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BioC 2.13: CHECK report for spliceR on zin1

This page was generated on 2014-04-05 09:48:40 -0700 (Sat, 05 Apr 2014).

Package 682/750HostnameOS / ArchBUILDCHECKBUILD BIN
spliceR 1.3.1
Johannes Waage , Kristoffer Vitting-Seerup
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/spliceR
Last Changed Rev: 86204 / Revision: 88450
Last Changed Date: 2014-02-07 00:40:18 -0800 (Fri, 07 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: spliceR
Version: 1.3.1
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings spliceR_1.3.1.tar.gz
StartedAt: 2014-04-05 04:08:21 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:12:46 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 264.3 seconds
RetCode: 0
Status:  OK 
CheckDir: spliceR.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/spliceR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spliceR/DESCRIPTION’ ... OK
* this is package ‘spliceR’ version ‘1.3.1’
* 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 ‘spliceR’ can be installed ... [22s/22s] 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
Packages in Depends field not imported from:
  ‘cummeRbund’ ‘methods’ ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘spliceR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
totalNumberOfAS 8.512  0.056   9.083
generateGTF     8.456  0.064   8.547
spliceRPlot     8.421  0.052   8.601
topIsoShift     7.945  0.056   8.017
spliceR         7.872  0.044   7.947
conditions      5.885  0.080   6.067
* 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/spliceR.Rcheck/00check.log’
for details.

spliceR.Rcheck/00install.out:

* installing *source* package ‘spliceR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/local/lib -o spliceR.so utils.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/spliceR.Rcheck/spliceR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spliceR)

spliceR.Rcheck/spliceR-Ex.timings:

nameusersystemelapsed
annotatePTC.R0.0080.0000.007
conditions5.8850.0806.067
generateGTF8.4560.0648.547
getCDS0.0000.0000.001
preSpliceRFilter4.0600.0404.126
prepareCuff4.3530.0324.392
prepareCuffExample3.5240.0283.561
spliceR7.8720.0447.947
spliceRPlot8.4210.0528.601
tools4.2560.0484.344
topIsoShift7.9450.0568.017
totalNumberOfAS8.5120.0569.083