Package: ramwas

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ramwas_1.2.0.tar.gz

StartedAt: 2018-04-12 08:17:22 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:20:48 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 206.2 seconds

RetCode: 0

Status:  OK

CheckDir: ramwas.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ramwas_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ramwas.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* 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 ‘ramwas’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
* 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
* 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-3.6-bioc/meat/ramwas.Rcheck/00check.log’
for details.

* 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 /Users/biocbuild/bbs-3.6-bioc/meat/ramwas.Rcheck/ramwas/libs
** R
** inst
** preparing 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
QCs	0.062	0.003	0.067
cachedRDSload	0.661	0.001	0.695
findBestNpvs	0.002	0.000	0.002
getCpGset	4.581	0.136	4.919
getDataByLocation	0.000	0.000	0.001
getTestsByLocation	0.001	0.000	0.000
injectSNPsMAF	0.408	0.006	0.427
insilicoFASTQ	0.003	0.000	0.002
isAbsolutePath	0.001	0.000	0.001
makefullpath	0.001	0.000	0.002
orthonormalizeCovariates	0.028	0.000	0.029
parameterDump	0.025	0.001	0.027
parameterPreprocess	0.006	0.003	0.010
parametersFromFile	0.002	0.001	0.003
pipeline	0.003	0.000	0.003
plotROC	0.004	0.001	0.004
processCommandLine	0.003	0.000	0.002
pvalue2qvalue	0.001	0.000	0.001
qqplotFast	0.691	0.052	0.763
ramwas0createArtificialData	0.264	0.025	0.293
ramwasAnnotateLocations	0.285	0.012	3.808
ramwasParameters	0.000	0.000	0.001
rowcolSumSq	0.002	0.000	0.002
testPhenotype	0.080	0.001	0.081