BioC 3.1: CHECK report for TEQC on petty

Package: TEQC

Version: 3.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.8.0.tar.gz

StartedAt: 2015-10-09 02:19:57 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:23:32 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 214.7 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 TEQC_3.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/TEQC.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘3.8.0’
* 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 ... [16s/17s] 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 ... 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 ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
duplicates.barplot 7.892  0.018   7.922
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/TEQC.Rcheck/00check.log’
for details.

* installing *source* package ‘TEQC’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (TEQC)

name	user	system	elapsed
TEQCreport	0.002	0.000	0.003
chrom.barplot	0.995	0.034	1.035
coverage.GC	2.320	0.013	2.336
coverage.correlation	3.062	0.042	3.107
coverage.density	1.539	0.006	1.545
coverage.hist	1.464	0.007	1.472
coverage.plot	1.613	0.007	1.623
coverage.target	1.414	0.005	1.421
coverage.targetlength.plot	1.796	0.007	1.804
coverage.uniformity	1.734	0.005	1.739
covered.k	1.635	0.007	1.644
duplicates.barplot	7.892	0.018	7.922
fraction.reads.target	0.689	0.005	0.695
fraction.target	0.183	0.001	0.184
get.baits	0.03	0.00	0.03
get.reads	0.225	0.003	0.228
get.targets	0.235	0.000	0.236
insert.size.hist	3.187	0.008	3.196
make.wigfiles	1.575	0.008	1.584
multiTEQCreport	0.537	0.003	0.542
reads2pairs	3.111	0.005	3.117
readsPerTarget	1.155	0.004	1.158