Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:32:52 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the PubScore package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1411/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PubScore 1.2.0 (landing page) Tiago Lubiana
| 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: PubScore |
Version: 1.2.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PubScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PubScore_1.2.0.tar.gz |
StartedAt: 2021-05-06 05:47:57 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 05:56:03 -0400 (Thu, 06 May 2021) |
EllapsedTime: 486.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PubScore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PubScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PubScore_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PubScore.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'PubScore/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PubScore' version '1.2.0' * 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 'PubScore' 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 ... NOTE get_literature_score: no visible binding for global variable 'gene2pubmed_db' get_literature_score: no visible binding for global variable 'hgcn_entrez_reference' get_sum_of_weights: no visible binding for global variable 'Genes' get_sum_of_weights: no visible binding for global variable 'Topic' plot_literature_score: no visible binding for global variable 'Genes' plot_literature_score: no visible binding for global variable 'Topic' plot_literature_score: no visible binding for global variable 'number_of_articles' show,PubScore: no visible binding for global variable 'pub' Undefined global functions or variables: Genes Topic gene2pubmed_db hgcn_entrez_reference number_of_articles pub * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed test_score 33.19 0.26 41.03 plot_literature_graph 0.68 0.00 5.89 plot_literature_score 0.44 0.02 23.09 get_literature_score 0.10 0.00 9.17 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed test_score 30.40 0.11 37.25 plot_literature_graph 0.52 0.00 5.47 plot_literature_score 0.50 0.00 24.57 get_literature_score 0.06 0.00 9.34 * 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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PubScore.Rcheck/00check.log' for details.
PubScore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/PubScore_1.2.0.tar.gz && rm -rf PubScore.buildbin-libdir && mkdir PubScore.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PubScore.buildbin-libdir PubScore_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL PubScore_1.2.0.zip && rm PubScore_1.2.0.tar.gz PubScore_1.2.0.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 3061k 100 3061k 0 0 45.4M 0 --:--:-- --:--:-- --:--:-- 45.9M install for i386 * installing *source* package 'PubScore' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'PubScore' finding HTML links ... done PubScore-class html all_counts html dot-getSimulation_test html dot-query_pubmed html gene2pubmed_db html getScore html get_all_counts html get_literature_score html heatmapViz html hgcn_entrez_reference html initialize-PubScore-method html networkViz html plot_literature_graph html plot_literature_score html pubscore html set_all_counts html test_score 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 'PubScore' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'PubScore' as PubScore_1.2.0.zip * DONE (PubScore) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'PubScore' successfully unpacked and MD5 sums checked
PubScore.Rcheck/tests_i386/testthat.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" 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(PubScore) > > test_check("PubScore") ~~~ Initializing PubScore Object ~~~ ~~~ Initializing PubScore Object ~~~ ~~~ Initializing PubScore Object ~~~ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] > > proc.time() user system elapsed 41.73 0.34 115.76 |
PubScore.Rcheck/tests_x64/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-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(PubScore) > > test_check("PubScore") ~~~ Initializing PubScore Object ~~~ ~~~ Initializing PubScore Object ~~~ ~~~ Initializing PubScore Object ~~~ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] > > proc.time() user system elapsed 50.78 0.53 123.17 |
PubScore.Rcheck/examples_i386/PubScore-Ex.timings
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PubScore.Rcheck/examples_x64/PubScore-Ex.timings
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