Lihua Julie Zhu
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CRISPRseek |
| Branch: RELEASE_3_7 |
| Last Commit: eef2c5a |
| Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:52:16 -0400 (Wed, 17 Oct 2018).
| Package 321/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CRISPRseek 1.20.0 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: CRISPRseek |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CRISPRseek_1.20.0.tar.gz |
| StartedAt: 2018-10-16 20:43:32 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:52:22 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 530.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CRISPRseek_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CRISPRseek.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.20.0’
* package encoding: UTF-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 ... WARNING
Found the following significant warnings:
Note: possible error in 'fold(s = gRNA.backbone, ': unused arguments (s = gRNA.backbone, t = temperature)
Note: possible error in 'fold(paste(gRNAs[i], ': unused argument (t = temperature)
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/CRISPRseek.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CRISPRseek-package 212.996 9.644 224.752
offTargetAnalysis 54.204 0.901 55.582
annotateOffTargets 12.487 0.180 12.817
filterOffTarget 12.253 0.177 12.532
compare2Sequences 6.930 0.251 7.233
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘CRISPRseek’ ... ** R ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'fold(s = gRNA.backbone, ': unused arguments (s = gRNA.backbone, t = temperature) Note: possible error in 'fold(paste(gRNAs[i], ': unused argument (t = temperature) ** 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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
0.247 0.060 0.273
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 212.996 | 9.644 | 224.752 | |
| annotateOffTargets | 12.487 | 0.180 | 12.817 | |
| buildFeatureVectorForScoring | 0.097 | 0.001 | 0.099 | |
| calculategRNAEfficiency | 0.032 | 0.006 | 0.039 | |
| compare2Sequences | 6.930 | 0.251 | 7.233 | |
| filterOffTarget | 12.253 | 0.177 | 12.532 | |
| filtergRNA | 1.054 | 0.018 | 1.085 | |
| findgRNAs | 0.187 | 0.008 | 0.197 | |
| foldgRNAs | 0.001 | 0.000 | 0.001 | |
| getOfftargetScore | 0.120 | 0.001 | 0.122 | |
| isPatternUnique | 0.019 | 0.000 | 0.019 | |
| offTargetAnalysis | 54.204 | 0.901 | 55.582 | |
| searchHits | 0.010 | 0.001 | 0.010 | |
| searchHits2 | 3.141 | 0.283 | 3.457 | |
| translatePattern | 0.002 | 0.001 | 0.002 | |
| uniqueREs | 0.427 | 0.004 | 0.437 | |
| writeHits | 0.003 | 0.000 | 0.004 | |
| writeHits2 | 0.192 | 0.007 | 0.200 | |