BioC 2.12: CHECK report for TEQC on petty

Package: TEQC

Version: 2.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_2.9.2.tar.gz

StartedAt: 2013-10-09 00:03:29 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:08:08 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 279.1 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 3.0.1 (2013-05-16)
* 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 '2.9.2'
* 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 ... [21s/22s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [73s/73s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
duplicates.barplot   13.723  0.060  13.873
insert.size.hist      5.606  0.028   5.688
coverage.correlation  5.211  0.062   5.321
reads2pairs           5.234  0.025   5.468
* 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
** testing if installed package can be loaded
* DONE (TEQC)

name	user	system	elapsed
TEQCreport	0.015	0.004	0.020
chrom.barplot	1.012	0.022	1.044
coverage.GC	3.887	0.042	3.983
coverage.correlation	5.211	0.062	5.321
coverage.density	2.587	0.025	2.632
coverage.hist	2.620	0.026	2.662
coverage.plot	2.949	0.027	2.993
coverage.target	2.528	0.021	2.557
coverage.targetlength.plot	3.225	0.028	3.298
coverage.uniformity	3.016	0.023	3.066
covered.k	2.681	0.023	2.728
duplicates.barplot	13.723	0.060	13.873
fraction.reads.target	1.316	0.018	1.339
fraction.target	0.282	0.003	0.285
get.baits	0.075	0.003	0.078
get.reads	0.575	0.014	0.606
get.targets	0.272	0.003	0.277
insert.size.hist	5.606	0.028	5.688
make.wigfiles	2.702	0.028	2.740
reads2pairs	5.234	0.025	5.468
readsPerTarget	1.927	0.016	1.958