Package: ramwas

Version: 1.4.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ramwas.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ramwas_1.4.0.tar.gz

StartedAt: 2018-10-16 03:02:56 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:05:28 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 151.6 seconds

RetCode: 0

Status:  OK

CheckDir: ramwas.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:ramwas.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ramwas_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ramwas.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 ‘ramwas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ramwas’ 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 ‘ramwas’ 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 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 ... 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
manhattan 6.564  0.456   7.029
* 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-3.7-bioc/meat/ramwas.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 ramwas
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ramwas’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rw_c_code.c -o rw_c_code.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o ramwas.so rw_c_code.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/ramwas/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ramwas)

name	user	system	elapsed
MakeBED	0	0	0
QCs	0.032	0.004	0.045
cachedRDSload	1.040	0.000	1.044
findBestNpvs	0.000	0.004	0.001
get	0.000	0.000	0.002
getCpGset	2.912	0.048	3.093
injectSNPsMAF	0.648	0.000	0.652
insilicoFASTQ	0.000	0.000	0.001
isAbsolutePath	0.000	0.000	0.001
makefullpath	0.000	0.000	0.001
manhattan	6.564	0.456	7.029
mat2cols	0.004	0.000	0.001
orthonormalizeCovariates	0.008	0.000	0.008
parameterDump	0.004	0.000	0.003
parameterPreprocess	0.000	0.056	0.062
parametersFromFile	0.000	0.000	0.001
pipeline	0.004	0.000	0.002
plotCV	0.192	0.008	0.199
plotFragmentSizeDistributionEstimate	0.024	0.000	0.025
plotPC	0.008	0.000	0.006
processCommandLine	0.004	0.000	0.002
pvalue2qvalue	0	0	0
qqplotFast	0.656	0.080	0.735
ramwas0createArtificialData	0.192	0.004	0.197
ramwasAnnotateLocations	0.004	0.000	0.001
ramwasParameters	0.000	0.000	0.001
rowcolSumSq	0.004	0.000	0.002
rwDataClass-class	0.032	0.004	0.036
subsetData	0	0	0
testPhenotype	0.020	0.000	0.018