Package: ramwas

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ramwas.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ramwas_1.6.0.tar.gz

StartedAt: 2019-04-16 02:11:32 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:15:15 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 223.1 seconds

RetCode: 0

Status:  OK

CheckDir: ramwas.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ramwas.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ramwas_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ramwas.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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 7.185  0.766   7.994
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/ramwas.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ramwas
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ramwas’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rw_c_code.c -o rw_c_code.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 ramwas.so rw_c_code.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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	0.001	0.000	0.000
QCs	0.041	0.004	0.045
cachedRDSload	1.014	0.003	1.023
findBestNpvs	0.002	0.001	0.002
get	0.000	0.000	0.001
getCpGset	3.178	0.176	3.388
injectSNPsMAF	0.593	0.010	0.605
insilicoFASTQ	0.002	0.000	0.002
isAbsolutePath	0.001	0.001	0.002
makefullpath	0.001	0.000	0.001
manhattan	7.185	0.766	7.994
mat2cols	0.002	0.001	0.001
orthonormalizeCovariates	0.012	0.001	0.013
parameterDump	0.005	0.001	0.005
parameterPreprocess	0.009	0.005	0.015
parametersFromFile	0.002	0.001	0.003
pipeline	0.003	0.000	0.004
plotCV	0.224	0.013	0.249
plotFragmentSizeDistributionEstimate	0.029	0.000	0.030
plotPC	0.006	0.002	0.007
processCommandLine	0.001	0.000	0.001
pvalue2qvalue	0.001	0.000	0.000
qqplotFast	0.726	0.200	0.935
ramwas0createArtificialData	0.292	0.023	0.318
ramwasAnnotateLocations	0.000	0.000	0.001
ramwasParameters	0.001	0.000	0.001
rowcolSumSq	0.002	0.001	0.002
rwDataClass-class	0.039	0.000	0.039
subsetData	0.001	0.000	0.001
testPhenotype	0.022	0.002	0.024