Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the bioCancer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.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 157/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bioCancer 1.20.02 (landing page) Karim Mezhoud
| 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: bioCancer |
Version: 1.20.02 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioCancer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings bioCancer_1.20.02.tar.gz |
StartedAt: 2021-10-14 20:08:56 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:14:11 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 315.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bioCancer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioCancer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings bioCancer_1.20.02.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/bioCancer.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 'bioCancer/DESCRIPTION' ... OK * this is package 'bioCancer' version '1.20.02' * 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 'bioCancer' can be installed ... OK * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: app 3.3Mb extdata 1.6Mb * 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 ... NOTE Namespaces in Imports field not imported from: 'AlgDesign' 'GO.db' 'import' 'methods' 'org.Bt.eg.db' 'shinythemes' All declared Imports should be used. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/bioCancer.Rcheck/00check.log' for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/bioCancer_1.20.02.tar.gz && rm -rf bioCancer.buildbin-libdir && mkdir bioCancer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bioCancer.buildbin-libdir bioCancer_1.20.02.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL bioCancer_1.20.02.zip && rm bioCancer_1.20.02.tar.gz bioCancer_1.20.02.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 24 6708k 24 1676k 0 0 1683k 0 0:00:03 --:--:-- 0:00:03 1683k 38 6708k 38 2557k 0 0 1365k 0 0:00:04 0:00:01 0:00:03 1365k 71 6708k 71 4781k 0 0 1660k 0 0:00:04 0:00:02 0:00:02 1660k 100 6708k 100 6708k 0 0 1873k 0 0:00:03 0:00:03 --:--:-- 1873k install for i386 * installing *source* package 'bioCancer' ... ** 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 'bioCancer' finding HTML links ... done AnnotationFuncs-package html Edges_Diseases_obj html Mutation_obj html Node_Diseases_obj html Node_df_FreqIn html Node_obj_CNA_ProfData html Node_obj_FreqIn html Node_obj_Met_ProfData html Node_obj_mRNA_Classifier html Studies_obj html UnifyRowNames html attriColorGene html attriColorValue html attriColorVector html attriShape2Gene html attriShape2Node html bioCancer html checkDimensions html coffeewheel html coffeewheelOutput html displayTable html dot-dbEscapeString html dot-getTableName html dot-pickRef html epiGenomics html findPhantom html getEvidenceCodes html getFreqMutData html getGenesClassification html getListProfData html getList_Cases html getList_GenProfs html getMegaProfData html getOrthologs html getSequensed_SampleSize html grepRef html mapLists html metabologram html metabologramOutput html pickGO html pickRefSeq html reStrColorGene html reStrDimension html reStrDisease html removeNAs html renderCoffeewheel html renderMetabologram html returnTextAreaInput html switchButton html translate html user_CNA html user_MetHM27 html user_MetHM450 html user_Mut html user_mRNA html whichGeneList html widgetThumbnail 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 'bioCancer' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'bioCancer' as bioCancer_1.20.02.zip * DONE (bioCancer) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'bioCancer' successfully unpacked and MD5 sums checked
bioCancer.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(bioCancer) Loading required package: radiant.data Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Loading required package: ggplot2 Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:magrittr': extract The following object is masked from 'package:testthat': matches Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'radiant.data' The following objects are masked from 'package:lubridate': month, wday The following object is masked from 'package:ggplot2': diamonds The following object is masked from 'package:magrittr': set_attr The following object is masked from 'package:testthat': describe The following object is masked from 'package:base': date Loading required package: cgdsr Please send questions to cbioportal@googlegroups.com Loading required package: XML > > test_check("bioCancer") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK ReactomeFI connection... OK == Skipped tests =============================================================== * empty test (2) [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ] > > proc.time() user system elapsed 10.25 0.96 12.23 |
bioCancer.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(bioCancer) Loading required package: radiant.data Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Loading required package: ggplot2 Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:magrittr': extract The following object is masked from 'package:testthat': matches Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'radiant.data' The following objects are masked from 'package:lubridate': month, wday The following object is masked from 'package:ggplot2': diamonds The following object is masked from 'package:magrittr': set_attr The following object is masked from 'package:testthat': describe The following object is masked from 'package:base': date Loading required package: cgdsr Please send questions to cbioportal@googlegroups.com Loading required package: XML > > test_check("bioCancer") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK ReactomeFI connection... OK == Skipped tests =============================================================== * empty test (2) [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ] > > proc.time() user system elapsed 10.98 0.56 12.32 |
bioCancer.Rcheck/examples_i386/bioCancer-Ex.timings
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bioCancer.Rcheck/examples_x64/bioCancer-Ex.timings
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