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CHECK report for ramwas on veracruz1

This page was generated on 2018-04-12 13:44:07 -0400 (Thu, 12 Apr 2018).

Package 1117/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.2.0
Andrey A Shabalin
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ramwas
Branch: RELEASE_3_6
Last Commit: d9374a2
Last Changed Date: 2017-10-30 12:41:24 -0400 (Mon, 30 Oct 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  WARNINGS  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: 1.2.0
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

Command output

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


* 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.



Installation output

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-3.6-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)

Tests output


Example timings

ramwas.Rcheck/ramwas-Ex.timings

nameusersystemelapsed
QCs0.0620.0030.067
cachedRDSload0.6610.0010.695
findBestNpvs0.0020.0000.002
getCpGset4.5810.1364.919
getDataByLocation0.0000.0000.001
getTestsByLocation0.0010.0000.000
injectSNPsMAF0.4080.0060.427
insilicoFASTQ0.0030.0000.002
isAbsolutePath0.0010.0000.001
makefullpath0.0010.0000.002
orthonormalizeCovariates0.0280.0000.029
parameterDump0.0250.0010.027
parameterPreprocess0.0060.0030.010
parametersFromFile0.0020.0010.003
pipeline0.0030.0000.003
plotROC0.0040.0010.004
processCommandLine0.0030.0000.002
pvalue2qvalue0.0010.0000.001
qqplotFast0.6910.0520.763
ramwas0createArtificialData0.2640.0250.293
ramwasAnnotateLocations0.2850.0123.808
ramwasParameters0.0000.0000.001
rowcolSumSq0.0020.0000.002
testPhenotype0.0800.0010.081