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This page was generated on 2021-06-23 15:05:57 -0400 (Wed, 23 Jun 2021).

CHECK results for GAPGOM on machv2

To the developers/maintainers of the GAPGOM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GAPGOM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 688/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GAPGOM 1.8.0  (landing page)
Rezvan Ehsani
Snapshot Date: 2021-06-22 04:50:12 -0400 (Tue, 22 Jun 2021)
URL: https://git.bioconductor.org/packages/GAPGOM
Branch: RELEASE_3_13
Last Commit: e8e35ed
Last Changed Date: 2021-05-19 12:40:41 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GAPGOM
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2021-06-22 18:57:46 -0400 (Tue, 22 Jun 2021)
EndedAt: 2021-06-22 19:04:14 -0400 (Tue, 22 Jun 2021)
EllapsedTime: 387.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GAPGOM.Rcheck
Warnings: 0

Command output

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### Running 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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GAPGOM.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 LazyData ... 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 (user + system) or elapsed time > 5s
                     user system elapsed
topo_ic_sim_genes 101.566  2.830 104.500
topo_ic_sim_term   33.336  0.853  34.219
set_go_data        31.274  0.942  32.241
fantom_to_expset    5.371  0.062   5.457
fantom_load_raw     5.059  0.065   5.129
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GAPGOM.Rcheck/00check.log’
for details.



Installation output

GAPGOM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GAPGOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 v1.8.0
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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• R cmd check time constraints (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 11.574   0.522  12.082 

Example timings

GAPGOM.Rcheck/GAPGOM-Ex.timings

nameusersystemelapsed
expression_prediction0.8960.0160.912
expression_semantic_scoring0.4600.0250.485
fantom_download0.9360.0580.995
fantom_load_raw5.0590.0655.129
fantom_to_expset5.3710.0625.457
set_go_data31.274 0.94232.241
topo_ic_sim_genes101.566 2.830104.500
topo_ic_sim_term33.336 0.85334.219