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CHECK report for blima on nebbiolo1

This page was generated on 2020-10-18 12:27:41 -0400 (Sun, 18 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 187/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blima 1.23.0
Vojtěch Kulvait
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/blima
Branch: master
Last Commit: aa0de00
Last Changed Date: 2020-04-27 14:40:34 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: blima
Version: 1.23.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:blima.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings blima_1.23.0.tar.gz
StartedAt: 2020-10-17 19:58:23 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 20:00:36 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 132.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: blima.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:blima.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings blima_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/blima.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.23.0’
* 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 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/blima.Rcheck/00check.log’
for details.



Installation output

blima.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL blima
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘blima’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c interpolateSortedVector.cpp -o interpolateSortedVector.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o blima.so RcppExports.o interpolateSortedVector.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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
bacgroundCorrect0.0220.0000.022
backgroundChannelSubtract0.0060.0000.006
chipArrayStatistics0.0060.0000.006
createSummarizedMatrix0.2910.0160.307
doProbeTTests0.0700.0040.074
doTTests0.0730.0040.077
log2TransformPositive0.3390.0000.339
nonPositiveCorrect0.0070.0000.007
plotBackgroundImageAfterCorrection0.0050.0000.005
plotBackgroundImageBeforeCorrection0.0020.0040.006
quantileNormalize0.0070.0000.007
selectedChannelTransform0.0060.0000.006
varianceBeadStabilise0.0060.0000.007
writeBackgroundImages0.0060.0000.005
xieBacgroundCorrect0.0060.0000.006