Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:53:16 -0400 (Wed, 16 Oct 2019).
Package 178/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
blima 1.18.0 Vojtěch Kulvait
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: blima |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:blima.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings blima_1.18.0.tar.gz |
StartedAt: 2019-10-16 01:00:50 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 01:03:35 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 164.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: blima.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:blima.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings blima_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/blima.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘blima/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘blima’ version ‘1.18.0’ * 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 for sufficient/correct file permissions ... 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 * 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 is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/blima.Rcheck/00check.log’ for details.
blima.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL blima ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘blima’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c interpolateSortedVector.cpp -o interpolateSortedVector.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o blima.so RcppExports.o interpolateSortedVector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-blima/00new/blima/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (blima)
blima.Rcheck/blima-Ex.timings
name | user | system | elapsed | |
bacgroundCorrect | 0.021 | 0.003 | 0.025 | |
backgroundChannelSubtract | 0.023 | 0.001 | 0.025 | |
chipArrayStatistics | 0.018 | 0.001 | 0.019 | |
createSummarizedMatrix | 0.705 | 0.044 | 0.757 | |
doProbeTTests | 0.272 | 0.017 | 0.289 | |
doTTests | 0.213 | 0.013 | 0.226 | |
log2TransformPositive | 0.212 | 0.014 | 0.225 | |
nonPositiveCorrect | 0.021 | 0.001 | 0.022 | |
plotBackgroundImageAfterCorrection | 0.020 | 0.001 | 0.021 | |
plotBackgroundImageBeforeCorrection | 0.019 | 0.002 | 0.020 | |
quantileNormalize | 0.024 | 0.002 | 0.025 | |
selectedChannelTransform | 0.023 | 0.001 | 0.024 | |
varianceBeadStabilise | 0.025 | 0.001 | 0.027 | |
writeBackgroundImages | 0.020 | 0.001 | 0.021 | |
xieBacgroundCorrect | 0.049 | 0.001 | 0.051 | |