Lihua Julie Zhu
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CRISPRseek |
| Branch: RELEASE_3_6 |
| Last Commit: f83f8b0 |
| Last Changed Date: 2017-10-30 12:40:10 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:37:50 -0400 (Thu, 12 Apr 2018).
| Package 308/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CRISPRseek 1.18.0 Lihua Julie Zhu
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CRISPRseek |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CRISPRseek_1.18.0.tar.gz |
| StartedAt: 2018-04-12 02:19:57 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:26:46 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 409.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CRISPRseek_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CRISPRseek.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 151.088 7.894 162.032
offTargetAnalysis 32.596 0.524 33.747
compare2Sequences 5.785 0.089 6.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/Users/biocbuild/bbs-3.6-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/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #BiocGenerics:::testPackage("CRISPRseek")
>
> proc.time()
user system elapsed
0.231 0.042 0.260
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 151.088 | 7.894 | 162.032 | |
| annotateOffTargets | 3.950 | 0.139 | 4.193 | |
| buildFeatureVectorForScoring | 0.087 | 0.001 | 0.089 | |
| calculategRNAEfficiency | 0.026 | 0.003 | 0.029 | |
| compare2Sequences | 5.785 | 0.089 | 6.018 | |
| filterOffTarget | 4.369 | 0.169 | 4.627 | |
| filtergRNA | 0.752 | 0.002 | 0.765 | |
| findgRNAs | 0.199 | 0.007 | 0.211 | |
| foldgRNAs | 0.000 | 0.000 | 0.002 | |
| getOfftargetScore | 0.098 | 0.002 | 0.100 | |
| isPatternUnique | 0.017 | 0.000 | 0.019 | |
| offTargetAnalysis | 32.596 | 0.524 | 33.747 | |
| searchHits | 0.005 | 0.001 | 0.006 | |
| searchHits2 | 2.393 | 0.165 | 2.602 | |
| translatePattern | 0.001 | 0.001 | 0.001 | |
| uniqueREs | 0.393 | 0.005 | 0.406 | |
| writeHits | 0.002 | 0.000 | 0.002 | |
| writeHits2 | 0.193 | 0.032 | 0.231 | |