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This page was generated on 2021-09-21 12:06:03 -0400 (Tue, 21 Sep 2021).

CHECK results for GAPGOM on riesling1

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
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raw results

Package 680/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GAPGOM 1.9.0  (landing page)
Rezvan Ehsani
Snapshot Date: 2021-09-20 14:50:09 -0400 (Mon, 20 Sep 2021)
git_url: https://git.bioconductor.org/packages/GAPGOM
git_branch: master
git_last_commit: c8c74ff
git_last_commit_date: 2021-05-19 12:40:41 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GAPGOM
Version: 1.9.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GAPGOM_1.9.0.tar.gz
StartedAt: 2021-09-21 00:54:04 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 00:59:20 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 316.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GAPGOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GAPGOM.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GAPGOM_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-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 '1.9.0'
* 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 59.50   0.39   59.94
topo_ic_sim_term  19.39   0.16   19.55
set_go_data       18.88   0.11   18.98
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
topo_ic_sim_genes 25.50   0.61   26.11
set_go_data        7.45   0.20    7.65
topo_ic_sim_term   7.44   0.19    7.63
* 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


Installation output

GAPGOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GAPGOM_1.9.0.tar.gz && rm -rf GAPGOM.buildbin-libdir && mkdir GAPGOM.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GAPGOM.buildbin-libdir GAPGOM_1.9.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GAPGOM_1.9.0.zip && rm GAPGOM_1.9.0.tar.gz GAPGOM_1.9.0.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
100  751k  100  751k    0     0  2235k      0 --:--:-- --:--:-- --:--:-- 2235k

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_1.9.0.zip
* DONE (GAPGOM)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'GAPGOM' successfully unpacked and MD5 sums checked

Tests output

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 v1.9.0
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 
   4.92    0.28    5.18 

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 v1.9.0
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 
   5.29    0.42    5.71 

Example timings

GAPGOM.Rcheck/examples_i386/GAPGOM-Ex.timings

nameusersystemelapsed
expression_prediction0.210.000.20
expression_semantic_scoring0.150.000.16
fantom_download0.390.000.39
fantom_load_raw1.200.041.25
fantom_to_expset1.250.011.27
set_go_data18.88 0.1118.98
topo_ic_sim_genes59.50 0.3959.94
topo_ic_sim_term19.39 0.1619.55

GAPGOM.Rcheck/examples_x64/GAPGOM-Ex.timings

nameusersystemelapsed
expression_prediction0.520.000.51
expression_semantic_scoring0.140.000.14
fantom_download0.410.010.42
fantom_load_raw1.220.001.22
fantom_to_expset1.220.001.22
set_go_data7.450.207.65
topo_ic_sim_genes25.50 0.6126.11
topo_ic_sim_term7.440.197.63