BioC 3.0: CHECK report for polyester on perceval

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

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### Running command:
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###   /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

* 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)

name	user	system	elapsed
NB	0.001	0.000	0.001
add_error	0.659	0.028	0.700
count_transcripts	0.168	0.015	0.183
create_read_numbers	14.303	0.413	14.733
fpkm_to_counts	0.848	0.011	0.863
generate_fragments	0.516	0.032	0.549
getAttributeField	2.622	0.026	2.648
get_params	0.121	0.012	0.133
get_reads	0.428	0.022	0.451
reverse_complement	0.474	0.024	0.499
seq_gtf	10.919	0.237	16.689
simulate_experiment	0.001	0.000	0.000
simulate_experiment_countmat	0.001	0.000	0.001
write_reads	0.385	0.016	0.402