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BioC 2.12: CHECK report for TEQC on petty

This page was generated on 2013-10-09 09:39:55 -0700 (Wed, 09 Oct 2013).

Package 634/671HostnameOS / ArchBUILDCHECKBUILD BIN
TEQC 2.9.2
Manuela Hummel
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/TEQC
Last Changed Rev: 78626 / Revision: 81334
Last Changed Date: 2013-07-16 23:29:08 -0700 (Tue, 16 Jul 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: TEQC
Version: 2.9.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEQC_2.9.2.tar.gz
StartedAt: 2013-10-09 00:03:29 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:08:08 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 279.1 seconds
RetCode: 0
Status:  OK 
CheckDir: TEQC.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/TEQC.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'TEQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TEQC' version '2.9.2'
* 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 ... [21s/22s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
get.reads: no visible binding for global variable 'pos'
get.reads: no visible binding for global variable 'qname'
* 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 examples ... [73s/73s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
duplicates.barplot   13.723  0.060  13.873
insert.size.hist      5.606  0.028   5.688
coverage.correlation  5.211  0.062   5.321
reads2pairs           5.234  0.025   5.468
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
TEQCreport0.0150.0040.020
chrom.barplot1.0120.0221.044
coverage.GC3.8870.0423.983
coverage.correlation5.2110.0625.321
coverage.density2.5870.0252.632
coverage.hist2.6200.0262.662
coverage.plot2.9490.0272.993
coverage.target2.5280.0212.557
coverage.targetlength.plot3.2250.0283.298
coverage.uniformity3.0160.0233.066
covered.k2.6810.0232.728
duplicates.barplot13.723 0.06013.873
fraction.reads.target1.3160.0181.339
fraction.target0.2820.0030.285
get.baits0.0750.0030.078
get.reads0.5750.0140.606
get.targets0.2720.0030.277
insert.size.hist5.6060.0285.688
make.wigfiles2.7020.0282.740
reads2pairs5.2340.0255.468
readsPerTarget1.9270.0161.958