BioC 3.5: CHECK report for ramwas on veracruz2
This page was generated on 2017-08-16 13:35:19 -0400 (Wed, 16 Aug 2017).
ramwas 1.0.0 Andrey A Shabalin
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ramwas | Last Changed Rev: 129126 / Revision: 131943 | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
Summary
Package: ramwas |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ramwas_1.0.0.tar.gz |
StartedAt: 2017-08-16 07:04:35 -0400 (Wed, 16 Aug 2017) |
EndedAt: 2017-08-16 07:08:02 -0400 (Wed, 16 Aug 2017) |
EllapsedTime: 206.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ramwas.Rcheck |
Warnings: 0 |
Command output
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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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ramwas.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.0.0’
* 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 ‘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 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: OK
ramwas.Rcheck/00install.out:
* 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-3.5-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)
ramwas.Rcheck/ramwas-Ex.timings:
name | user | system | elapsed
|
QCs | 0.063 | 0.010 | 0.073 |
|
cachedRDSload | 0.704 | 0.002 | 0.720 |
|
findBestNpvs | 0.002 | 0.000 | 0.003 |
|
getCpGset | 4.354 | 0.144 | 4.665 |
|
getDataByLocation | 0.001 | 0.000 | 0.001 |
|
getTestsByLocation | 0.001 | 0.001 | 0.001 |
|
injectSNPsMAF | 0.436 | 0.005 | 0.449 |
|
insilicoFASTQ | 0.001 | 0.000 | 0.001 |
|
isAbsolutePath | 0.001 | 0.001 | 0.001 |
|
makefullpath | 0.002 | 0.000 | 0.001 |
|
orthonormalizeCovariates | 0.031 | 0.001 | 0.031 |
|
parameterDump | 0.024 | 0.001 | 0.032 |
|
parameterPreprocess | 0.006 | 0.003 | 0.012 |
|
parametersFromFile | 0.002 | 0.001 | 0.003 |
|
pipeline | 0.003 | 0.000 | 0.004 |
|
plotROC | 0.004 | 0.001 | 0.004 |
|
processCommandLine | 0.002 | 0.000 | 0.004 |
|
pvalue2qvalue | 0.001 | 0.000 | 0.001 |
|
qqplotFast | 0.762 | 0.053 | 0.839 |
|
ramwas0createArtificialData | 0.278 | 0.022 | 0.305 |
|
ramwasAnnotateLocations | 0.294 | 0.009 | 3.566 |
|
ramwasParameters | 0.000 | 0.001 | 0.001 |
|
rowcolSumSq | 0.002 | 0.000 | 0.002 |
|
testPhenotype | 0.090 | 0.003 | 0.093 |
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