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BioC 3.2: CHECK report for TEQC on perceval

This page was generated on 2015-11-10 14:46:50 -0800 (Tue, 10 Nov 2015).

Package 1048/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEQC 3.10.0
Manuela Hummel
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TEQC
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TEQC
Version: 3.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.10.0.tar.gz
StartedAt: 2015-11-10 10:09:43 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 10:12:25 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 161.5 seconds
RetCode: 0
Status:  OK 
CheckDir: TEQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TEQC.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘3.10.0’
* 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 ... [12s/12s] 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 ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
duplicates.barplot 5.037   0.01   5.048
* 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-3.2-bioc/meat/TEQC.Rcheck/00check.log’
for details.


TEQC.Rcheck/00install.out:

* 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)

TEQC.Rcheck/TEQC-Ex.timings:

nameusersystemelapsed
TEQCreport0.0010.0010.002
chrom.barplot0.4510.0170.468
coverage.GC1.5560.0061.562
coverage.correlation2.3430.0352.379
coverage.density1.1780.0071.186
coverage.hist1.0470.0051.052
coverage.plot1.0460.0031.050
coverage.target1.0260.0061.031
coverage.targetlength.plot1.2510.0071.258
coverage.uniformity1.0180.0051.023
covered.k0.9880.0050.993
duplicates.barplot5.0370.0105.048
fraction.reads.target0.5170.0030.519
fraction.target0.1640.0000.165
get.baits0.0170.0010.018
get.reads0.1750.0020.176
get.targets0.1680.0000.167
insert.size.hist1.9280.0031.931
make.wigfiles1.1170.0091.126
multiTEQCreport0.6920.0060.697
reads2pairs1.9920.0081.999
readsPerTarget0.7040.0040.707