Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the sigsquared package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sigsquared.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 1765/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sigsquared 1.24.0 (landing page) UnJin Lee
| 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: sigsquared |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigsquared.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sigsquared_1.24.0.tar.gz |
StartedAt: 2021-10-15 05:43:38 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 05:45:34 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 116.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sigsquared.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigsquared.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sigsquared_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sigsquared.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 'sigsquared/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'sigsquared' version '1.24.0' * 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 'sigsquared' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Non-standard license specification: GPL version 3 Standardizable: TRUE Standardized license specification: GPL-3 * 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 Package in Depends field not imported from: 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE analysisPipeline,ExpressionSet-geneSignature: no visible binding for global variable 'nCores' analysisPipeline,ExpressionSet-geneSignature: no visible global function definition for 'mcparallel' analysisPipeline,ExpressionSet-geneSignature: no visible global function definition for 'mccollect' applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible binding for global variable 'mc' applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible binding for global variable 'nCores' applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible global function definition for 'mcparallel' applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible global function definition for 'mccollect' eJPDF,ExpressionSet-geneSignature-numeric: no visible global function definition for 'new' eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for global variable 'mc' eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for global variable 'nCores' eJPDF,ExpressionSet-geneSignature-numeric: no visible global function definition for 'rnorm' eJPDF,ExpressionSet-geneSignature-numeric: no visible global function definition for 'mcparallel' eJPDF,ExpressionSet-geneSignature-numeric: no visible global function definition for 'mccollect' genGeneDirect,matrix: no visible global function definition for 'sd' optCF,ExpressionSet-geneSignature: no visible global function definition for 'new' optCF,ExpressionSet-geneSignature: no visible global function definition for 'rnorm' optCF,ExpressionSet-geneSignature: no visible global function definition for 'optim' summarizeSolnSpace,solnSpace: no visible global function definition for 'sd' Undefined global functions or variables: mc mccollect mcparallel nCores new optim rnorm sd Consider adding importFrom("methods", "new") importFrom("stats", "optim", "rnorm", "sd") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 analysisPipeline 14.87 0.13 15 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analysisPipeline 17.03 0.05 17.08 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sigsquared.Rcheck/00check.log' for details.
sigsquared.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/sigsquared_1.24.0.tar.gz && rm -rf sigsquared.buildbin-libdir && mkdir sigsquared.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigsquared.buildbin-libdir sigsquared_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sigsquared_1.24.0.zip && rm sigsquared_1.24.0.tar.gz sigsquared_1.24.0.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 149k 100 149k 0 0 751k 0 --:--:-- --:--:-- --:--:-- 756k install for i386 * installing *source* package 'sigsquared' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for 'ensembleCostFcn' with signature 'dataSet="ExpressionSet",geneSig="geneSignature",jpdf="solnSpace"': no definition for class "solnSpace" in method for 'getCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace" in method for 'summarizeCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace" ** help *** installing help indices converting help for package 'sigsquared' finding HTML links ... done BrCa443 html analysisPipeline html ensembleAdjustable html geneSignature-class html setGeneSignature html sigsquared 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 'sigsquared' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'sigsquared' as sigsquared_1.24.0.zip * DONE (sigsquared) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'sigsquared' successfully unpacked and MD5 sums checked
sigsquared.Rcheck/tests_i386/runTests.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. > BiocGenerics:::testPackage("sigsquared") RUNIT TEST PROTOCOL -- Fri Oct 15 05:45:24 2021 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 1.90 0.15 2.04 |
sigsquared.Rcheck/tests_x64/runTests.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. > BiocGenerics:::testPackage("sigsquared") RUNIT TEST PROTOCOL -- Fri Oct 15 05:45:26 2021 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 1.56 0.12 1.67 |
sigsquared.Rcheck/examples_i386/sigsquared-Ex.timings
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sigsquared.Rcheck/examples_x64/sigsquared-Ex.timings
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