CRISPRseek 1.9.8
Lihua Julie Zhu
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CRISPRseek | | Last Changed Rev: 107089 / Revision: 107602 | | Last Changed Date: 2015-08-04 08:50:18 -0700 (Tue, 04 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 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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### rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.9.8.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.9.8.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CRISPRseek.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CRISPRseek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRISPRseek' version '1.9.8'
* 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 whether package 'CRISPRseek' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by 'seqinr::translate' when loading 'CRISPRseek'
See 'D:/biocbld/bbs-3.2-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 ... WARNING
Invalid citation information in 'inst/CITATION':
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'library' or 'require' call not declared from: 'GeneRfold'
'library' or 'require' call to 'GeneRfold' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateOffTargets: no visible global function definition for 'GRanges'
annotateOffTargets: no visible global function definition for 'Rle'
annotateOffTargets: no visible global function definition for 'IRanges'
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
'seqlevels<-'
annotateOffTargets: no visible global function definition for
'seqlevels'
annotateOffTargets: no visible global function definition for
'overlapsAny'
annotateOffTargets: no visible global function definition for 'genes'
annotateOffTargets: no visible global function definition for
'findOverlaps'
annotateOffTargets: no visible global function definition for
'queryHits'
annotateOffTargets: no visible global function definition for
'subjectHits'
annotateOffTargets: no visible global function definition for 'toTable'
filterOffTarget: no visible global function definition for 'seqlengths'
foldgRNAs: no visible global function definition for 'fold'
foldgRNAs : <anonymous>: no visible global function definition for
'fold'
getSeqFromBed: no visible global function definition for 'seqlengths'
uniqueREs: no visible global function definition for 'seqlengths'
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:47-49: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:59-61: Dropping empty section \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:150-152: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:192-194: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:98-100: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:112-114: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:48-50: Dropping empty section \details
prepare_Rd: filtergRNA.Rd:62-64: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:56-58: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:92-94: Dropping empty section \references
prepare_Rd: foldgRNAs.Rd:28-30: Dropping empty section \details
prepare_Rd: foldgRNAs.Rd:44-46: Dropping empty section \note
prepare_Rd: foldgRNAs.Rd:38-40: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:73-75: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:22-24: Dropping empty section \details
prepare_Rd: isPatternUnique.Rd:34-36: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:28-30: Dropping empty section \references
prepare_Rd: isPatternUnique.Rd:40-41: Dropping empty section \seealso
prepare_Rd: offTargetAnalysis.Rd:223-225: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:245-247: Dropping empty section \note
prepare_Rd: offTargetAnalysisOfPeakRegions.Rd:82-84: Dropping empty section \details
prepare_Rd: offTargetAnalysisOfPeakRegions.Rd:102-104: Dropping empty section \note
prepare_Rd: searchHits.Rd:55-57: Dropping empty section \details
prepare_Rd: searchHits.Rd:77-79: Dropping empty section \note
prepare_Rd: searchHits.Rd:71-73: 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: uniqueREs.Rd:40-42: Dropping empty section \details
prepare_Rd: uniqueREs.Rd:53-55: Dropping empty section \note
prepare_Rd: uniqueREs.Rd:47-49: Dropping empty section \references
prepare_Rd: uniqueREs.Rd:59-60: 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 ...
** running examples for arch 'i386' ... [12m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 558.28 5.18 591.10
offTargetAnalysis 49.86 0.34 50.25
offTargetAnalysisOfPeakRegions 30.07 0.05 30.15
filterOffTarget 16.09 0.06 16.17
annotateOffTargets 14.47 0.28 14.76
searchHits 12.19 0.16 12.34
** running examples for arch 'x64' ... [12m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 609.74 5.25 616.41
offTargetAnalysis 42.54 0.15 42.70
offTargetAnalysisOfPeakRegions 35.97 0.05 36.04
filterOffTarget 14.85 0.06 14.91
annotateOffTargets 13.51 0.10 13.60
searchHits 5.78 0.05 5.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [0s]
[1s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [0s]
[1s] 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: 3 WARNINGs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/CRISPRseek.Rcheck/00check.log'
for details.
install for i386
* 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'
install for x64
* installing *source* package 'CRISPRseek' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'seqinr::translate' when loading 'CRISPRseek'
* MD5 sums
packaged installation of 'CRISPRseek' as CRISPRseek_1.9.8.zip
* DONE (CRISPRseek)