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BioC 3.6: CHECK report for ramwas on malbec1

This page was generated on 2017-08-16 13:25:16 -0400 (Wed, 16 Aug 2017).

Package 1075/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.1.0
Andrey A Shabalin
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ramwas
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ramwas
Version: 1.1.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ramwas_1.1.0.tar.gz
StartedAt: 2017-08-16 01:42:39 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:45:25 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 166.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ramwas.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ramwas_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ramwas.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.1.0’
* 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
gcc -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o ramwas.so rw_c_code.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/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)

ramwas.Rcheck/ramwas-Ex.timings:

nameusersystemelapsed
QCs0.0440.0040.048
cachedRDSload0.7360.0000.734
findBestNpvs0.0000.0000.002
getCpGset4.1960.0524.387
getDataByLocation000
getTestsByLocation0.0000.0000.001
injectSNPsMAF0.4760.0000.476
insilicoFASTQ0.0040.0000.002
isAbsolutePath0.0000.0000.001
makefullpath0.0040.0000.001
orthonormalizeCovariates0.0200.0000.022
parameterDump0.0160.0000.016
parameterPreprocess0.0040.0160.026
parametersFromFile0.0000.0000.003
pipeline0.0040.0000.003
plotROC0.0040.0000.005
processCommandLine0.0000.0000.002
pvalue2qvalue000
qqplotFast0.7840.0680.852
ramwas0createArtificialData0.1920.0120.207
ramwasAnnotateLocations0.3560.0123.659
ramwasParameters0.0000.0000.001
rowcolSumSq0.0040.0000.002
testPhenotype0.0920.0000.097