Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-20 11:05:38 -0400 (Mon, 20 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4297 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4286 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4150 |
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 crisprDesign package: - Please 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 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 445/2189 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprDesign 1.1.24 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: crisprDesign |
Version: 1.1.24 |
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crisprDesign_1.1.24.tar.gz |
StartedAt: 2023-03-20 00:40:21 -0400 (Mon, 20 Mar 2023) |
EndedAt: 2023-03-20 00:49:39 -0400 (Mon, 20 Mar 2023) |
EllapsedTime: 557.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprDesign.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crisprDesign_1.1.24.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/crisprDesign.Rcheck' * using R Under development (unstable) (2023-03-15 r83984 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * 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 '1.1.24' * 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 ... 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 ... 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 11.36 0.20 11.56 addEditedAlleles 10.20 0.26 10.47 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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: 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc/meat/crisprDesign.Rcheck/00check.log' for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. > 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 1018 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (69) • long run time (8) • no del for guideSetExample (1) [ FAIL 0 | WARN 0 | SKIP 78 | PASS 1018 ] > > proc.time() user system elapsed 180.37 5.40 193.59
crisprDesign.Rcheck/crisprDesign-Ex.timings
name | user | system | elapsed | |
GuideSet-class | 0.11 | 0.03 | 0.14 | |
GuideSet2DataFrames | 1.01 | 0.07 | 1.11 | |
PairedGuideSet-class | 0.53 | 0.04 | 0.58 | |
TxDb2GRangesList | 0 | 0 | 0 | |
addCompositeScores | 2.03 | 0.03 | 2.06 | |
addDistanceToTss | 0.05 | 0.02 | 0.06 | |
addEditedAlleles | 10.20 | 0.26 | 10.47 | |
addExonTable | 0 | 0 | 0 | |
addGeneAnnotation | 1.64 | 0.08 | 2.84 | |
addIsoformAnnotation | 0.13 | 0.00 | 0.12 | |
addNtcs | 0.39 | 0.05 | 0.44 | |
addOffTargetScores | 0.25 | 0.00 | 0.25 | |
addOnTargetScores | 0 | 0 | 0 | |
addOpsBarcodes | 0.03 | 0.00 | 0.04 | |
addPamScores | 0.47 | 0.00 | 0.46 | |
addRepeats | 0.24 | 0.02 | 0.25 | |
addRestrictionEnzymes | 0.70 | 0.00 | 0.71 | |
addSNPAnnotation | 11.36 | 0.20 | 11.56 | |
addSequenceFeatures | 0.46 | 0.01 | 0.48 | |
addSpacerAlignments | 0 | 0 | 0 | |
addTssAnnotation | 0.18 | 0.00 | 0.17 | |
addTxTable | 0 | 0 | 0 | |
completeSpacers | 0.34 | 0.04 | 0.38 | |
convertToMinMaxGRanges | 0.05 | 0.00 | 0.04 | |
convertToProtospacerGRanges | 0.23 | 0.00 | 0.24 | |
designOpsLibrary | 0.10 | 0.01 | 0.11 | |
findSpacerPairs | 1.96 | 0.11 | 2.08 | |
findSpacers | 1.27 | 0.13 | 1.39 | |
getBarcodeDistanceMatrix | 1.41 | 0.03 | 1.43 | |
getConsensusIsoform | 0.07 | 0.00 | 0.08 | |
getMrnaSequences | 0.29 | 0.03 | 0.31 | |
getPreMrnaSequences | 0.28 | 0.01 | 0.30 | |
getTssObjectFromTxObject | 0.05 | 0.00 | 0.04 | |
getTxDb | 0 | 0 | 0 | |
getTxInfoDataFrame | 1.66 | 0.08 | 1.73 | |
preparePfamTable | 0 | 0 | 0 | |
queryTss | 0.03 | 0.00 | 0.03 | |
queryTxObject | 0.03 | 0.00 | 0.04 | |
rankSpacers | 1.78 | 0.05 | 1.82 | |
removeRepeats | 0.22 | 0.03 | 0.25 | |
updateOpsLibrary | 0.16 | 0.00 | 0.16 | |
validateOpsLibrary | 0.14 | 0.02 | 0.16 | |