Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE blima PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 193/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
blima 1.22.0 Vojtěch Kulvait
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK |
Package: blima |
Version: 1.22.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blima.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings blima_1.22.0.tar.gz |
StartedAt: 2020-10-17 02:04:57 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 02:08:04 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 186.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: blima.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blima.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings blima_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/blima.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'blima/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'blima' version '1.22.0' * 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 'blima' 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 nonParametricEstimator: no visible global function definition for 'var' performXieCorrection: no visible global function definition for 'dnorm' performXieCorrection: no visible global function definition for 'pnorm' vstFromLumi: no visible global function definition for 'lm' vstFromLumi: no visible global function definition for 'predict' Undefined global functions or variables: dnorm lm pnorm predict var Consider adding importFrom("stats", "dnorm", "lm", "pnorm", "predict", "var") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (5) interpolateSortedVectorRcpp_.Rd:0-21: Must have a \description * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/blima/libs/i386/blima.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/blima/libs/x64/blima.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/blima.Rcheck/00check.log' for details.
blima.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/blima_1.22.0.tar.gz && rm -rf blima.buildbin-libdir && mkdir blima.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=blima.buildbin-libdir blima_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL blima_1.22.0.zip && rm blima_1.22.0.tar.gz blima_1.22.0.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 36868 100 36868 0 0 562k 0 --:--:-- --:--:-- --:--:-- 631k install for i386 * installing *source* package 'blima' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interpolateSortedVector.cpp -o interpolateSortedVector.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o blima.dll tmp.def RcppExports.o interpolateSortedVector.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/blima.buildbin-libdir/00LOCK-blima/00new/blima/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'blima' finding HTML links ... done aggregateAndPreprocess html bacgroundCorrect html bacgroundCorrectSingleArray html backgroundChannelSubtract html backgroundChannelSubtractSingleArray html blima-package html channelExistsIntegrityWithLogicalVectorList html checkIntegrity html checkIntegrityLogical html checkIntegrityOfListOfBeadLevelDataObjects html checkIntegrityOfSingleBeadLevelDataObject html chipArrayStatistics html createSummarizedMatrix html doAction html doProbeTTests html doTTests html filterBg html getNextVector html initMeanDistribution html insertColumn html interpolateSortedVector html interpolateSortedVectorRcpp_ html log2TransformPositive html meanDistribution html nonParametricEstimator html nonPositiveCorrect html nonPositiveCorrectSingleArray html numberOfDistributionElements html performXieCorrection html plotBackgroundImageAfterCorrection html plotBackgroundImageBeforeCorrection html quantileNormalize html readToVector html selectedChannelTransform html selectedChannelTransformSingleArray html singleArrayNormalize html singleChannelExistsIntegrityWithLogicalVector html singleCheckIntegrityLogicalVector html singleNumberOfDistributionElements html updateMeanDistribution html varianceBeadStabilise html varianceBeadStabiliseSingleArray html vstFromLumi html writeBackgroundImages html xieBacgroundCorrect html xieBacgroundCorrectSingleArray 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 'blima' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interpolateSortedVector.cpp -o interpolateSortedVector.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o blima.dll tmp.def RcppExports.o interpolateSortedVector.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/blima.buildbin-libdir/blima/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'blima' as blima_1.22.0.zip * DONE (blima) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'blima' successfully unpacked and MD5 sums checked
blima.Rcheck/examples_i386/blima-Ex.timings
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blima.Rcheck/examples_x64/blima-Ex.timings
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