Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 453/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprDesign 1.7.2 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.7.2 |
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings crisprDesign_1.7.2.tar.gz |
StartedAt: 2024-08-20 23:46:52 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:58:11 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 678.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprDesign.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings crisprDesign_1.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/crisprDesign.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'crisprDesign/DESCRIPTION' ... OK * this is package 'crisprDesign' version '1.7.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: 'crisprBwa', 'Rbwa' * 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 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 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 addSNPAnnotation 15.03 0.19 15.39 addEditedAlleles 14.14 0.36 14.51 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/crisprDesign.Rcheck/00check.log' for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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") Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 Failed with error: 'there is no package called 'crisprBwa'' [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 230.82 8.21 245.81
crisprDesign.Rcheck/crisprDesign-Ex.timings
name | user | system | elapsed | |
GuideSet-class | 0.26 | 0.00 | 0.27 | |
GuideSet2DataFrames | 2.68 | 0.14 | 3.05 | |
PairedGuideSet-class | 0.52 | 0.07 | 0.60 | |
TxDb2GRangesList | 0 | 0 | 0 | |
addCompositeScores | 1.12 | 0.04 | 1.17 | |
addDistanceToTss | 0.05 | 0.00 | 0.05 | |
addEditedAlleles | 14.14 | 0.36 | 14.51 | |
addExonTable | 0.02 | 0.00 | 0.02 | |
addGeneAnnotation | 1.93 | 0.17 | 3.83 | |
addIsoformAnnotation | 0.18 | 0.00 | 0.17 | |
addNtcs | 0.51 | 0.04 | 0.54 | |
addOffTargetScores | 0.24 | 0.00 | 0.27 | |
addOnTargetScores | 0 | 0 | 0 | |
addOpsBarcodes | 0.04 | 0.00 | 0.04 | |
addPamScores | 0.56 | 0.00 | 0.56 | |
addRepeats | 0.32 | 0.05 | 0.38 | |
addRestrictionEnzymes | 0.75 | 0.01 | 0.77 | |
addSNPAnnotation | 15.03 | 0.19 | 15.39 | |
addSequenceFeatures | 0.58 | 0.02 | 0.59 | |
addSpacerAlignments | 0 | 0 | 0 | |
addTssAnnotation | 0.23 | 0.00 | 0.23 | |
addTxTable | 0 | 0 | 0 | |
completeSpacers | 0.53 | 0.03 | 0.60 | |
convertToMinMaxGRanges | 0.05 | 0.01 | 0.06 | |
convertToProtospacerGRanges | 0.30 | 0.02 | 0.33 | |
designOpsLibrary | 0.14 | 0.00 | 0.14 | |
findSpacerPairs | 2.63 | 0.20 | 2.83 | |
findSpacers | 1.58 | 0.10 | 1.69 | |
getBarcodeDistanceMatrix | 1.62 | 0.07 | 1.70 | |
getConsensusIsoform | 0.06 | 0.02 | 0.08 | |
getMrnaSequences | 0.36 | 0.11 | 0.47 | |
getPreMrnaSequences | 0.33 | 0.08 | 0.41 | |
getTssObjectFromTxObject | 0.06 | 0.00 | 0.06 | |
getTxDb | 0 | 0 | 0 | |
getTxInfoDataFrame | 1.03 | 0.14 | 1.18 | |
preparePfamTable | 0 | 0 | 0 | |
queryTss | 0.03 | 0.00 | 0.03 | |
queryTxObject | 0.05 | 0.00 | 0.05 | |
rankSpacers | 2.16 | 0.05 | 2.20 | |
removeRepeats | 0.37 | 0.03 | 0.41 | |
updateOpsLibrary | 0.27 | 0.00 | 0.26 | |
validateOpsLibrary | 0.20 | 0.03 | 0.24 | |