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BioC 3.0: CHECK report for polyester on perceval

This page was generated on 2015-04-10 10:00:25 -0700 (Fri, 10 Apr 2015).

Package 673/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
polyester 1.0.2
Alyssa Frazee , Jeff Leek
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/polyester
Last Changed Rev: 96808 / Revision: 102249
Last Changed Date: 2014-11-16 18:27:45 -0800 (Sun, 16 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: polyester
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch polyester_1.0.2.tar.gz
StartedAt: 2015-04-10 04:57:30 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:00:40 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 190.6 seconds
RetCode: 0
Status:  OK 
CheckDir: polyester.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch polyester_1.0.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/polyester.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘polyester/DESCRIPTION’ ... OK
* this is package ‘polyester’ version ‘1.0.2’
* 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 ‘polyester’ can be installed ... [13s/14s] 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 ... OK
* 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 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 ... [39s/45s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
create_read_numbers 14.303  0.413  14.733
seq_gtf             10.919  0.237  16.689
* 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

polyester.Rcheck/00install.out:

* installing *source* package ‘polyester’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (polyester)

polyester.Rcheck/polyester-Ex.timings:

nameusersystemelapsed
NB0.0010.0000.001
add_error0.6590.0280.700
count_transcripts0.1680.0150.183
create_read_numbers14.303 0.41314.733
fpkm_to_counts0.8480.0110.863
generate_fragments0.5160.0320.549
getAttributeField2.6220.0262.648
get_params0.1210.0120.133
get_reads0.4280.0220.451
reverse_complement0.4740.0240.499
seq_gtf10.919 0.23716.689
simulate_experiment0.0010.0000.000
simulate_experiment_countmat0.0010.0000.001
write_reads0.3850.0160.402