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CHECK report for methimpute on malbec1

This page was generated on 2018-04-12 13:16:50 -0400 (Thu, 12 Apr 2018).

Package 831/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methimpute 1.0.0
Aaron Taudt
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/methimpute
Branch: RELEASE_3_6
Last Commit: 0d0322b
Last Changed Date: 2017-10-30 12:42:01 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methimpute
Version: 1.0.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings methimpute_1.0.0.tar.gz
StartedAt: 2018-04-12 00:58:10 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:00:54 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 164.2 seconds
RetCode: 0
Status:  OK 
CheckDir: methimpute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings methimpute_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/methimpute.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methimpute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methimpute’ version ‘1.0.0’
* 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 ‘methimpute’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
* 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
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotting        19.36  0.020  19.054
exportMethylome  5.00  0.068   4.712
* 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-3.6-bioc/meat/methimpute.Rcheck/00check.log’
for details.



Installation output

methimpute.Rcheck/00install.out

* installing *source* package ‘methimpute’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c densities.cpp -o densities.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c fitHMM.cpp -o fitHMM.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c fitHMM_context.cpp -o fitHMM_context.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c hmm_context.cpp -o hmm_context.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c methimpute_init.c -o methimpute_init.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/methimpute.Rcheck/methimpute/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 (methimpute)

Tests output


Example timings

methimpute.Rcheck/methimpute-Ex.timings

nameusersystemelapsed
arabidopsis_TEs0.1720.0080.177
arabidopsis_chromosomes0.0000.0000.003
arabidopsis_genes0.0640.0000.064
arabidopsis_toydata0.3720.0080.378
binomialTestMethylation0.3960.0040.399
callMethylation3.9600.0363.363
callMethylationSeparate4.6240.0204.280
collapseBins3.2000.0043.211
distanceCorrelation2.1640.0002.169
estimateTransDist2.1000.0202.124
exportMethylome5.0000.0684.712
extractCytosinesFromFASTA4.4480.0004.450
getDistinctColors0.020.000.02
getStateColors0.0120.0000.013
import0.5480.0040.553
importRene0.0160.0000.016
inflateMethylome0.6320.0040.634
loadFromFiles0.1520.0040.155
plotting19.360 0.02019.054