BioC 3.5: CHECK report for CRISPRseek on tokay2
This page was generated on 2017-08-16 13:22:51 -0400 (Wed, 16 Aug 2017).
CRISPRseek 1.16.0 Lihua Julie Zhu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CRISPRseek | Last Changed Rev: 129126 / Revision: 131943 | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Package: CRISPRseek
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Version: 1.16.0
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Command: rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.16.0.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.16.0.tar.gz
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StartedAt: 2017-08-15 23:01:40 -0400 (Tue, 15 Aug 2017)
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EndedAt: 2017-08-15 23:15:36 -0400 (Tue, 15 Aug 2017)
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EllapsedTime: 836.2 seconds
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RetCode: 0
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Status: OK
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CheckDir: CRISPRseek.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.16.0.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CRISPRseek.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.16.0'
* 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 ... 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
* 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
* 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 dependencies in R code ... NOTE
':::' call which should be '::': 'S4Vectors:::orderIntegerPairs'
See the note in ?`:::` about the use of this operator.
* 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 'as'
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 'genes'
annotateOffTargets: no visible global function definition for 'toTable'
buildFeatureVectorForScoring: no visible global function definition for
'as'
buildFeatureVectorForScoring2: no visible global function definition
for 'as'
filterOffTarget: no visible global function definition for 'seqlengths'
foldgRNAs: no visible global function definition for 'fold'
getSeqFromBed: no visible global function definition for 'seqlengths'
uniqueREs: no visible global function definition for 'seqlengths'
writeHits: no visible global function definition for 'as'
writeHits2: no visible global function definition for 'as'
Undefined global functions or variables:
GRanges as exons fold genes seqlengths seqlevels seqlevels<- toTable
Consider adding
importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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:48-50: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:77-79: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:71-73: Dropping empty section \references
prepare_Rd: calculategRNAEfficiency.Rd:49-51: Dropping empty section \note
prepare_Rd: compare2Sequences.Rd:217-219: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:259-261: 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:110-112: 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:284-286: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:307-309: Dropping empty section \note
prepare_Rd: searchHits.Rd:58-60: Dropping empty section \details
prepare_Rd: searchHits.Rd:80-82: Dropping empty section \note
prepare_Rd: searchHits.Rd:74-76: Dropping empty section \references
prepare_Rd: searchHits2.Rd:66-68: Dropping empty section \details
prepare_Rd: searchHits2.Rd:88-90: Dropping empty section \note
prepare_Rd: searchHits2.Rd:82-84: 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:73-75: Dropping empty section \details
prepare_Rd: writeHits.Rd:85-87: Dropping empty section \note
prepare_Rd: writeHits2.Rd:76-78: Dropping empty section \details
prepare_Rd: writeHits2.Rd:88-90: 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 203.50 6.99 276.05
offTargetAnalysis 40.21 0.69 40.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 171.70 6.44 178.14
offTargetAnalysis 33.53 0.55 34.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/CRISPRseek.Rcheck/00check.log'
for details.
CRISPRseek.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'CRISPRseek' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRISPRseek' as CRISPRseek_1.16.0.zip
* DONE (CRISPRseek)
CRISPRseek.Rcheck/examples_i386/CRISPRseek-Ex.timings:
name | user | system | elapsed
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CRISPRseek-package | 203.50 | 6.99 | 276.05 |
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annotateOffTargets | 3.75 | 0.12 | 3.87 |
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buildFeatureVectorForScoring | 0.11 | 0.02 | 0.12 |
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calculategRNAEfficiency | 0.02 | 0.00 | 0.02 |
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compare2Sequences | 2.14 | 0.01 | 2.15 |
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filterOffTarget | 4.37 | 0.04 | 4.41 |
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filtergRNA | 0.61 | 0.01 | 0.63 |
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findgRNAs | 0.16 | 0.00 | 0.15 |
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foldgRNAs | 0 | 0 | 0 |
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getOfftargetScore | 0.11 | 0.00 | 0.11 |
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isPatternUnique | 0.01 | 0.00 | 0.02 |
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offTargetAnalysis | 40.21 | 0.69 | 40.92 |
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searchHits | 0 | 0 | 0 |
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searchHits2 | 2.53 | 0.12 | 2.65 |
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translatePattern | 0 | 0 | 0 |
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uniqueREs | 0.23 | 0.05 | 0.29 |
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writeHits | 0 | 0 | 0 |
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writeHits2 | 0.14 | 0.02 | 0.15 |
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CRISPRseek.Rcheck/examples_x64/CRISPRseek-Ex.timings:
name | user | system | elapsed
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CRISPRseek-package | 171.70 | 6.44 | 178.14 |
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annotateOffTargets | 3.86 | 0.03 | 3.89 |
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buildFeatureVectorForScoring | 0.08 | 0.00 | 0.08 |
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calculategRNAEfficiency | 0.01 | 0.00 | 0.01 |
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compare2Sequences | 2.24 | 0.02 | 2.25 |
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filterOffTarget | 3.64 | 0.09 | 3.74 |
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filtergRNA | 0.66 | 0.08 | 0.74 |
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findgRNAs | 0.17 | 0.00 | 0.17 |
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foldgRNAs | 0 | 0 | 0 |
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getOfftargetScore | 0.11 | 0.00 | 0.11 |
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isPatternUnique | 0.02 | 0.00 | 0.01 |
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offTargetAnalysis | 33.53 | 0.55 | 34.08 |
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searchHits | 0.01 | 0.00 | 0.02 |
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searchHits2 | 2.03 | 0.06 | 2.09 |
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translatePattern | 0 | 0 | 0 |
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uniqueREs | 0.36 | 0.00 | 0.36 |
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writeHits | 0 | 0 | 0 |
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writeHits2 | 0.14 | 0.03 | 0.17 |
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