BioC 3.0: CHECK report for TEQC on perceval

Package: TEQC

Version: 3.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_3.6.0.tar.gz

StartedAt: 2015-04-10 06:58:23 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 07:02:34 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 250.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TEQC.Rcheck

Warnings: 1

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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_3.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/TEQC.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘3.6.0’
* 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 ... [20s/22s] 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
coverage.plot: no visible global function definition for ‘Rle’
coverage.target: no visible global function definition for ‘Rle’
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’
multfun: no visible global function definition for ‘Rle’
multfun: no visible global function definition for ‘runValue’
reads2pairs: no visible global function definition for ‘Rle’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'coverage.GC.Rd':
  ‘[IRanges:Rle-class]{RleList}’ ‘[IRanges:Rle-class]{Rle}’

Missing link or links in documentation object 'coverage.hist.Rd':
  ‘[IRanges:Rle-class]{RleList}’ ‘[IRanges:Rle-class]{Rle}’

Missing link or links in documentation object 'coverage.plot.Rd':
  ‘[IRanges:Rle-class]{RleList}’ ‘[IRanges:Rle-class]{Rle}’

Missing link or links in documentation object 'coverage.target.Rd':
  ‘[IRanges:Rle-class]{RleList}’ ‘[IRanges:Rle-class]{Rle}’

Missing link or links in documentation object 'covered.k.Rd':
  ‘[IRanges:Rle-class]{RleList}’ ‘[IRanges:Rle-class]{Rle}’

Missing link or links in documentation object 'make.wigfiles.Rd':
  ‘[IRanges:Rle-class]{RleList}’ ‘[IRanges:Rle-class]{Rle}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
duplicates.barplot 6.864  0.013   6.911
* 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
* DONE

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.003	0.001	0.004
chrom.barplot	0.511	0.012	0.523
coverage.GC	1.980	0.018	2.011
coverage.correlation	2.405	0.012	2.426
coverage.density	1.708	0.012	1.734
coverage.hist	1.268	0.012	1.773
coverage.plot	1.149	0.010	1.166
coverage.target	1.417	0.012	1.429
coverage.targetlength.plot	1.449	0.012	1.474
coverage.uniformity	1.209	0.010	1.233
covered.k	1.169	0.007	1.175
duplicates.barplot	6.864	0.013	6.911
fraction.reads.target	0.636	0.003	0.640
fraction.target	0.196	0.001	0.197
get.baits	0.019	0.001	0.020
get.reads	0.185	0.004	0.189
get.targets	0.211	0.002	0.213
insert.size.hist	2.966	0.008	2.990
make.wigfiles	1.235	0.011	1.246
multiTEQCreport	0.532	0.005	0.537
reads2pairs	2.518	0.007	2.524
readsPerTarget	0.990	0.005	0.996