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BioC 2.14: CHECK report for easyRNASeq on morelia

This page was generated on 2014-10-08 09:05:20 -0700 (Wed, 08 Oct 2014).

Package 244/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easyRNASeq 2.0.8
Nicolas Delhomme
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/easyRNASeq
Last Changed Rev: 92539 / Revision: 95116
Last Changed Date: 2014-07-15 22:43:36 -0700 (Tue, 15 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: easyRNASeq
Version: 2.0.8
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch easyRNASeq_2.0.8.tar.gz
StartedAt: 2014-10-07 22:33:24 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:40:05 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 400.6 seconds
RetCode: 0
Status:  OK 
CheckDir: easyRNASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch easyRNASeq_2.0.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.0.8’
* 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 ‘easyRNASeq’ can be installed ... [29s/30s] 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.convertToUCSC’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [97s/102s]
 [97s/103s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

easyRNASeq.Rcheck/00install.out:

* installing *source* package ‘easyRNASeq’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’
Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’
Creating a generic function for ‘print’ from package ‘base’ in package ‘easyRNASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (easyRNASeq)

easyRNASeq.Rcheck/easyRNASeq-Ex.timings:

nameusersystemelapsed
DESeq-methods0.0000.0000.001
GenomicRanges-methods0.5520.0240.673
IRanges-methods0.0010.0000.001
Rsamtools-methods0.1310.0050.213
ShortRead-methods0.0020.0010.002
easyRNASeq-AnnotParam-accessors0.0060.0010.007
easyRNASeq-AnnotParam-class0.0010.0000.001
easyRNASeq-AnnotParam0.0020.0000.003
easyRNASeq-BamFileList0.3200.0100.331
easyRNASeq-BamParam-accessors0.0020.0000.004
easyRNASeq-BamParam-class0.0010.0000.001
easyRNASeq-BamParam0.0040.0000.005
easyRNASeq-RnaSeqParam-accessors0.0080.0010.009
easyRNASeq-RnaSeqParam-class0.0020.0000.002
easyRNASeq-RnaSeqParam0.0120.0010.013
easyRNASeq-accessors0.0040.0000.004
easyRNASeq-annotation-methods0.0010.0000.001
easyRNASeq-class0.0020.0000.001
easyRNASeq-correction-methods0.0020.0000.002
easyRNASeq-count0.0010.0000.001
easyRNASeq-coverage-methods0.0010.0000.002
easyRNASeq-deprecated-annotation-methods0.0020.0010.003
easyRNASeq-easyRNASeq0.0010.0000.001
easyRNASeq-island-methods0.0010.0000.001
easyRNASeq-package0.0010.0000.001
easyRNASeq-simpleRNASeq0.0010.0000.001
easyRNASeq-summarization-methods0.0010.0010.001
edgeR-methods0.0010.0000.001
genomeIntervals-methods0.0000.0000.001
parallel-methods0.0010.0000.001