CRISPRseek 1.4.2
Lihua Julie Zhu
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CRISPRseek | | Last Changed Rev: 95787 / Revision: 102249 | | Last Changed Date: 2014-10-20 11:08:31 -0700 (Mon, 20 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CRISPRseek_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/CRISPRseek.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.4.2’
* 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 ‘CRISPRseek’ can be installed ... [19s/19s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘seqinr::translate’ when loading ‘CRISPRseek’
See ‘/home/biocbuild/bbs-3.0-bioc/meat/CRISPRseek.Rcheck/00install.out’ for details.
* 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
filterOffTarget: no visible global function definition for ‘GRanges’
filterOffTarget: no visible global function definition for ‘Rle’
filterOffTarget: no visible global function definition for ‘IRanges’
filterOffTarget: no visible global function definition for ‘exons’
filterOffTarget: no visible global function definition for
‘overlapsAny’
filterOffTarget: no visible global function definition for
‘intronsByTranscript’
filterOffTarget: no visible global function definition for
‘findOverlaps’
filterOffTarget: no visible global function definition for
‘subjectHits’
filterOffTarget: no visible global function definition for ‘queryHits’
filterOffTarget: no visible global function definition for ‘seqlengths’
* 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: calculategRNAEfficiency.Rd:40-42: Dropping empty section \note
prepare_Rd: compare2Sequences.Rd:107-109: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:145-147: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:98-100: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:111-113: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:44-46: Dropping empty section \details
prepare_Rd: filtergRNA.Rd:58-60: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:52-54: 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:180-182: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:201-203: 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 ... WARNING
Bad \usage lines found in documentation object 'calculategRNAEfficiency':
calculategRNAEfficiency <- function(extendedSequence, baseBeforegRNA, featureWeightMatrix, gRNA.size = 20)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [455s/459s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 359.895 7.472 371.323
offTargetAnalysis 61.636 0.976 62.954
filterOffTarget 7.628 0.228 7.870
* 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
* DONE
WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.
* installing *source* package ‘CRISPRseek’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘seqinr::translate’ when loading ‘CRISPRseek’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘seqinr::translate’ when loading ‘CRISPRseek’
* DONE (CRISPRseek)