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BioC 3.1: CHECK report for ballgown on moscato2

This page was generated on 2015-10-09 09:31:24 -0700 (Fri, 09 Oct 2015).

Package 68/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.0.0
Alyssa Frazee
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ballgown
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ballgown
Version: 2.0.0
Command: rm -rf ballgown.buildbin-libdir ballgown.Rcheck && mkdir ballgown.buildbin-libdir ballgown.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ballgown.buildbin-libdir ballgown_2.0.0.tar.gz >ballgown.Rcheck\00install.out 2>&1 && cp ballgown.Rcheck\00install.out ballgown-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ballgown.buildbin-libdir --install="check:ballgown-install.out" --force-multiarch --no-vignettes --timings ballgown_2.0.0.tar.gz
StartedAt: 2015-10-08 23:28:18 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:35:18 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 419.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ballgown.buildbin-libdir ballgown.Rcheck && mkdir ballgown.buildbin-libdir ballgown.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ballgown.buildbin-libdir ballgown_2.0.0.tar.gz >ballgown.Rcheck\00install.out 2>&1 && cp ballgown.Rcheck\00install.out ballgown-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ballgown.buildbin-libdir --install="check:ballgown-install.out" --force-multiarch --no-vignettes --timings ballgown_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ballgown.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ballgown/DESCRIPTION' ... OK
* this is package 'ballgown' version '2.0.0'
* 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 'ballgown' 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
subset,ballgown : .local: no visible binding for global variable 'i_id'
subset,ballgown : .local: no visible binding for global variable 'e_id'
subset,ballgown : .local: no visible binding for global variable 't_id'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
annotate_assembly 5.46   0.02    5.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [35s]
 [35s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [39s]
 [39s] 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 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/ballgown.Rcheck/00check.log'
for details.


ballgown.Rcheck/00install.out:


install for i386

* installing *source* package 'ballgown' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a new generic function for 'structure' in package 'ballgown'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'ballgown' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'ballgown' as ballgown_2.0.0.zip
* DONE (ballgown)

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

nameusersystemelapsed
annotate_assembly4.070.004.08
ballgown-class0.080.000.08
ballgown-constructor0.410.000.41
ballgownrsem3.490.003.49
bg0.030.000.03
checkAssembledTx0.020.000.02
clusterTranscripts0.150.000.15
collapseTranscripts0.270.000.27
contains2.390.002.39
dirs0.040.000.04
eexpr0.050.000.05
expr-replace0.050.000.05
expr0.030.000.03
exprfilter0.080.000.08
geneIDs0.030.020.04
geneNames1.100.001.11
getAttributeField1.370.001.37
getGenes1.390.001.39
gexpr0.090.000.10
gffRead0.340.000.34
gffReadGR1.410.001.40
iexpr0.030.000.03
indexes-replace0.040.000.03
indexes0.040.000.05
last000
mergedDate0.030.000.03
pData-replace0.030.020.05
pData0.050.000.04
pctOverlap1.410.001.41
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.040.000.04
seqnames0.030.000.03
stattest0.10.00.1
structure0.060.000.06
subset0.120.000.13
tGene0.050.000.04
texpr0.050.000.05
transcriptIDs0.030.000.03
transcriptNames0.050.000.05
writeFiles000

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

nameusersystemelapsed
annotate_assembly5.460.025.48
ballgown-class0.080.000.08
ballgown-constructor0.360.010.37
ballgownrsem4.180.034.21
bg0.030.000.04
checkAssembledTx000
clusterTranscripts0.190.000.18
collapseTranscripts0.290.000.30
contains2.860.002.85
dirs0.030.000.04
eexpr0.040.000.04
expr-replace0.050.000.05
expr0.030.000.03
exprfilter0.080.000.08
geneIDs0.030.020.04
geneNames1.270.001.27
getAttributeField1.600.001.61
getGenes1.660.001.65
gexpr0.100.000.11
gffRead0.320.000.31
gffReadGR1.850.001.86
iexpr0.030.000.03
indexes-replace0.030.000.03
indexes0.050.000.05
last000
mergedDate0.030.000.03
pData-replace0.050.000.05
pData0.030.000.03
pctOverlap1.230.001.23
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.030.000.03
seqnames0.030.000.03
stattest0.090.000.09
structure0.060.000.07
subset0.180.000.17
tGene0.030.010.05
texpr0.030.000.03
transcriptIDs0.040.000.04
transcriptNames0.040.000.03
writeFiles000