| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:14 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CRISPRseek package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRseek.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 416/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRISPRseek 1.34.2 (landing page) Lihua Julie Zhu
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CRISPRseek |
| Version: 1.34.2 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CRISPRseek_1.34.2.tar.gz |
| StartedAt: 2022-04-12 06:59:37 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:07:38 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 481.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CRISPRseek_1.34.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.34.2’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 12.8Mb
sub-directories of 1Mb or more:
extdata 12.3Mb
* 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 ... OK
* 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 ‘exons’
annotateOffTargets: no visible global function definition for
‘seqlevels<-’
annotateOffTargets: no visible global function definition for ‘genes’
predictRelativeFreqIndels : <anonymous>: no visible global function
definition for ‘predIndelFreq’
Undefined global functions or variables:
exons genes predIndelFreq seqlevels<-
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:64-66: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:67-69: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:86-88: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:89-91: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:99-101: Dropping empty section \references
prepare_Rd: compare2Sequences.Rd:263-265: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:266-268: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:151-153: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:154-156: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:48-50: Dropping empty section \details
prepare_Rd: filtergRNAs.Rd:51-53: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:70-72: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:308-310: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:79-81: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:23-25: Dropping empty section \details
prepare_Rd: isPatternUnique.Rd:26-28: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:37-39: Dropping empty section \references
prepare_Rd: isPatternUnique.Rd:40-42: Dropping empty section \seealso
prepare_Rd: offTargetAnalysis.Rd:438-440: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \note
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:440-442: Dropping empty section \details
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:443-445: Dropping empty section \note
prepare_Rd: searchHits.Rd:99-101: Dropping empty section \details
prepare_Rd: searchHits.Rd:102-104: Dropping empty section \note
prepare_Rd: searchHits.Rd:130-132: Dropping empty section \references
prepare_Rd: searchHits2.Rd:116-118: Dropping empty section \details
prepare_Rd: searchHits2.Rd:119-121: Dropping empty section \note
prepare_Rd: searchHits2.Rd:152-154: Dropping empty section \references
prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details
prepare_Rd: translatePattern.Rd:25-27: Dropping empty section \note
prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \references
prepare_Rd: translatePattern.Rd:36-38: Dropping empty section \seealso
prepare_Rd: uniqueREs.Rd:46-48: Dropping empty section \details
prepare_Rd: uniqueREs.Rd:49-51: Dropping empty section \note
prepare_Rd: uniqueREs.Rd:61-63: Dropping empty section \references
prepare_Rd: uniqueREs.Rd:64-66: Dropping empty section \seealso
prepare_Rd: writeHits.Rd:89-91: Dropping empty section \details
prepare_Rd: writeHits.Rd:92-94: Dropping empty section \note
prepare_Rd: writeHits2.Rd:99-101: Dropping empty section \details
prepare_Rd: writeHits2.Rd:102-104: 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CRISPRseek-package 148.414 7.837 156.315
offTargetAnalysis 55.768 2.108 57.566
offTargetAnalysisWithoutBSgenome 33.177 0.200 33.374
compare2Sequences 6.686 0.133 6.842
* 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
‘/home/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘CRISPRseek’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CRISPRseek)
CRISPRseek.Rcheck/tests/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
0.182 0.026 0.194
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 148.414 | 7.837 | 156.315 | |
| annotateOffTargets | 2.907 | 0.076 | 2.984 | |
| buildFeatureVectorForScoring | 0.073 | 0.000 | 0.073 | |
| calculategRNAEfficiency | 0.017 | 0.008 | 0.042 | |
| compare2Sequences | 6.686 | 0.133 | 6.842 | |
| deepCpf1 | 0.000 | 0.000 | 0.001 | |
| filterOffTarget | 3.283 | 0.029 | 3.310 | |
| filtergRNAs | 0.493 | 0.000 | 0.493 | |
| findgRNAs | 0.240 | 0.001 | 0.241 | |
| getOfftargetScore | 0.076 | 0.000 | 0.076 | |
| isPatternUnique | 0.013 | 0.000 | 0.012 | |
| offTargetAnalysis | 55.768 | 2.108 | 57.566 | |
| offTargetAnalysisWithoutBSgenome | 33.177 | 0.200 | 33.374 | |
| predictRelativeFreqIndels | 0.021 | 0.000 | 0.021 | |
| searchHits | 0.18 | 0.00 | 0.18 | |
| searchHits2 | 3.177 | 0.296 | 3.473 | |
| translatePattern | 0.014 | 0.000 | 0.015 | |
| uniqueREs | 0.352 | 0.000 | 0.353 | |
| writeHits | 0.032 | 0.016 | 0.048 | |
| writeHits2 | 0.180 | 0.000 | 0.181 | |