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 12:06 -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 923/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GUIDEseq 1.36.0 (landing page) Lihua Julie Zhu
| 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 GUIDEseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GUIDEseq.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: GUIDEseq |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GUIDEseq_1.36.0.tar.gz |
StartedAt: 2024-12-20 04:25:26 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:42:21 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1015.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GUIDEseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GUIDEseq_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GUIDEseq.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GUIDEseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GUIDEseq’ version ‘1.36.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GUIDEseq’ can be installed ... OK * checking installed package size ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: extdata 12.0Mb * 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 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 ... NOTE .maskSubSeq: no visible global function definition for '.getMatchedInd' .nucleotideSubstitutionMatrix: no visible binding for global variable 'IUPAC_CODE_MAP' .nucleotideSubstitutionMatrix: no visible binding for global variable 'DNA_BASES' GUIDEseqAnalysis: no visible binding for global variable 'offTarget' GUIDEseqAnalysis: no visible binding for global variable 'peak_score' GUIDEseqAnalysis: no visible binding for global variable 'predicted_cleavage_score' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.name' GUIDEseqAnalysis: no visible binding for global variable 'gRNAPlusPAM' GUIDEseqAnalysis: no visible binding for global variable 'offTarget_sequence' GUIDEseqAnalysis: no visible binding for global variable 'guideAlignment2OffTarget' GUIDEseqAnalysis: no visible binding for global variable 'offTargetStrand' GUIDEseqAnalysis: no visible binding for global variable 'mismatch.distance2PAM' GUIDEseqAnalysis: no visible binding for global variable 'n.guide.mismatch' GUIDEseqAnalysis: no visible binding for global variable 'offTarget_Start' GUIDEseqAnalysis: no visible binding for global variable 'offTarget_End' GUIDEseqAnalysis: no visible binding for global variable 'chromosome' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.insertion' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.deletion' GUIDEseqAnalysis: no visible binding for global variable 'pos.insertion' GUIDEseqAnalysis: no visible binding for global variable 'pos.deletion' GUIDEseqAnalysis: no visible binding for global variable 'n.insertion' GUIDEseqAnalysis: no visible binding for global variable 'n.deletion' GUIDEseqAnalysis: no visible binding for global variable 'n.RNA.bulge' GUIDEseqAnalysis: no visible binding for global variable 'n.DNA.bulge' GUIDEseqAnalysis: no visible binding for global variable 'feature' GUIDEseqAnalysis: no visible binding for global variable 'n.distinct.UMIs' annotateOffTargets: no visible binding for global variable 'offTarget_Start' getAlnWithBulge : <anonymous>: no visible binding for global variable 'pa.f1' getAlnWithBulge : <anonymous>: no visible binding for global variable 'pa.r2' getPeaks: no visible binding for global variable 'adjusted.p.value' getPeaks: no visible binding for global variable 'SNratio' getUniqueCleavageEvents: no visible binding for global variable 'width.first' getUniqueCleavageEvents: no visible binding for global variable 'width.last' getUniqueCleavageEvents: no visible binding for global variable 'qwidth.last' getUniqueCleavageEvents: no visible binding for global variable 'strand.last' getUniqueCleavageEvents: no visible binding for global variable 'qwidth.first' getUniqueCleavageEvents: no visible binding for global variable 'strand.first' getUniqueCleavageEvents: no visible binding for global variable 'readName' getUniqueCleavageEvents: no visible binding for global variable 'seqnames.last' getUniqueCleavageEvents: no visible binding for global variable 'seqnames.first' getUniqueCleavageEvents: no visible binding for global variable 'start.last' getUniqueCleavageEvents: no visible binding for global variable 'end.first' getUniqueCleavageEvents: no visible binding for global variable 'UMI' getUniqueCleavageEvents: no visible binding for global variable 'start.first' getUniqueCleavageEvents: no visible binding for global variable 'end.last' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'thePeak' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'gRNAPlusPAM' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'offTarget' plotAlignedOfftargets: no visible binding for global variable 'total.mismatch.bulge' plotAlignedOfftargets: no visible binding for global variable 'RIR' plotAlignedOfftargets: no visible binding for global variable 'guideAlignment2OffTarget' plotAlignedOfftargets: no visible binding for global variable 'DNA.bulge' plotAlignedOfftargets: no visible binding for global variable 'y' plotAlignedOfftargets: no visible binding for global variable 'h' plotAlignedOfftargets: no visible binding for global variable 'IR' plotHeatmapOfftargets: no visible binding for global variable 'total.mismatch.bulge' plotHeatmapOfftargets: no visible binding for global variable 'Offtargets' plotHeatmapOfftargets: no visible binding for global variable 'IR' plotHeatmapOfftargets: no visible binding for global variable 'Ontarget' plotHeatmapOfftargets: no visible binding for global variable 'IR.max' plotHeatmapOfftargets: no visible binding for global variable 'Samples' plotHeatmapOfftargets: no visible global function definition for 'guides' plotHeatmapOfftargets: no visible global function definition for 'guide_legend' plotHeatmapOfftargets: no visible global function definition for 'unit' plotTracks: no visible binding for global variable 'total.mismatch.bulge' plotTracks: no visible binding for global variable 'n.PAM.mismatch' plotTracks: no visible binding for global variable 'offTargetStrand' plotTracks: no visible binding for global variable 'offTarget_Start' plotTracks: no visible binding for global variable 'offTarget_End' plotTracks: no visible binding for global variable 'n.distinct.UMIs' plotTracks: no visible binding for global variable 'predicted_cleavage_score' plotTracks: no visible global function definition for 'geom_smooth' plotTracks: no visible binding for global variable 'chromosome' plotTracks: no visible binding for global variable 'chr.max' plotTracks: no visible binding for global variable 'chr.offset' plotTracks: no visible binding for global variable '.' plotTracks: no visible binding for global variable 'cum.cleavage.position' Undefined global functions or variables: . .getMatchedInd DNA.bulge DNA_BASES IR IR.max IUPAC_CODE_MAP Offtargets Ontarget RIR SNratio Samples UMI adjusted.p.value chr.max chr.offset chromosome cum.cleavage.position end.first end.last feature gRNA.deletion gRNA.insertion gRNA.name gRNAPlusPAM geom_smooth guideAlignment2OffTarget guide_legend guides h mismatch.distance2PAM n.DNA.bulge n.PAM.mismatch n.RNA.bulge n.deletion n.distinct.UMIs n.guide.mismatch n.insertion offTarget offTargetStrand offTarget_End offTarget_Start offTarget_sequence pa.f1 pa.r2 peak_score pos.deletion pos.insertion predicted_cleavage_score qwidth.first qwidth.last readName seqnames.first seqnames.last start.first start.last strand.first strand.last thePeak total.mismatch.bulge unit width.first width.last y * checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:35-37: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:63-65: Dropping empty section \references prepare_Rd: createBarcodeFasta.Rd:56-58: Dropping empty section \references prepare_Rd: getUsedBarcodes.Rd:53-55: Dropping empty section \references checkRd: (-1) mergePlusMinusPeaks.Rd:72: Escaped LaTeX specials: \_ * 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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PEtagAnalysis 24.636 1.413 26.787 annotateOffTargets 12.736 0.403 14.443 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/GUIDEseq.Rcheck/00check.log’ for details.
GUIDEseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GUIDEseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GUIDEseq’ ... ** using staged installation ** R ** data ** 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 (GUIDEseq)
GUIDEseq.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-apple-darwin20 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(GUIDEseq) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb > library(org.Hs.eg.db) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > > test_check("GUIDEseq") Loading required package: GenomicFeatures Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat GUIDEseqAnalysis without bulge. Remove duplicate reads ... Peak calling ... computing coverage for plus strand ... computing coverage for minus strand ... call peaks ... finding local max for chromosome: chr13 combine plus and minus peaks ... keep peaks not in merged.gr but present in both peaks1 and peaks2 Find unmerged peaks with very high reads one-library protocol offtarget analysis ... search for gRNAs for input file1... [1] "Scoring ..." >>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ... >>> DONE searching >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ... >>> DONE searching >>> Finding all hits in sequence chr13+:30964712:30964730 ... >>> DONE searching >>> Finding all hits in sequence chr13+:67161908:67161923 ... >>> DONE searching >>> Finding all hits in sequence chr13-:29087136:29087137 ... >>> DONE searching >>> Finding all hits in sequence chr13-:115084360:115084375 ... >>> DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" Extract PAM sequence and n.PAM.mismatch. Done with offtarget search! Add gene and exon information to offTargets .... Order offtargets. Add sequence depth information. Get the number of unique UMIs for each offtarget. Save offtargets. Please check output file in directory GUIDEseqTestResults Remove duplicate reads ... offtarget analysis ... Done with offtarget search! Add gene and exon information to offTargets .... Order offtargets. Add sequence depth information. Get the number of unique UMIs for each offtarget. Save offtargets. Please check output file in directory GUIDEseqTestResults GUIDEseqAnalysis with offtargets containing no bulge and with bulge. Remove duplicate reads ... Peak calling ... computing coverage for plus strand ... computing coverage for minus strand ... call peaks ... finding local max for chromosome: chr13 combine plus and minus peaks ... keep peaks not in merged.gr but present in both peaks1 and peaks2 Find unmerged peaks with very high reads one-library protocol offtarget analysis ... search for gRNAs for input file1... [1] "Scoring ..." >>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ... >>> DONE searching >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ... >>> DONE searching >>> Finding all hits in sequence chr13+:30964712:30964730 ... >>> DONE searching >>> Finding all hits in sequence chr13+:67161908:67161923 ... >>> DONE searching >>> Finding all hits in sequence chr13-:29087136:29087137 ... >>> DONE searching >>> Finding all hits in sequence chr13-:115084360:115084375 ... >>> DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" Extract PAM sequence and n.PAM.mismatch. Finding offtargets with bulges ...Done with offtarget search! Add gene and exon information to offTargets .... Order offtargets. Add sequence depth information. Get the number of unique UMIs for each offtarget. Save offtargets. Please check output file in directory GUIDEseqTestResults2 Remove duplicate reads ... offtarget analysis ... Finding offtargets with bulges ...Done with offtarget search! Add gene and exon information to offTargets .... Order offtargets. Add sequence depth information. Get the number of unique UMIs for each offtarget. Save offtargets. Please check output file in directory GUIDEseqTestResults2 GUIDEseqAnalysis with bulge containing offtargets where no offtargets contain no bulge. Remove duplicate reads ... Peak calling ... computing coverage for plus strand ... computing coverage for minus strand ... call peaks ... finding local max for chromosome: chr13 combine plus and minus peaks ... keep peaks not in merged.gr but present in both peaks1 and peaks2 Find unmerged peaks with very high reads one-library protocol offtarget analysis ... search for gRNAs for input file1... [1] "Scoring ..." >>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ... >>> DONE searching >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ... >>> DONE searching >>> Finding all hits in sequence chr13+:30964712:30964730 ... >>> DONE searching >>> Finding all hits in sequence chr13+:66687218:66687225 ... >>> DONE searching >>> Finding all hits in sequence chr13+:67161908:67161923 ... >>> DONE searching >>> Finding all hits in sequence chr13+:98226906:98226924 ... >>> DONE searching >>> Finding all hits in sequence chr13-:29087136:29087137 ... >>> DONE searching >>> Finding all hits in sequence chr13-:97395652:97395666 ... >>> DONE searching >>> Finding all hits in sequence chr13-:115084360:115084375 ... >>> DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 Remove duplicate reads ... Peak calling ... computing coverage for plus strand ... computing coverage for minus strand ... call peaks ... finding local max for chromosome: chr13 combine plus and minus peaks ... keep peaks not in merged.gr but present in both peaks1 and peaks2 Find unmerged peaks with very high reads one-library protocol offtarget analysis ... search for gRNAs for input file1... [1] "Scoring ..." >>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629399:27629417 ... >>> DONE searching >>> Finding all hits in sequence chr13+:39262920:39262939:chr13-:39262918:39262918 ... >>> DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" Extract PAM sequence and n.PAM.mismatch. Done with offtarget search! Add gene and exon information to offTargets .... Order offtargets. Add sequence depth information. Get the number of unique UMIs for each offtarget. Save offtargets. Please check output file in directory PEtagTestResults search for gRNAs for input file1... [1] "Scoring ..." >>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ... >>> DONE searching >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ... >>> DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" bulge on gRNA and offtarget on the minus strand worksStart testing offtarget on the minus strand ...test sequence not long enough for allowing large stretch of bulge[ FAIL 0 | WARN 6 | SKIP 0 | PASS 259 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 259 ] > > proc.time() user system elapsed 239.054 6.521 264.514
GUIDEseq.Rcheck/GUIDEseq-Ex.timings
name | user | system | elapsed | |
GUIDEseq-package | 0.002 | 0.001 | 0.003 | |
GUIDEseqAnalysis | 0.002 | 0.001 | 0.002 | |
PEtagAnalysis | 24.636 | 1.413 | 26.787 | |
annotateOffTargets | 12.736 | 0.403 | 14.443 | |
buildFeatureVectorForScoringBulge | 0.001 | 0.002 | 0.003 | |
combineOfftargets | 0.177 | 0.047 | 1.509 | |
createBarcodeFasta | 0.047 | 0.003 | 0.053 | |
getPeaks | 0.000 | 0.001 | 0.001 | |
getUniqueCleavageEvents | 0.002 | 0.001 | 0.002 | |
getUsedBarcodes | 0.082 | 0.005 | 0.095 | |
mergePlusMinusPeaks | 0.001 | 0.000 | 0.002 | |
offTargetAnalysisOfPeakRegions | 0.002 | 0.001 | 0.002 | |
offTargetAnalysisWithBulge | 0.001 | 0.001 | 0.003 | |
peaks.gr | 0.054 | 0.017 | 0.073 | |
plotAlignedOfftargets | 1.807 | 0.035 | 2.627 | |
plotHeatmapOfftargets | 0.010 | 0.003 | 0.014 | |
plotTracks | 0.025 | 0.003 | 0.036 | |
uniqueCleavageEvents | 0.093 | 0.014 | 0.114 | |