Package: TEQC

Version: 2.4.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings TEQC_2.4.0.tar.gz

StartedAt: 2012-04-01 03:41:46 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:43:54 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 128.9 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/TEQC.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TEQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TEQC' version '2.4.0'
* 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 installed files from '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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-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	0.004	0.000	0.009
chrom.barplot	0.320	0.008	0.335
coverage.GC	1.472	0.004	1.480
coverage.correlation	1.936	0.016	1.958
coverage.density	1.112	0.000	1.116
coverage.hist	0.956	0.000	0.961
coverage.plot	0.948	0.000	0.952
coverage.target	0.924	0.000	0.931
coverage.targetlength.plot	1.344	0.004	1.350
coverage.uniformity	0.944	0.000	0.948
covered.k	0.932	0.004	0.940
duplicates.barplot	4.949	0.004	4.957
fraction.reads.target	0.388	0.000	0.393
fraction.target	0.108	0.000	0.112
get.baits	0.016	0.000	0.021
get.reads	0.132	0.000	0.136
get.targets	0.120	0.000	0.123
insert.size.hist	2.080	0.008	2.091
make.wigfiles	0.936	0.000	0.941
reads2pairs	1.868	0.000	1.872
readsPerTarget	0.756	0.000	0.764