Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:30:26 -0400 (Wed, 15 Apr 2020).
Package 1710/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TCGAutils 1.6.2 Marcel Ramos
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: TCGAutils |
Version: 1.6.2 |
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TCGAutils_1.6.2.tar.gz |
StartedAt: 2020-04-15 07:03:27 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 07:17:05 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 818.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCGAutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TCGAutils_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TCGAutils.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'TCGAutils/DESCRIPTION' ... OK * this is package 'TCGAutils' version '1.6.2' * 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 'TCGAutils' 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 ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'GenomicRanges:::.normarg_field' See the note in ?`:::` about the use of this operator. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed simplifyTCGA 35.15 2.15 38.22 TCGAprimaryTumors 28.88 3.00 33.80 curatedTCGAData-helpers 20.52 1.23 22.72 imputeAssay 18.31 0.80 19.97 oncoPrintTCGA 15.49 1.02 17.27 trimColData 13.08 2.99 16.80 makeSummarizedExperimentFromGISTIC 5.44 0.63 21.85 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed simplifyTCGA 57.29 3.52 70.37 TCGAprimaryTumors 31.94 2.03 34.89 trimColData 26.57 0.81 36.93 imputeAssay 26.66 0.70 29.38 oncoPrintTCGA 24.34 0.86 32.87 curatedTCGAData-helpers 23.35 0.81 24.88 makeSummarizedExperimentFromGISTIC 9.55 0.63 30.11 * 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-3.10-bioc/meat/TCGAutils.Rcheck/00check.log' for details.
TCGAutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TCGAutils_1.6.2.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.6.2.zip && rm TCGAutils_1.6.2.tar.gz TCGAutils_1.6.2.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 64208 100 64208 0 0 648k 0 --:--:-- --:--:-- --:--:-- 674k install for i386 * installing *source* package 'TCGAutils' ... ** 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 'TCGAutils' finding HTML links ... done ID-translation html TCGAbarcode html TCGAbiospec html TCGAprimaryTumors html finding level-2 HTML links ... done TCGAsampleSelect html TCGAutils-package html builds html clinicalNames html curatedTCGAData-helpers html diseaseCodes html findGRangesCols html generateMap html getFileName html hidden-helpers html imputeAssay html makeGRangesListFromCopyNumber html makeGRangesListFromExonFiles html makeSummarizedExperimentFromGISTIC html mergeColData html oncoPrintTCGA html sampleTypes html simplifyTCGA html trimColData 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 'TCGAutils' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'TCGAutils' as TCGAutils_1.6.2.zip * DONE (TCGAutils) * installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library' package 'TCGAutils' successfully unpacked and MD5 sums checked
TCGAutils.Rcheck/tests_i386/testthat.Rout R version 3.6.3 (2020-02-29) -- "Holding the Windsock" 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(TCGAutils) > > test_check("TCGAutils") == testthat results =========================================================== [ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 12.14 1.23 20.70 |
TCGAutils.Rcheck/tests_x64/testthat.Rout R version 3.6.3 (2020-02-29) -- "Holding the Windsock" 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(TCGAutils) > > test_check("TCGAutils") == testthat results =========================================================== [ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 16.23 0.70 20.34 |
TCGAutils.Rcheck/examples_i386/TCGAutils-Ex.timings
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TCGAutils.Rcheck/examples_x64/TCGAutils-Ex.timings
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