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BioC 3.5: CHECK report for blima on veracruz2

This page was generated on 2017-08-16 13:32:01 -0400 (Wed, 16 Aug 2017).

Package 144/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blima 1.10.0
Vojtěch Kulvait
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/blima
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: blima
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings blima_1.10.0.tar.gz
StartedAt: 2017-08-16 00:22:47 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:24:43 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: blima.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings blima_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/blima.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.10.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/blima.Rcheck/00check.log’
for details.


blima.Rcheck/00install.out:

* installing *source* package ‘blima’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c interpolateSortedVector.cpp -o interpolateSortedVector.o
clang++ -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 /Users/biocbuild/bbs-3.5-bioc/meat/blima.Rcheck/blima/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (blima)

blima.Rcheck/blima-Ex.timings:

nameusersystemelapsed
bacgroundCorrect0.0140.0010.017
backgroundChannelSubtract0.0080.0010.008
chipArrayStatistics0.0130.0010.014
createSummarizedMatrix0.9250.0270.989
doProbeTTests0.1450.0090.154
doTTests0.1340.0060.144
log2TransformPositive0.1350.0060.144
nonPositiveCorrect0.0140.0010.015
plotBackgroundImageAfterCorrection0.0090.0010.010
plotBackgroundImageBeforeCorrection0.0100.0010.012
quantileNormalize0.0150.0000.015
selectedChannelTransform0.0110.0000.013
varianceBeadStabilise0.0150.0000.019
writeBackgroundImages0.0090.0000.010
xieBacgroundCorrect0.0120.0010.013