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CHECK report for blima on celaya2

This page was generated on 2020-01-16 13:39:03 -0500 (Thu, 16 Jan 2020).

Package 188/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blima 1.21.0
Vojtěch Kulvait
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/blima
Branch: master
Last Commit: 6e131e7
Last Changed Date: 2019-10-29 13:37:32 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: blima
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2020-01-16 02:17:46 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:20:58 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 192.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: blima.Rcheck
Warnings: 1

Command output

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### 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_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/blima.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.21.0’
* 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-3.11-bioc/meat/blima.Rcheck/00check.log’
for details.



Installation output

blima.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL blima
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/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)

Tests output


Example timings

blima.Rcheck/blima-Ex.timings

nameusersystemelapsed
bacgroundCorrect0.0280.0030.032
backgroundChannelSubtract0.0240.0010.025
chipArrayStatistics0.0230.0010.024
createSummarizedMatrix1.1600.0461.215
doProbeTTests0.2980.0170.315
doTTests0.2980.0150.314
log2TransformPositive0.3020.0170.321
nonPositiveCorrect0.0270.0010.028
plotBackgroundImageAfterCorrection0.0230.0010.024
plotBackgroundImageBeforeCorrection0.0240.0010.026
quantileNormalize0.0220.0020.023
selectedChannelTransform0.0210.0010.022
varianceBeadStabilise0.0240.0020.025
writeBackgroundImages0.0150.0010.016
xieBacgroundCorrect0.0210.0020.023