Casper van Mourik
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GAPGOM |
| Branch: RELEASE_3_11 |
| Last Commit: 8968608 |
| Last Changed Date: 2020-04-27 15:22:56 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:37 -0400 (Sat, 17 Oct 2020).
| 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 652/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GAPGOM 1.4.0 Casper van Mourik
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: GAPGOM |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GAPGOM_1.4.0.tar.gz |
| StartedAt: 2020-10-17 04:12:47 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:20:29 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 462.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GAPGOM.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GAPGOM_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GAPGOM.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.0'
* 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 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 (user + system) or elapsed time > 5s
user system elapsed
topo_ic_sim_genes 101.92 1.18 106.13
set_go_data 30.80 0.36 33.62
topo_ic_sim_term 30.89 0.19 31.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
topo_ic_sim_genes 36.28 0.61 37.00
topo_ic_sim_term 11.26 0.28 11.55
set_go_data 9.35 0.36 9.76
* 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
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GAPGOM_1.4.0.tar.gz && rm -rf GAPGOM.buildbin-libdir && mkdir GAPGOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GAPGOM.buildbin-libdir GAPGOM_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GAPGOM_1.4.0.zip && rm GAPGOM_1.4.0.tar.gz GAPGOM_1.4.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 748k 100 748k 0 0 10.6M 0 --:--:-- --:--:-- --:--:-- 11.7M
install for i386
* 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
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_1.4.0.zip
* DONE (GAPGOM)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GAPGOM' successfully unpacked and MD5 sums checked
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GAPGOM.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 v1.4.0
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")
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.35 0.51 8.01
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GAPGOM.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 v1.4.0
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")
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.84 0.60 8.32
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GAPGOM.Rcheck/examples_i386/GAPGOM-Ex.timings
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GAPGOM.Rcheck/examples_x64/GAPGOM-Ex.timings
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