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CHECK report for blima on tokay1

This page was generated on 2020-10-22 12:28:18 -0400 (Thu, 22 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 193/1952HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blima 1.23.0
Vojtěch Kulvait
Snapshot Date: 2020-10-21 14:52:01 -0400 (Wed, 21 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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blima.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings blima_1.23.0.tar.gz
StartedAt: 2020-10-22 00:46:21 -0400 (Thu, 22 Oct 2020)
EndedAt: 2020-10-22 00:49:16 -0400 (Thu, 22 Oct 2020)
EllapsedTime: 174.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: blima.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blima.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings blima_1.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-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 '1.23.0'
* 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 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-3.12-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-3.12-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-3.12-bioc/meat/blima.Rcheck/00check.log'
for details.



Installation output

blima.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/blima_1.23.0.tar.gz && rm -rf blima.buildbin-libdir && mkdir blima.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=blima.buildbin-libdir blima_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL blima_1.23.0.zip && rm blima_1.23.0.tar.gz blima_1.23.0.zip
###
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  % 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 35942  100 35942    0     0   974k      0 --:--:-- --:--:-- --:--:-- 1096k

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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/blima.buildbin-libdir/blima/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'blima' as blima_1.23.0.zip
* DONE (blima)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'blima' successfully unpacked and MD5 sums checked

Tests output


Example timings

blima.Rcheck/examples_i386/blima-Ex.timings

nameusersystemelapsed
bacgroundCorrect0.030.000.21
backgroundChannelSubtract0.030.000.03
chipArrayStatistics0.020.000.02
createSummarizedMatrix0.580.022.05
doProbeTTests0.190.030.22
doTTests0.230.000.23
log2TransformPositive0.180.030.20
nonPositiveCorrect0.010.000.02
plotBackgroundImageAfterCorrection0.020.000.02
plotBackgroundImageBeforeCorrection0.010.000.01
quantileNormalize000
selectedChannelTransform000
varianceBeadStabilise0.020.000.01
writeBackgroundImages0.010.000.02
xieBacgroundCorrect000

blima.Rcheck/examples_x64/blima-Ex.timings

nameusersystemelapsed
bacgroundCorrect0.010.000.02
backgroundChannelSubtract0.020.000.01
chipArrayStatistics0.010.000.02
createSummarizedMatrix0.530.030.56
doProbeTTests0.140.000.14
doTTests0.080.030.11
log2TransformPositive0.090.030.12
nonPositiveCorrect0.020.000.02
plotBackgroundImageAfterCorrection000
plotBackgroundImageBeforeCorrection000
quantileNormalize0.020.000.02
selectedChannelTransform000
varianceBeadStabilise000
writeBackgroundImages0.010.000.02
xieBacgroundCorrect000