Rezvan Ehsani
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/GAPGOM |
| git_branch: RELEASE_3_13 |
| git_last_commit: e8e35ed |
| git_last_commit_date: 2021-05-19 12:40:41 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 688/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GAPGOM 1.8.0 (landing page) Rezvan Ehsani
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GAPGOM_1.8.0.tar.gz |
| StartedAt: 2021-10-14 23:22:21 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:29:37 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 436.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GAPGOM.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GAPGOM_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GAPGOM.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.8.0'
* 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 ... 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 LazyData ... 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 77.67 1.08 78.76
set_go_data 25.92 0.46 26.40
topo_ic_sim_term 25.66 0.21 25.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
topo_ic_sim_genes 29.86 0.65 30.52
set_go_data 9.69 0.25 16.85
topo_ic_sim_term 8.93 0.19 9.11
fantom_to_expset 1.72 0.03 6.95
* 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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/GAPGOM_1.8.0.tar.gz && rm -rf GAPGOM.buildbin-libdir && mkdir GAPGOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GAPGOM.buildbin-libdir GAPGOM_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GAPGOM_1.8.0.zip && rm GAPGOM_1.8.0.tar.gz GAPGOM_1.8.0.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 751k 100 751k 0 0 2191k 0 --:--:-- --:--:-- --:--:-- 2197k
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_1.8.0.zip
* DONE (GAPGOM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GAPGOM' successfully unpacked and MD5 sums checked
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GAPGOM.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 v1.8.0
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
8.31 0.68 8.98
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GAPGOM.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 v1.8.0
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
8.78 0.37 9.14
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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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