CRISPRseek 1.9.8
Lihua Julie Zhu
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CRISPRseek | | Last Changed Rev: 107089 / Revision: 107696 | | 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 ] | |  |
| 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CRISPRseek_1.9.8.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CRISPRseek.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 ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘CRISPRseek’ can be installed ... [14s/14s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘seqinr::translate’ when loading ‘CRISPRseek’
See ‘/home/biocbuild/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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [383s/387s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 288.701 6.060 297.684
offTargetAnalysis 31.440 0.016 31.510
offTargetAnalysisOfPeakRegions 23.566 0.017 23.578
filterOffTarget 10.058 0.012 10.227
annotateOffTargets 8.551 0.056 8.600
* 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
Status: 3 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-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)