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BioC 3.4: CHECK report for JunctionSeq on tokay1

This page was generated on 2017-04-15 16:20:38 -0400 (Sat, 15 Apr 2017).

Package 656/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
JunctionSeq 1.4.0
Stephen Hartley
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/JunctionSeq
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: JunctionSeq
Version: 1.4.0
Command: rm -rf JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && mkdir JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=JunctionSeq.buildbin-libdir JunctionSeq_1.4.0.tar.gz >JunctionSeq.Rcheck\00install.out 2>&1 && cp JunctionSeq.Rcheck\00install.out JunctionSeq-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=JunctionSeq.buildbin-libdir --install="check:JunctionSeq-install.out" --force-multiarch --no-vignettes --timings JunctionSeq_1.4.0.tar.gz
StartedAt: 2017-04-14 23:09:48 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:16:32 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 404.2 seconds
RetCode: 0
Status:  OK  
CheckDir: JunctionSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && mkdir JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=JunctionSeq.buildbin-libdir JunctionSeq_1.4.0.tar.gz >JunctionSeq.Rcheck\00install.out 2>&1 && cp JunctionSeq.Rcheck\00install.out JunctionSeq-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=JunctionSeq.buildbin-libdir --install="check:JunctionSeq-install.out" --force-multiarch --no-vignettes --timings JunctionSeq_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/JunctionSeq.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'JunctionSeq/DESCRIPTION' ... OK
* this is package 'JunctionSeq' version '1.4.0'
* 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 'JunctionSeq' 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 ... NOTE
Foreign function calls to a different package:
  .Call("DESeq2_fitBeta", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_fitDisp", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_fitDispGrid", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_rlogGrid", ..., PACKAGE = "DESeq2")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
testFeatureForDJU.fromRow.simpleNormDist: no visible global function
  definition for 'glm.fit'
Undefined global functions or variables:
  glm.fit
Consider adding
  importFrom("stats", "glm.fit")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
buildAllPlots        9.56  52.80   63.57
defaultColorList     1.91   5.99    7.97
buildAllPlotsForGene 1.20   5.73    6.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
buildAllPlots        8.94  47.72   56.77
defaultColorList     1.25   5.04    6.88
buildAllPlotsForGene 1.14   4.65    5.93
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/JunctionSeq.Rcheck/00check.log'
for details.


JunctionSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'JunctionSeq' ...
** 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 'JunctionSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'JunctionSeq' as JunctionSeq_1.4.0.zip
* DONE (JunctionSeq)

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

nameusersystemelapsed
JunctionSeqCountSet-class0.020.000.02
buildAllPlots 9.5652.8063.57
buildAllPlotsForGene1.205.736.97
defaultColorList1.915.997.97
estimateEffectSizes4.490.004.48
estimateJunctionSeqDispersions0.010.000.02
estimateJunctionSeqSizeFactors0.210.000.20
fitJunctionSeqDispersionFunction1.020.001.01
plotDispEsts0.100.010.11
plotJunctionSeqResultsForGene0.160.020.17
plotMA0.640.030.68
readAnnotationData0.950.001.01
readJunctionSeqCounts0.690.001.44
runJunctionSeqAnalyses000
testForDiffUsage0.910.000.90
writeBedTrack0.080.000.08
writeCompleteResults0.390.000.39

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

nameusersystemelapsed
JunctionSeqCountSet-class000
buildAllPlots 8.9447.7256.77
buildAllPlotsForGene1.144.655.93
defaultColorList1.255.046.88
estimateEffectSizes3.730.013.75
estimateJunctionSeqDispersions000
estimateJunctionSeqSizeFactors0.140.020.16
fitJunctionSeqDispersionFunction0.410.000.40
plotDispEsts0.090.000.10
plotJunctionSeqResultsForGene0.110.000.11
plotMA0.710.040.75
readAnnotationData0.640.000.64
readJunctionSeqCounts0.440.000.43
runJunctionSeqAnalyses000
testForDiffUsage0.640.000.64
writeBedTrack0.480.000.48
writeCompleteResults0.380.000.57