BioC 2.13: CHECK report for TEQC on perceval

Package: TEQC

Version: 3.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_3.2.0.tar.gz

StartedAt: 2014-04-05 04:45:10 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:49:17 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 246.7 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/TEQC.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘3.2.0’
* 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 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/20s] 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 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘TEQC.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [59s/60s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
duplicates.barplot   9.331  0.037   9.454
coverage.correlation 5.002  0.058   5.164
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (TEQC)

name	user	system	elapsed
TEQCreport	0.011	0.004	0.016
chrom.barplot	0.531	0.023	0.554
coverage.GC	3.709	0.038	3.765
coverage.correlation	5.002	0.058	5.164
coverage.density	2.231	0.016	2.253
coverage.hist	2.520	0.028	2.553
coverage.plot	2.014	0.027	2.053
coverage.target	2.056	0.021	2.086
coverage.targetlength.plot	3.159	0.028	3.211
coverage.uniformity	2.151	0.015	2.180
covered.k	2.032	0.013	2.056
duplicates.barplot	9.331	0.037	9.454
fraction.reads.target	0.713	0.014	0.734
fraction.target	0.216	0.005	0.226
get.baits	0.049	0.003	0.053
get.reads	0.238	0.009	0.249
get.targets	0.199	0.003	0.204
insert.size.hist	4.480	0.027	4.551
make.wigfiles	2.187	0.029	2.248
multiTEQCreport	0.921	0.018	0.966
reads2pairs	4.430	0.032	4.522
readsPerTarget	0.852	0.015	0.873