Package: TEQC

Version: 2.7.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings TEQC_2.7.3.tar.gz

StartedAt: 2013-01-16 06:43:11 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:46:21 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 190.1 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/TEQC.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘2.7.3’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
duplicates.barplot 8.813      0   8.817
* 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
  ‘/loc/home/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	0.284	0.004	0.290
chrom.barplot	0.520	0.012	0.534
coverage.GC	2.524	0.004	2.529
coverage.correlation	3.164	0.020	3.188
coverage.density	1.872	0.004	1.874
coverage.hist	1.529	0.012	1.542
coverage.plot	1.556	0.004	1.565
coverage.target	1.552	0.004	1.553
coverage.targetlength.plot	1.856	0.000	1.859
coverage.uniformity	1.536	0.004	1.543
covered.k	1.568	0.004	1.575
duplicates.barplot	8.813	0.000	8.817
fraction.reads.target	0.992	0.000	0.993
fraction.target	0.188	0.000	0.187
get.baits	0.052	0.000	0.053
get.reads	0.188	0.004	0.192
get.targets	0.188	0.000	0.191
insert.size.hist	3.264	0.000	3.266
make.wigfiles	1.932	0.004	1.941
reads2pairs	3.456	0.004	3.460
readsPerTarget	1.188	0.008	1.195