘DNAshapeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.6Mb
* 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
Examples with CPU or elapsed time > 5s
            user system elapsed
plotShape 12.528  0.076  12.612
getShape  12.484  0.108  12.597
heatShape 11.720  0.220  11.996
getFasta   6.796  0.080   6.973
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/DNAshapeR.Rcheck/00check.log’
for details.


DNAshapeR.Rcheck/00install.out:

* installing *source* package ‘DNAshapeR’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c OptionParser.cpp -o OptionParser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Output.cpp -o Output.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -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  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadData.cpp -o ReadData.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SNP.cpp -o SNP.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ShapePrediction.cpp -o ShapePrediction.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c TableCompiler.cpp -o TableCompiler.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c map.cpp -o map.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c prediction.cpp -o prediction.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c properties.cpp -o properties.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.cpp -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o DNAshapeR.so OptionParser.o Output.o RcppExports.o ReadData.o SNP.o ShapePrediction.o TableCompiler.o map.o prediction.o properties.o utilities.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/DNAshapeR.Rcheck/DNAshapeR/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 (DNAshapeR)

DNAshapeR.Rcheck/DNAshapeR-Ex.timings:

nameusersystemelapsed
encodeSeqShape0.1640.0000.166
getFasta6.7960.0806.973
getShape12.484 0.10812.597
heatShape11.720 0.22011.996
plotShape12.528 0.07612.612
readShape0.2920.0040.296
trackShape0.1600.0000.158