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BioC 3.2: CHECK report for TEQC on oaxaca

This page was generated on 2016-04-23 10:24:56 -0700 (Sat, 23 Apr 2016).

Package 1048/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEQC 3.10.0
Manuela Hummel
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TEQC
Last Changed Rev: 109589 / Revision: 116712
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
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 2016-04-23 04:56:46 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:59:09 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 143.9 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 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [11s/11s] 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 ... [32s/32s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
duplicates.barplot 5.235   0.02   5.259
* 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
TEQCreport0.0020.0000.002
chrom.barplot0.6580.0120.672
coverage.GC1.8830.0111.925
coverage.correlation2.1200.0092.130
coverage.density1.4350.0231.460
coverage.hist1.1980.0071.273
coverage.plot1.1900.0061.196
coverage.target1.1980.0061.205
coverage.targetlength.plot1.3690.0061.377
coverage.uniformity1.1870.0111.199
covered.k1.1580.0051.165
duplicates.barplot5.2350.0205.259
fraction.reads.target0.7060.0050.711
fraction.target0.1430.0010.144
get.baits0.0190.0000.020
get.reads0.3220.0030.324
get.targets0.1410.0010.140
insert.size.hist2.0970.0092.107
make.wigfiles1.2040.0101.215
multiTEQCreport0.6790.0040.683
reads2pairs2.0050.0052.013
readsPerTarget0.8740.0100.885