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BioC 3.6: CHECK report for DiffLogo on tokay1

This page was generated on 2017-08-16 13:35:08 -0400 (Wed, 16 Aug 2017).

Package 352/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.00.1
Hendrik Treutler
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DiffLogo
Last Changed Rev: 131064 / Revision: 131943
Last Changed Date: 2017-07-10 03:40:11 -0400 (Mon, 10 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DiffLogo
Version: 2.00.1
Command: rm -rf DiffLogo.buildbin-libdir DiffLogo.Rcheck && mkdir DiffLogo.buildbin-libdir DiffLogo.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DiffLogo.buildbin-libdir DiffLogo_2.00.1.tar.gz >DiffLogo.Rcheck\00install.out 2>&1 && cp DiffLogo.Rcheck\00install.out DiffLogo-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DiffLogo.buildbin-libdir --install="check:DiffLogo-install.out" --force-multiarch --no-vignettes --timings DiffLogo_2.00.1.tar.gz
StartedAt: 2017-08-15 23:00:22 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:01:21 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 59.8 seconds
RetCode: 0
Status:  OK  
CheckDir: DiffLogo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DiffLogo.buildbin-libdir DiffLogo.Rcheck && mkdir DiffLogo.buildbin-libdir DiffLogo.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DiffLogo.buildbin-libdir DiffLogo_2.00.1.tar.gz >DiffLogo.Rcheck\00install.out 2>&1 && cp DiffLogo.Rcheck\00install.out DiffLogo-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DiffLogo.buildbin-libdir --install="check:DiffLogo-install.out" --force-multiarch --no-vignettes --timings DiffLogo_2.00.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DiffLogo.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DiffLogo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DiffLogo' version '2.00.1'
* 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 'DiffLogo' 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
** checking loading without being on the library search path ... 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 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 ... OK
* checking Rd files ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: OK

DiffLogo.Rcheck/00install.out:


install for i386

* installing *source* package 'DiffLogo' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DiffLogo' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DiffLogo' as DiffLogo_2.00.1.zip
* DONE (DiffLogo)

DiffLogo.Rcheck/examples_i386/DiffLogo-Ex.timings:

nameusersystemelapsed
ASN000
Alphabet000
DNA0.020.000.01
FULL_ALPHABET000
RNA000
calculatePvalue0.030.000.03
createDiffLogoObject0.120.000.13
diffLogo0.160.000.15
diffLogoFromPwm0.080.000.08
diffLogoTable2.010.002.02
diffLogoTableConfiguration000
differenceOfICs0.410.000.40
drawDiffLogoTable1.760.011.78
enrichDiffLogoObjectWithPvalues0.250.020.27
enrichDiffLogoTableWithPvalues3.750.003.75
extendPwmsFromAlignmentVector0.050.000.04
getAlphabetFromCharacters000
getAlphabetFromSequences0.010.000.02
getPwmFromAlignment0.520.010.53
getPwmFromAlignmentFile0.010.000.02
getPwmFromFastaFile0.000.020.01
getPwmFromFile000
getPwmFromHomerFile000
getPwmFromPfmOrJasparFile000
getPwmFromPwmFile000
getSequencesFromAlignmentFile000
getSequencesFromFastaFile0.010.000.01
informationContent0.10.00.1
lossOfAbsICDifferences0.060.010.07
multipleLocalPwmsAlignment0.030.000.04
normalizePWM000
normalizedDifferenceOfProbabilities0.080.000.07
prepareDiffLogoTable1.480.001.49
probabilities0.080.000.08
seqLogo0.100.000.09
shannonDivergence0.110.000.11
sumOfAbsICDifferences0.140.000.14
sumOfAbsProbabilityDifferences0.090.020.11
sumProbabilities0.080.000.08

DiffLogo.Rcheck/examples_x64/DiffLogo-Ex.timings:

nameusersystemelapsed
ASN000
Alphabet000
DNA000
FULL_ALPHABET000
RNA000
calculatePvalue0.030.000.03
createDiffLogoObject0.130.010.14
diffLogo0.170.000.18
diffLogoFromPwm0.080.000.07
diffLogoTable2.090.002.10
diffLogoTableConfiguration000
differenceOfICs0.330.030.36
drawDiffLogoTable2.090.052.14
enrichDiffLogoObjectWithPvalues0.270.000.26
enrichDiffLogoTableWithPvalues3.900.003.91
extendPwmsFromAlignmentVector0.080.000.08
getAlphabetFromCharacters000
getAlphabetFromSequences0.020.000.01
getPwmFromAlignment0.590.000.60
getPwmFromAlignmentFile0.030.000.03
getPwmFromFastaFile000
getPwmFromFile0.020.000.01
getPwmFromHomerFile000
getPwmFromPfmOrJasparFile000
getPwmFromPwmFile000
getSequencesFromAlignmentFile000
getSequencesFromFastaFile000
informationContent0.100.000.09
lossOfAbsICDifferences0.060.000.07
multipleLocalPwmsAlignment0.050.000.04
normalizePWM000
normalizedDifferenceOfProbabilities0.060.020.08
prepareDiffLogoTable1.730.001.74
probabilities0.040.010.04
seqLogo0.060.000.06
shannonDivergence0.090.000.10
sumOfAbsICDifferences0.060.000.06
sumOfAbsProbabilityDifferences0.080.000.08
sumProbabilities0.060.000.06