Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-07 12:26:18 -0400 (Sun, 07 Apr 2019).
Package 594/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GAPGOM 0.99.36 Casper Peters
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: GAPGOM |
Version: 0.99.36 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GAPGOM_0.99.36.tar.gz |
StartedAt: 2019-04-07 03:04:25 -0400 (Sun, 07 Apr 2019) |
EndedAt: 2019-04-07 03:10:09 -0400 (Sun, 07 Apr 2019) |
EllapsedTime: 344.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GAPGOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GAPGOM_0.99.36.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GAPGOM.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed topo_ic_sim_genes 31.39 1.14 32.51 topo_ic_sim_term 9.97 0.15 10.13 set_go_data 7.89 0.24 8.13 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed topo_ic_sim_genes 37.31 0.92 38.19 set_go_data 11.77 0.32 12.08 topo_ic_sim_term 10.94 0.15 11.09 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GAPGOM_0.99.36.tar.gz && rm -rf GAPGOM.buildbin-libdir && mkdir GAPGOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GAPGOM.buildbin-libdir GAPGOM_0.99.36.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GAPGOM_0.99.36.zip && rm GAPGOM_0.99.36.tar.gz GAPGOM_0.99.36.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 748k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 748k 100 748k 0 0 4452k 0 --:--:-- --:--:-- --:--:-- 4619k install for i386 * installing *source* package 'GAPGOM' ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GAPGOM' finding HTML links ... done ambiguous_functions html dag_funcs html dot-enrichment_analysis html dot-entrezraw_to_entrez html dot-ext_id_to_term_id html dot-fantom_filter_entrez html dot-generate_translation_df html dot-get_package_version html dot-go_ids_lookup html dot-organism_to_species_lib html dot-prepare_score_df html dot-prepare_score_matrix_topoicsim html dot-prepare_variables_topoicsim html dot-resolve_genes_unique_gos html dot-resolve_keys_col html dot-set_identical_items html dot-set_values html dot-term_id_to_ext_id html dot-topo_ic_sim_g1g2 html dot-topo_ic_sim_geneset html dot-topo_ic_sim_titj html dot-unique_combos html expression_prediction html expression_semantic_scoring html expset html fantom_download html fantom_load_raw html fantom_to_expset html geometrical_measures html glb_checks html id_translation_df html misc_functions html set_go_data html topo_ic_sim_genes html topo_ic_sim_term html ** 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 install for x64 * installing *source* package 'GAPGOM' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GAPGOM' as GAPGOM_0.99.36.zip * DONE (GAPGOM) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'GAPGOM' successfully unpacked and MD5 sums checked
GAPGOM.Rcheck/tests_i386/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 18.40 1.07 19.45 |
GAPGOM.Rcheck/tests_x64/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 17.51 1.01 18.56 |
GAPGOM.Rcheck/examples_i386/GAPGOM-Ex.timings
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GAPGOM.Rcheck/examples_x64/GAPGOM-Ex.timings
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