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BioC 2.14: CHECK report for CRISPRseek on zin2

This page was generated on 2014-10-08 08:50:19 -0700 (Wed, 08 Oct 2014).

Package 198/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.0.3
Lihua Julie Zhu
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CRISPRseek
Last Changed Rev: 92691 / Revision: 95116
Last Changed Date: 2014-07-21 19:34:24 -0700 (Mon, 21 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CRISPRseek
Version: 1.0.3
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CRISPRseek_1.0.3.tar.gz
StartedAt: 2014-10-07 22:56:54 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:01:49 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 294.9 seconds
RetCode: 0
Status:  OK 
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CRISPRseek_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/CRISPRseek.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.0.3’
* 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 ‘CRISPRseek’ can be installed ... [10s/10s] 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: buildFeatureVectorForScoring.Rd:35-37: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:64-66: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:58-60: Dropping empty section \references
prepare_Rd: compare2Sequences.Rd:96-98: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:134-136: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:84-86: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:97-99: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:91-93: Dropping empty section \references
prepare_Rd: filtergRNA.Rd:43-45: Dropping empty section \details
prepare_Rd: filtergRNA.Rd:57-59: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:51-53: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:70-72: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:73-75: Dropping empty section \note
prepare_Rd: offTargetAnalysis.Rd:158-160: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:178-180: Dropping empty section \note
prepare_Rd: searchHits.Rd:45-47: Dropping empty section \details
prepare_Rd: searchHits.Rd:67-69: Dropping empty section \note
prepare_Rd: searchHits.Rd:61-63: Dropping empty section \references
prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details
prepare_Rd: translatePattern.Rd:34-36: Dropping empty section \note
prepare_Rd: translatePattern.Rd:28-30: Dropping empty section \references
prepare_Rd: translatePattern.Rd:40-42: Dropping empty section \seealso
prepare_Rd: writeHits.Rd:50-52: Dropping empty section \details
prepare_Rd: writeHits.Rd:62-64: Dropping empty section \note
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [185s/186s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CRISPRseek-package 124.012  2.680 127.365
offTargetAnalysis   38.075  0.748  38.992
searchHits           4.976  0.120   5.109
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [0s/0s]
 [0s/0s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.

CRISPRseek.Rcheck/00install.out:

* installing *source* package ‘CRISPRseek’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CRISPRseek)

CRISPRseek.Rcheck/CRISPRseek-Ex.timings:

nameusersystemelapsed
CRISPRseek-package124.012 2.680127.365
buildFeatureVectorForScoring0.0600.0000.059
compare2Sequences3.2160.0123.234
filterOffTarget4.5680.2764.851
filtergRNA0.9360.0040.945
findgRNAs0.0400.0000.046
getOfftargetScore0.0760.0000.076
offTargetAnalysis38.075 0.74838.992
searchHits4.9760.1205.109
translatePattern0.0000.0000.001
writeHits0.040.000.04