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CHECK report for GAPGOM on celaya2

This page was generated on 2019-04-07 13:12:45 -0400 (Sun, 07 Apr 2019).

Package 594/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GAPGOM 0.99.36
Casper Peters
Snapshot Date: 2019-04-06 17:01:31 -0400 (Sat, 06 Apr 2019)
URL: https://git.bioconductor.org/packages/GAPGOM
Branch: master
Last Commit: 36592a8
Last Changed Date: 2019-04-04 08:08:32 -0400 (Thu, 04 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: GAPGOM
Version: 0.99.36
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GAPGOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GAPGOM_0.99.36.tar.gz
StartedAt: 2019-04-07 01:58:15 -0400 (Sun, 07 Apr 2019)
EndedAt: 2019-04-07 02:03:45 -0400 (Sun, 07 Apr 2019)
EllapsedTime: 329.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GAPGOM.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 --install=check:GAPGOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GAPGOM_0.99.36.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GAPGOM.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GAPGOM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GAPGOM’ version ‘0.99.36’
* package encoding: UTF-8
* 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 ‘GAPGOM’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
topo_ic_sim_genes     54.462  9.474  56.681
topo_ic_sim_term      16.132  2.450  17.795
set_go_data           13.972  2.153  15.783
fantom_to_expset      12.684  1.075  11.868
fantom_load_raw       10.961  0.089  11.052
expression_prediction  3.960  3.078   1.727
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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


Installation output

GAPGOM.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GAPGOM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GAPGOM’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GAPGOM)

Tests output

GAPGOM.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GAPGOM)


Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

GAPGOM v0.99.36
For help/issues, refer to the readme FAQ or report an issue on the issue page: https://github.com/Berghopper/GAPGOM/issues

If you use GAPGOM in any sort of publication, please cite:
[1] Ehsani R, Drabløs F: TopoICSim: a new semantic similarity measure based on gene ontology. BMC Bioinformatics 2016, 17(1):296
[2] Ehsani R, Drabløs F: Measures of co-expression for improved function prediction of long non-coding RNAs, 2018. BMC Bioinformatics, 2018 Accepted.
> 
> test_check("GAPGOM")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 10 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 34.573   6.566  31.884 

Example timings

GAPGOM.Rcheck/GAPGOM-Ex.timings

nameusersystemelapsed
expression_prediction3.9603.0781.727
expression_semantic_scoring0.9310.5570.528
fantom_download0.6650.0680.735
fantom_load_raw10.961 0.08911.052
fantom_to_expset12.684 1.07511.868
set_go_data13.972 2.15315.783
topo_ic_sim_genes54.462 9.47456.681
topo_ic_sim_term16.132 2.45017.795