Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:39 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the GAPGOM package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 662/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GAPGOM 1.6.0 (landing page) Rezvan Ehsani
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GAPGOM |
Version: 1.6.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GAPGOM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GAPGOM_1.6.0.tar.gz |
StartedAt: 2021-05-06 01:42:57 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:46:46 -0400 (Thu, 06 May 2021) |
EllapsedTime: 228.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GAPGOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GAPGOM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GAPGOM_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GAPGOM.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’ * 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 ... 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 (user + system) or elapsed time > 5s user system elapsed topo_ic_sim_genes 37.800 0.276 38.292 topo_ic_sim_term 12.116 0.052 12.192 set_go_data 9.832 0.080 10.079 fantom_to_expset 5.476 0.008 5.501 fantom_load_raw 5.328 0.044 5.486 * 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
GAPGOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GAPGOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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)
GAPGOM.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 v1.6.0 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 9.028 0.304 9.313
GAPGOM.Rcheck/GAPGOM-Ex.timings
name | user | system | elapsed | |
expression_prediction | 0.848 | 0.000 | 0.819 | |
expression_semantic_scoring | 0.444 | 0.020 | 0.465 | |
fantom_download | 1.048 | 0.028 | 1.103 | |
fantom_load_raw | 5.328 | 0.044 | 5.486 | |
fantom_to_expset | 5.476 | 0.008 | 5.501 | |
set_go_data | 9.832 | 0.080 | 10.079 | |
topo_ic_sim_genes | 37.800 | 0.276 | 38.292 | |
topo_ic_sim_term | 12.116 | 0.052 | 12.192 | |