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BioC 3.5: CHECK report for ramwas on toluca2

This page was generated on 2017-04-23 14:42:29 -0400 (Sun, 23 Apr 2017).

Package 1055/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 0.99.19
Andrey A Shabalin
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ramwas
Last Changed Rev: 128895 / Revision: 129046
Last Changed Date: 2017-04-19 11:31:36 -0400 (Wed, 19 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ramwas
Version: 0.99.19
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ramwas_0.99.19.tar.gz
StartedAt: 2017-04-23 08:35:38 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 08:39:40 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 242.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ramwas.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ramwas_0.99.19.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ramwas.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.19’
* 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
Examples with CPU or elapsed time > 5s
                         user system elapsed
getCpGset               4.672  0.155   5.445
ramwasAnnotateLocations 1.304  0.015   6.790
* 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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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:

nameusersystemelapsed
QCs0.0690.0030.091
cachedRDSload0.7200.0020.818
findBestNpvs0.0020.0000.002
getCpGset4.6720.1555.445
getDataByLocation0.0010.0000.001
getTestsByLocation0.0010.0000.001
injectSNPsMAF0.4450.0050.455
insilicoFASTQ0.0020.0000.003
isAbsolutePath0.0010.0000.002
makefullpath0.0020.0010.002
orthonormalizeCovariates0.0360.0000.037
parameterDump0.0250.0000.026
parameterPreprocess0.0060.0040.011
parametersFromFile0.0020.0010.002
pipeline0.0040.0000.004
plotROC0.0050.0000.006
processCommandLine0.0020.0010.002
pvalue2qvalue0.0010.0000.001
qqplotFast0.7690.0480.847
ramwas0createArtificialData0.3040.0300.334
ramwasAnnotateLocations1.3040.0156.790
ramwasParameters0.0000.0000.001
rowcolSumSq0.0010.0010.002
testPhenotype0.1040.0030.108