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BioC 3.6: CHECK report for branchpointer on tokay1

This page was generated on 2017-08-16 13:37:40 -0400 (Wed, 16 Aug 2017).

Package 150/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
branchpointer 1.3.1
Beth Signal
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/branchpointer
Last Changed Rev: 131222 / Revision: 131943
Last Changed Date: 2017-07-13 20:51:31 -0400 (Thu, 13 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: branchpointer
Version: 1.3.1
Command: rm -rf branchpointer.buildbin-libdir branchpointer.Rcheck && mkdir branchpointer.buildbin-libdir branchpointer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=branchpointer.buildbin-libdir branchpointer_1.3.1.tar.gz >branchpointer.Rcheck\00install.out 2>&1 && cp branchpointer.Rcheck\00install.out branchpointer-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=branchpointer.buildbin-libdir --install="check:branchpointer-install.out" --force-multiarch --no-vignettes --timings branchpointer_1.3.1.tar.gz
StartedAt: 2017-08-15 22:06:29 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:12:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 370.8 seconds
RetCode: 0
Status:  OK  
CheckDir: branchpointer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf branchpointer.buildbin-libdir branchpointer.Rcheck && mkdir branchpointer.buildbin-libdir branchpointer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=branchpointer.buildbin-libdir branchpointer_1.3.1.tar.gz >branchpointer.Rcheck\00install.out 2>&1 && cp branchpointer.Rcheck\00install.out branchpointer-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=branchpointer.buildbin-libdir --install="check:branchpointer-install.out" --force-multiarch --no-vignettes --timings branchpointer_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/branchpointer.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 'branchpointer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'branchpointer' version '1.3.1'
* 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 'branchpointer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         4.0Mb
    extdata   1.1Mb
* 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 R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotBranchpointWindow    7   0.08    7.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotBranchpointWindow 6.43   0.08    6.52
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/branchpointer.Rcheck/00check.log'
for details.


branchpointer.Rcheck/00install.out:


install for i386

* installing *source* package 'branchpointer' ...
** 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 'branchpointer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'branchpointer' as branchpointer_1.3.1.zip
* DONE (branchpointer)

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

nameusersystemelapsed
gtfToExons0.860.000.86
makeBranchpointWindowForExons1.420.031.45
makeBranchpointWindowForSNP1.720.144.22
plotBranchpointWindow7.000.087.08
predictBranchpoints2.580.112.69
predictionsToSummary2.190.002.18
readQueryFile1.450.001.46

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

nameusersystemelapsed
gtfToExons1.100.001.11
makeBranchpointWindowForExons1.720.011.74
makeBranchpointWindowForSNP1.930.084.34
plotBranchpointWindow6.430.086.52
predictBranchpoints3.670.063.73
predictionsToSummary2.550.002.55
readQueryFile1.530.001.53