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BioC 2.14: CHECK report for spliceR on petty

This page was generated on 2014-10-08 09:00:59 -0700 (Wed, 08 Oct 2014).

Package 749/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spliceR 1.6.2
Johannes Waage , Kristoffer Vitting-Seerup
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/spliceR
Last Changed Rev: 94417 / Revision: 95116
Last Changed Date: 2014-09-23 04:05:10 -0700 (Tue, 23 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: spliceR
Version: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spliceR_1.6.2.tar.gz
StartedAt: 2014-10-08 00:16:48 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:28:08 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 680.7 seconds
RetCode: 0
Status:  OK 
CheckDir: spliceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spliceR_1.6.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/spliceR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spliceR/DESCRIPTION’ ... OK
* this is package ‘spliceR’ version ‘1.6.2’
* 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 ... [56s/60s] 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [163s/171s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
spliceRPlot        17.494  0.322  18.154
generateGTF        17.466  0.332  18.315
totalNumberOfAS    17.458  0.336  17.919
topIsoShift        16.373  0.321  16.937
spliceR            15.884  0.311  16.449
conditions         12.020  0.428  12.867
preSpliceRFilter    9.738  0.298  12.764
prepareCuff         9.569  0.298  12.336
tools               9.220  0.294   9.686
prepareCuffExample  7.949  0.290   8.623
* 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/spliceR.Rcheck/00check.log’
for details.

spliceR.Rcheck/00install.out:

* installing *source* package ‘spliceR’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c utils.c -o utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spliceR.so utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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.R0.0020.0000.099
conditions12.020 0.42812.867
generateGTF17.466 0.33218.315
getCDS0.0000.0010.001
preSpliceRFilter 9.738 0.29812.764
prepareCuff 9.569 0.29812.336
prepareCuffExample7.9490.2908.623
spliceR15.884 0.31116.449
spliceRPlot17.494 0.32218.154
tools9.2200.2949.686
topIsoShift16.373 0.32116.937
totalNumberOfAS17.458 0.33617.919