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BioC 3.2: CHECK report for TEQC on zin1

This page was generated on 2015-08-24 10:47:53 -0700 (Mon, 24 Aug 2015).

Package 1014/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEQC 3.9.0
Manuela Hummel
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TEQC
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 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: 3.9.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TEQC_3.9.0.tar.gz
StartedAt: 2015-08-24 04:18:19 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:20:08 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 109.0 seconds
RetCode: 0
Status:  OK 
CheckDir: TEQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TEQC_3.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/TEQC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘3.9.0’
* 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 ... [9s/9s] 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 ... [23s/23s] OK
* 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
  ‘/home/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
TEQCreport0.0010.0000.001
chrom.barplot0.3330.0080.339
coverage.GC1.1200.0041.124
coverage.correlation1.5880.0001.606
coverage.density1.1080.0111.137
coverage.hist0.7530.0040.756
coverage.plot0.7760.0000.777
coverage.target0.7190.0000.718
coverage.targetlength.plot0.8970.0040.901
coverage.uniformity0.7320.0000.731
covered.k0.8050.0000.804
duplicates.barplot4.0710.0044.116
fraction.reads.target0.3730.0000.396
fraction.target0.1490.0000.151
get.baits0.0140.0000.014
get.reads0.1100.0000.114
get.targets0.1500.0000.152
insert.size.hist1.4880.0001.486
make.wigfiles0.9220.0040.931
multiTEQCreport0.3380.0000.337
reads2pairs1.6490.0001.648
readsPerTarget0.4670.0000.467