Package: TEQC

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_2.2.0.tar.gz

StartedAt: 2012-03-24 04:39:18 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 04:43:23 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 244.1 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/TEQC.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'TEQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TEQC' version '2.2.0'
* 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 whether package 'TEQC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* 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

* installing *source* package 'TEQC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'TEQC.Rnw' 
** testing if installed package can be loaded

* DONE (TEQC)

name	user	system	elapsed
TEQCreport	0.002	0.001	0.004
chrom.barplot	0.538	0.031	0.574
coverage.GC	2.419	0.054	2.547
coverage.correlation	3.304	0.093	3.797
coverage.density	1.850	0.052	1.949
coverage.hist	1.666	0.043	1.836
coverage.plot	1.844	0.040	2.000
coverage.target	1.763	0.034	1.845
coverage.targetlength.plot	2.026	0.055	2.196
coverage.uniformity	1.614	0.040	1.714
covered.k	1.871	0.041	1.937
duplicates.barplot	8.604	0.221	8.984
fraction.reads.target	0.693	0.032	0.729
fraction.target	0.189	0.002	0.196
get.baits	0.027	0.001	0.028
get.reads	0.235	0.022	0.258
get.targets	0.181	0.002	0.183
insert.size.hist	3.185	0.076	3.292
make.wigfiles	1.954	0.054	2.016
reads2pairs	3.197	0.074	3.344
readsPerTarget	1.470	0.040	1.551