Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for ballgown on morelia

This page was generated on 2015-10-09 09:42:02 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.0.0.tar.gz
StartedAt: 2015-10-08 23:21:22 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:25:47 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 265.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ballgown.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ballgown’ can be installed ... [19s/19s] 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
* 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 ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [39s/39s]
 [40s/40s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/ballgown.Rcheck/00check.log’
for details.


ballgown.Rcheck/00install.out:

* 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’
* DONE (ballgown)

ballgown.Rcheck/ballgown-Ex.timings:

nameusersystemelapsed
annotate_assembly4.5380.1644.705
ballgown-class0.0980.0050.103
ballgown-constructor0.4740.0270.501
ballgownrsem3.8110.1433.957
bg0.0300.0060.037
checkAssembledTx000
clusterTranscripts0.1830.0060.189
collapseTranscripts0.3530.0310.386
contains2.6380.0912.730
dirs0.0400.0080.048
eexpr0.0450.0020.047
expr-replace0.0440.0030.047
expr0.0380.0090.047
exprfilter0.0890.0020.092
geneIDs0.0350.0020.037
geneNames1.0550.0451.100
getAttributeField1.4660.0061.472
getGenes1.4390.1041.544
gexpr0.0920.0030.096
gffRead0.2590.0000.259
gffReadGR1.7890.0571.847
iexpr0.0390.0040.043
indexes-replace0.0350.0020.038
indexes0.0360.0020.040
last0.0000.0000.001
mergedDate0.0340.0030.038
pData-replace0.0290.0040.033
pData0.0350.0040.040
pctOverlap1.1770.0701.248
plotLatentTranscripts0.0000.0010.000
plotMeans0.0010.0000.000
plotTranscripts0.0010.0000.000
sampleNames0.0360.0130.049
seqnames0.0370.0140.051
stattest0.1030.0120.114
structure0.0590.0130.072
subset0.1060.0090.115
tGene0.0430.0110.055
texpr0.0380.0130.052
transcriptIDs0.0360.0110.047
transcriptNames0.0390.0130.053
writeFiles0.0010.0000.001