BioC 2.14: CHECK report for TEQC on petty

Package: TEQC

Version: 3.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_3.4.0.tar.gz

StartedAt: 2014-10-08 00:25:28 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:30:43 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 315.3 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_3.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/TEQC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘3.4.0’
* 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 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 ... [22s/23s] 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 loading without being on the library search path ... 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 ‘qwidth’
get.reads: no visible binding for global variable ‘qname’
get.reads: no visible binding for global variable ‘rname’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [80s/81s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
duplicates.barplot   13.406  0.028  13.497
coverage.correlation  6.672  0.026   6.706
reads2pairs           5.435  0.013   5.478
insert.size.hist      5.376  0.016   5.446
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.005	0.002	0.006
chrom.barplot	0.839	0.017	0.858
coverage.GC	4.872	0.017	4.896
coverage.correlation	6.672	0.026	6.706
coverage.density	3.463	0.011	3.483
coverage.hist	3.354	0.016	3.372
coverage.plot	3.280	0.013	3.299
coverage.target	3.219	0.010	3.232
coverage.targetlength.plot	3.918	0.012	3.942
coverage.uniformity	3.240	0.011	3.309
covered.k	3.311	0.016	3.442
duplicates.barplot	13.406	0.028	13.497
fraction.reads.target	1.254	0.007	1.263
fraction.target	0.343	0.002	0.344
get.baits	0.078	0.001	0.079
get.reads	0.339	0.005	0.345
get.targets	0.362	0.002	0.365
insert.size.hist	5.376	0.016	5.446
make.wigfiles	3.287	0.017	3.360
multiTEQCreport	1.124	0.009	1.164
reads2pairs	5.435	0.013	5.478
readsPerTarget	1.519	0.008	1.530