Package: TEQC

Version: 2.2.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings TEQC_2.2.0.tar.gz

StartedAt: 2012-03-24 03:01:09 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:04:27 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 197.6 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/TEQC.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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	0.004	0.000	0.003
chrom.barplot	0.360	0.008	0.367
coverage.GC	1.968	0.012	1.984
coverage.correlation	2.692	0.036	2.816
coverage.density	1.612	0.012	1.679
coverage.hist	1.113	0.016	1.129
coverage.plot	1.196	0.000	1.201
coverage.target	1.176	0.000	1.203
coverage.targetlength.plot	1.844	0.004	1.886
coverage.uniformity	1.156	0.000	1.156
covered.k	1.200	0.000	1.205
duplicates.barplot	6.852	0.020	6.930
fraction.reads.target	0.472	0.004	0.480
fraction.target	0.136	0.004	0.137
get.baits	0.020	0.000	0.022
get.reads	0.152	0.000	0.153
get.targets	0.144	0.000	0.143
insert.size.hist	2.433	0.004	2.437
make.wigfiles	1.620	0.008	1.639
reads2pairs	2.480	0.004	2.486
readsPerTarget	0.752	0.004	0.756