Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 450/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprDesign 1.9.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.9.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings crisprDesign_1.9.0.tar.gz |
StartedAt: 2024-12-22 21:08:00 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 21:17:37 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 576.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprDesign.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings crisprDesign_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/crisprDesign.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘1.9.0’ * 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 ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GuideSet-class.Rd: CrisprNuclease-class, BSgenome-class, DNAStringSet-class, Seqinfo-class PairedGuideSet-class.Rd: DNAStringSet-class TxDb2GRangesList.Rd: TxDb-class, GRangesList-class addCrispraiScores.Rd: GRanges-class addEditedAlleles.Rd: BaseEditor-class addExonTable.Rd: TxDb-class, GRangesList-class addGeneAnnotation.Rd: TxDb-class, GRangesList-class addNtcs.Rd: Seqinfo-class addPamScores.Rd: CrisprNuclease-class addPfamDomains.Rd: DataFrame-class addRepeats.Rd: GRanges-class addSNPAnnotation.Rd: VCF-class addSpacerAlignments.Rd: TxDb-class, GRangesList-class, GRanges-class, BSgenome-class, CrisprNuclease-class addTssAnnotation.Rd: GRanges-class addTxTable.Rd: TxDb-class, GRangesList-class completeSpacers.Rd: CrisprNuclease-class, BSgenome-class designCompleteAnnotation.Rd: BSgenome-class, GRanges-class, VCF-class, CrisprNuclease-class, TxDb-class, GRangesList-class, DataFrame-class findSpacerPairs.Rd: GRanges-class, DNAStringSet-class, DNAString-class, CrisprNuclease-class, BSgenome-class findSpacers.Rd: GRanges-class, DNAStringSet-class, DNAString-class, CrisprNuclease-class, BSgenome-class getConsensusIsoform.Rd: TxDb-class, GRangesList-class getMrnaSequences.Rd: TxDb-class, GRangesList-class, BSgenome-class, DNAStringSet-class getPreMrnaSequences.Rd: TxDb-class, GRangesList-class, BSgenome-class, DNAStringSet-class getTssObjectFromTxObject.Rd: TxDb-class, GRangesList-class getTxDb.Rd: TxDb-class, makeTxDbFromGFF, makeTxDbFromEnsembl getTxInfoDataFrame.Rd: TxDb-class, GRangesList-class, BSgenome-class, GRanges-class grListExample.Rd: TxDb-class, GRangesList-class grRepeatsExample.Rd: GRanges-class preparePfamTable.Rd: TxDb-class, GRangesList-class, DataFrame-class queryTss.Rd: GRanges-class queryTxObject.Rd: TxDb-class, GRangesList-class, GRanges-class removeRepeats.Rd: GRanges-class tssObjectExample.Rd: GRanges-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 11.308 0.373 11.681 addSNPAnnotation 10.834 0.038 10.873 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/crisprDesign.Rcheck/00check.log’ for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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 166.066 5.038 174.513
crisprDesign.Rcheck/crisprDesign-Ex.timings
name | user | system | elapsed | |
GuideSet-class | 0.117 | 0.004 | 0.122 | |
GuideSet2DataFrames | 2.139 | 0.142 | 2.281 | |
PairedGuideSet-class | 0.373 | 0.037 | 0.409 | |
TxDb2GRangesList | 0 | 0 | 0 | |
addCompositeScores | 0.973 | 0.007 | 0.984 | |
addDistanceToTss | 0.033 | 0.006 | 0.038 | |
addEditedAlleles | 11.308 | 0.373 | 11.681 | |
addExonTable | 0.000 | 0.000 | 0.001 | |
addGeneAnnotation | 1.283 | 0.027 | 1.310 | |
addIsoformAnnotation | 0.096 | 0.001 | 0.097 | |
addNtcs | 0.283 | 0.008 | 0.290 | |
addOffTargetScores | 0.220 | 0.007 | 0.227 | |
addOnTargetScores | 0 | 0 | 0 | |
addOpsBarcodes | 0.030 | 0.001 | 0.030 | |
addPamScores | 0.395 | 0.001 | 0.395 | |
addRepeats | 0.218 | 0.004 | 0.222 | |
addRestrictionEnzymes | 0.599 | 0.009 | 0.608 | |
addSNPAnnotation | 10.834 | 0.038 | 10.873 | |
addSequenceFeatures | 0.396 | 0.002 | 0.398 | |
addSpacerAlignments | 0.001 | 0.000 | 0.000 | |
addTssAnnotation | 0.151 | 0.003 | 0.154 | |
addTxTable | 0 | 0 | 0 | |
completeSpacers | 0.321 | 0.030 | 0.351 | |
convertToMinMaxGRanges | 0.056 | 0.000 | 0.056 | |
convertToProtospacerGRanges | 0.222 | 0.009 | 0.231 | |
designOpsLibrary | 0.106 | 0.002 | 0.108 | |
findSpacerPairs | 1.852 | 0.055 | 1.907 | |
findSpacers | 1.240 | 0.053 | 1.293 | |
getBarcodeDistanceMatrix | 1.826 | 0.057 | 1.885 | |
getConsensusIsoform | 0.065 | 0.002 | 0.067 | |
getMrnaSequences | 0.245 | 0.020 | 0.266 | |
getPreMrnaSequences | 0.216 | 0.018 | 0.235 | |
getTssObjectFromTxObject | 0.052 | 0.001 | 0.053 | |
getTxDb | 0 | 0 | 0 | |
getTxInfoDataFrame | 1.499 | 0.207 | 1.707 | |
preparePfamTable | 0.002 | 0.000 | 0.002 | |
queryTss | 0.020 | 0.001 | 0.021 | |
queryTxObject | 0.024 | 0.002 | 0.026 | |
rankSpacers | 1.482 | 0.014 | 1.496 | |
removeRepeats | 0.213 | 0.002 | 0.215 | |
updateOpsLibrary | 0.163 | 0.001 | 0.164 | |
validateOpsLibrary | 0.155 | 0.002 | 0.157 | |