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BioC 3.1: CHECK report for goseq on morelia

This page was generated on 2015-10-09 09:39:20 -0700 (Fri, 09 Oct 2015).

Package 424/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goseq 1.20.0
Nadia Davidson
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/goseq
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: goseq
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goseq_1.20.0.tar.gz
StartedAt: 2015-10-09 02:35:28 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:39:35 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 246.5 seconds
RetCode: 0
Status:  OK 
CheckDir: goseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/goseq.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 ‘goseq/DESCRIPTION’ ... OK
* this is package ‘goseq’ version ‘1.20.0’
* 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 ‘goseq’ can be installed ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘rtracklayer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
getgo: no visible global function definition for ‘toTable’
getlength: no visible global function definition for ‘toTable’
getlength: no visible global function definition for
  ‘transcriptLengths’
getlength: no visible global function definition for ‘browserSession’
getlength: no visible global function definition for ‘genome<-’
getlength: no visible global function definition for ‘ucscTableQuery’
getlength: no visible global function definition for ‘getTable’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [66s/74s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
goseq     24.776  2.479  27.338
getgo     12.762  1.638  14.409
nullp      5.135  0.528   5.666
getlength  3.809  0.279  11.676
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/goseq.Rcheck/00check.log’
for details.


goseq.Rcheck/00install.out:

* installing *source* package ‘goseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** 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 (goseq)

goseq.Rcheck/goseq-Ex.timings:

nameusersystemelapsed
genes0.0240.0010.025
getgo12.762 1.63814.409
getlength 3.809 0.27911.676
goseq24.776 2.47927.338
makespline0.0610.0160.203
nullp5.1350.5285.666
plotPWF4.5010.4344.939