Package: methimpute

Version: 1.2.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methimpute_1.2.0.tar.gz

StartedAt: 2018-10-16 01:52:36 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:54:32 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 116.6 seconds

RetCode: 0

Status:  OK

CheckDir: methimpute.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methimpute_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/methimpute.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
plotting 14.436   0.02  13.995
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/methimpute.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL methimpute
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘methimpute’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/methimpute/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methimpute)

name	user	system	elapsed
arabidopsis_TEs	0.048	0.004	0.054
arabidopsis_chromosomes	0.000	0.000	0.003
arabidopsis_genes	0.016	0.000	0.015
arabidopsis_toydata	0.168	0.004	0.172
binning	2.636	0.016	2.656
binomialTestMethylation	0.216	0.000	0.216
callMethylation	3.080	0.008	2.528
callMethylationSeparate	3.776	0.040	3.517
collapseBins	3.000	0.004	3.004
distanceCorrelation	1.220	0.000	1.221
estimateTransDist	1.120	0.012	1.131
exportMethylome	2.872	0.036	2.323
extractCytosinesFromFASTA	4.688	0.000	4.700
getDistinctColors	0.020	0.000	0.019
getStateColors	0.012	0.000	0.012
import	0.392	0.008	0.391
importRene	0.036	0.000	0.036
inflateMethylome	0.396	0.004	0.380
loadFromFiles	0.144	0.008	0.154
plotting	14.436	0.020	13.995