Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:32:38 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the openPrimeR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1269/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
openPrimeR 1.12.1 (landing page) Matthias Döring
| 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: openPrimeR |
Version: 1.12.1 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings openPrimeR_1.12.1.tar.gz |
StartedAt: 2021-05-06 05:15:23 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 05:23:19 -0400 (Thu, 06 May 2021) |
EllapsedTime: 475.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: openPrimeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings openPrimeR_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/openPrimeR.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 'openPrimeR/DESCRIPTION' ... OK * this is package 'openPrimeR' version '1.12.1' * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'openPrimeR' can be installed ... OK * checking installed package size ... NOTE installed size is 12.2Mb sub-directories of 1Mb or more: R 1.3Mb extdata 10.0Mb * 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 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 PrimerDesign 12.70 0.25 13.78 Output 9.84 1.19 22.48 Plots 6.32 0.52 6.83 PrimerEval 4.88 0.20 5.08 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PrimerDesign 17.17 0.31 17.48 Output 15.16 1.37 25.30 Plots 9.56 0.38 9.95 PrimerEval 7.16 0.41 7.57 * 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-3.12-bioc/meat/openPrimeR.Rcheck/00check.log' for details.
openPrimeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/openPrimeR_1.12.1.tar.gz && rm -rf openPrimeR.buildbin-libdir && mkdir openPrimeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openPrimeR.buildbin-libdir openPrimeR_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL openPrimeR_1.12.1.zip && rm openPrimeR_1.12.1.tar.gz openPrimeR_1.12.1.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 1771k 100 1771k 0 0 39.7M 0 --:--:-- --:--:-- --:--:-- 41.1M install for i386 * installing *source* package 'openPrimeR' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'openPrimeR' finding HTML links ... done AnalysisStats html Data html Input html Output html Plots html PrimerDesign html PrimerEval html Primers-method html Scoring html Settings html Templates-method html TemplatesFunctions html check_cvg_constraints html create_report-Primers-Templates-method html create_report-list-list-method html filterLimits-methods html filters-methods html get_cvg_stats-Primers-method html get_cvg_stats-list-method html openPrimeR-package html plot_constraint-Primers-method html plot_constraint-list-method html plot_constraint_deviation-Primers-method html plot_constraint_deviation-list-method html plot_constraint_fulfillment-Primers-method html plot_constraint_fulfillment-list-method html plot_cvg_constraints-Primers-method html plot_cvg_constraints-list-method html plot_primer_binding_regions-Primers-Templates-method html plot_primer_binding_regions-list-list-method html plot_primer_cvg-Primers-Templates-method html plot_primer_cvg-list-list-method html plot_template_cvg-Primers-Templates-method html plot_template_cvg-list-list-method html runTutorial 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 'openPrimeR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'openPrimeR' as openPrimeR_1.12.1.zip * DONE (openPrimeR) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'openPrimeR' successfully unpacked and MD5 sums checked
openPrimeR.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. > require(testthat) Loading required package: testthat > require(openPrimeR) Loading required package: openPrimeR There are missing/non-functioning external tools. To use the full potential of openPrimeR, please make sure that the required versions of the speciied tools are installed and that they are functional: o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/) o ViennaRNA (http://www.tbi.univie.ac.at/RNA/) o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php) o MAFFT (http://mafft.cbrc.jp/alignment/software/) > #test_package("openPrimeR") > test_check("openPrimeR") pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. == Skipped tests =============================================================== * MAFFT not available. (1) * OligoArrayAux not available. (5) * On Bioconductor (1) * Secondary structure tests require ViennaRNA. (1) [ FAIL 0 | WARN 2 | SKIP 8 | PASS 1467 ] > > proc.time() user system elapsed 52.04 2.53 58.26 |
openPrimeR.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. > require(testthat) Loading required package: testthat > require(openPrimeR) Loading required package: openPrimeR There are missing/non-functioning external tools. To use the full potential of openPrimeR, please make sure that the required versions of the speciied tools are installed and that they are functional: o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/) o ViennaRNA (http://www.tbi.univie.ac.at/RNA/) o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php) o MAFFT (http://mafft.cbrc.jp/alignment/software/) > #test_package("openPrimeR") > test_check("openPrimeR") pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. pdfcrop.exe: MiKTeX encountered an internal error. == Skipped tests =============================================================== * MAFFT not available. (1) * OligoArrayAux not available. (5) * On Bioconductor (1) * Secondary structure tests require ViennaRNA. (1) [ FAIL 0 | WARN 2 | SKIP 8 | PASS 1467 ] > > proc.time() user system elapsed 61.18 1.84 75.04 |
openPrimeR.Rcheck/examples_i386/openPrimeR-Ex.timings
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openPrimeR.Rcheck/examples_x64/openPrimeR-Ex.timings
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