Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 457/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprDesign 1.8.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the crisprDesign package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crisprDesign.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: crisprDesign |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings crisprDesign_1.8.0.tar.gz |
StartedAt: 2024-12-19 22:06:22 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 22:19:27 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 784.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprDesign.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings crisprDesign_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/crisprDesign.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘crisprDesign/DESCRIPTION’ ... OK * this is package ‘crisprDesign’ version ‘1.8.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘crisprDesign’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed addEditedAlleles 11.629 0.342 11.972 addSNPAnnotation 10.657 0.009 10.667 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/crisprDesign.Rcheck/00check.log’ for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘crisprDesign’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (crisprDesign)
crisprDesign.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > library(testthat) > library(crisprDesign) Loading required package: crisprBase > > test_check("crisprDesign") [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 7 # reads with at least one alignment: 6 (85.71%) # reads that failed to align: 1 (14.29%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 7 # reads with at least one alignment: 6 (85.71%) # reads that failed to align: 1 (14.29%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 6 # reads with at least one alignment: 6 (100.00%) # reads that failed to align: 0 (0.00%) Reported 6 alignments [ FAIL 0 | WARN 0 | SKIP 78 | PASS 1090 ] ══ Skipped tests (78) ══════════════════════════════════════════════════════════ • empty test (69): 'test-GuideSet-class.R:214:1', 'test-GuideSet-class.R:225:1', 'test-GuideSet-class.R:230:1', 'test-addGeneAnnotation.R:17:1', 'test-addGeneAnnotation.R:116:1', 'test-addGeneAnnotation.R:174:1', 'test-addNtcs.R:352:1', 'test-addNtcs.R:398:1', 'test-addOffTargetScores.R:21:1', 'test-addOnTargetScores.R:20:1', 'test-addOnTargetScores.R:67:1', 'test-addOnTargetScores.R:87:1', 'test-addOnTargetScores.R:101:1', 'test-addOnTargetScores.R:145:1', 'test-addOnTargetScores.R:157:1', 'test-addOnTargetScores.R:190:1', 'test-addPamScores.R:30:1', 'test-addRepeats.R:78:1', 'test-addRepeats.R:84:1', 'test-addRepeats.R:89:1', 'test-addRestrictionEnzymes.R:89:1', 'test-addRestrictionEnzymes.R:180:1', 'test-addRestrictionEnzymes.R:185:1', 'test-addRestrictionEnzymes.R:191:1', 'test-addRestrictionEnzymes.R:198:1', 'test-addSpacerAlignments.R:63:1', 'test-addSpacerAlignments.R:147:1', 'test-addSpacerAlignments.R:199:1', 'test-addSpacerAlignments.R:266:1', 'test-addSpacerAlignments.R:349:1', 'test-addSpacerAlignments.R:469:1', 'test-addSpacerAlignments.R:509:1', 'test-addSpacerAlignments.R:546:1', 'test-addSpacerAlignments.R:572:1', 'test-addSpacerAlignments.R:603:1', 'test-addSpacerAlignments.R:627:1', 'test-addSpacerAlignments.R:650:1', 'test-addSpacerAlignments.R:669:1', 'test-addSpacerAlignments.R:720:1', 'test-completeSpacers.R:27:1', 'test-completeSpacers.R:32:1', 'test-completeSpacers.R:37:1', 'test-completeSpacers.R:42:1', 'test-completeSpacers.R:47:1', 'test-completeSpacers.R:52:1', 'test-completeSpacers.R:60:1', 'test-completeSpacers.R:73:1', 'test-completeSpacers.R:78:1', 'test-completeSpacers.R:83:1', 'test-completeSpacers.R:88:1', 'test-completeSpacers.R:93:1', 'test-completeSpacers.R:113:1', 'test-completeSpacers.R:118:1', 'test-completeSpacers.R:123:1', 'test-completeSpacers.R:128:1', 'test-completeSpacers.R:133:1', 'test-completeSpacers.R:139:1', 'test-completeSpacers.R:144:1', 'test-completeSpacers.R:167:1', 'test-completeSpacers.R:172:1', 'test-completeSpacers.R:177:1', 'test-completeSpacers.R:182:1', 'test-completeSpacers.R:187:1', 'test-completeSpacers.R:193:1', 'test-completeSpacers.R:198:1', 'test-completeSpacers.R:203:1', 'test-completeSpacers.R:208:1', 'test-completeSpacers.R:213:1', 'test-queryTxObject.R:152:1' • long run time (8): 'test-TxDb2GRangesList.R:19:5', 'test-TxDb2GRangesList.R:36:5', 'test-TxDb2GRangesList.R:56:5', 'test-TxDb2GRangesList.R:77:5', 'test-addSNPAnnotation.R:33:5', 'test-addSNPAnnotation.R:70:5', 'test-addSNPAnnotation.R:79:5', 'test-addSNPAnnotation.R:124:5' • no del for guideSetExample (1): 'test-addSNPAnnotation.R:148:5' [ FAIL 0 | WARN 0 | SKIP 78 | PASS 1090 ] > > proc.time() user system elapsed 171.513 3.949 175.902
crisprDesign.Rcheck/crisprDesign-Ex.timings
name | user | system | elapsed | |
GuideSet-class | 0.141 | 0.002 | 0.142 | |
GuideSet2DataFrames | 2.648 | 0.244 | 2.892 | |
PairedGuideSet-class | 0.342 | 0.019 | 0.361 | |
TxDb2GRangesList | 0 | 0 | 0 | |
addCompositeScores | 0.960 | 0.036 | 0.996 | |
addDistanceToTss | 0.034 | 0.003 | 0.037 | |
addEditedAlleles | 11.629 | 0.342 | 11.972 | |
addExonTable | 0.001 | 0.000 | 0.000 | |
addGeneAnnotation | 1.302 | 0.015 | 1.316 | |
addIsoformAnnotation | 0.098 | 0.000 | 0.097 | |
addNtcs | 0.317 | 0.010 | 0.326 | |
addOffTargetScores | 0.238 | 0.001 | 0.238 | |
addOnTargetScores | 0 | 0 | 0 | |
addOpsBarcodes | 0.029 | 0.000 | 0.029 | |
addPamScores | 0.368 | 0.000 | 0.368 | |
addRepeats | 0.199 | 0.003 | 0.201 | |
addRestrictionEnzymes | 0.660 | 0.015 | 0.675 | |
addSNPAnnotation | 10.657 | 0.009 | 10.667 | |
addSequenceFeatures | 0.434 | 0.000 | 0.434 | |
addSpacerAlignments | 0.000 | 0.001 | 0.000 | |
addTssAnnotation | 0.171 | 0.001 | 0.172 | |
addTxTable | 0.001 | 0.000 | 0.001 | |
completeSpacers | 0.318 | 0.011 | 0.329 | |
convertToMinMaxGRanges | 0.053 | 0.000 | 0.053 | |
convertToProtospacerGRanges | 0.176 | 0.004 | 0.180 | |
designOpsLibrary | 0.097 | 0.001 | 0.098 | |
findSpacerPairs | 1.802 | 0.013 | 1.815 | |
findSpacers | 1.323 | 0.005 | 1.328 | |
getBarcodeDistanceMatrix | 1.592 | 0.057 | 1.649 | |
getConsensusIsoform | 0.072 | 0.000 | 0.072 | |
getMrnaSequences | 0.250 | 0.003 | 0.253 | |
getPreMrnaSequences | 0.204 | 0.004 | 0.208 | |
getTssObjectFromTxObject | 0.053 | 0.000 | 0.053 | |
getTxDb | 0 | 0 | 0 | |
getTxInfoDataFrame | 0.591 | 0.021 | 0.612 | |
preparePfamTable | 0.002 | 0.000 | 0.002 | |
queryTss | 0.022 | 0.000 | 0.022 | |
queryTxObject | 0.026 | 0.000 | 0.026 | |
rankSpacers | 1.637 | 0.003 | 1.641 | |
removeRepeats | 0.205 | 0.002 | 0.207 | |
updateOpsLibrary | 0.199 | 0.000 | 0.199 | |
validateOpsLibrary | 0.163 | 0.000 | 0.164 | |