Package: TEQC

Version: 2.7.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_2.7.3.tar.gz

StartedAt: 2013-03-24 10:46:10 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 10:50:06 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 236.1 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/TEQC.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'TEQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TEQC' version '2.7.3'
* 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 'TEQC' can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... NOTE
get.reads: no visible binding for global variable 'pos'
get.reads: no visible binding for global variable 'qname'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [58s/60s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
duplicates.barplot 10.156  0.062   10.25
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/TEQC.Rcheck/00check.log'
for details.

* installing *source* package 'TEQC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'TEQC.Rnw' 
** testing if installed package can be loaded
* DONE (TEQC)

name	user	system	elapsed
TEQCreport	0.016	0.004	0.020
chrom.barplot	0.895	0.024	0.929
coverage.GC	3.126	0.033	3.166
coverage.correlation	4.272	0.056	4.341
coverage.density	2.082	0.028	2.197
coverage.hist	2.357	0.039	2.575
coverage.plot	2.103	0.036	2.181
coverage.target	2.047	0.021	2.073
coverage.targetlength.plot	2.489	0.026	2.526
coverage.uniformity	2.127	0.019	2.154
covered.k	2.389	0.029	2.429
duplicates.barplot	10.156	0.062	10.250
fraction.reads.target	1.418	0.022	1.448
fraction.target	0.218	0.005	0.225
get.baits	0.056	0.005	0.063
get.reads	0.510	0.016	0.531
get.targets	0.207	0.003	0.210
insert.size.hist	4.007	0.033	4.071
make.wigfiles	2.200	0.031	2.241
reads2pairs	3.975	0.030	4.073
readsPerTarget	1.350	0.016	1.367