| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:28 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the hiReadsProcessor package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiReadsProcessor.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 877/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hiReadsProcessor 1.30.0 (landing page) Nirav V Malani
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ... NOT SUPPORTED ... | ||||||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: hiReadsProcessor |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.30.0.tar.gz |
| StartedAt: 2022-04-12 07:47:50 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:51:38 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 227.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hiReadsProcessor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/hiReadsProcessor.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK * this is package ‘hiReadsProcessor’ version ‘1.30.0’ * 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 ‘hiReadsProcessor’ 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 ... NOTE chunkize: no visible global function definition for ‘breakInChunks’ chunkize: no visible global function definition for ‘detectCores’ clusterSites : <anonymous>: no visible binding for global variable ‘queryHits’ clusterSites: no visible binding for global variable ‘clusteredValue’ clusterSites: no visible binding for global variable ‘clusteredValue.freq’ crossOverCheck: no visible binding for global variable ‘queryHits’ decodeByBarcode: no visible global function definition for ‘metadata<-’ decodeByBarcode: no visible global function definition for ‘metadata’ extractSeqs : <anonymous>: no visible global function definition for ‘metadata’ extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘IRanges’ extractSeqs : <anonymous> : <anonymous>: no visible global function definition for ‘IRanges’ findBarcodes: no visible global function definition for ‘metadata<-’ findBarcodes: no visible global function definition for ‘metadata’ findIntegrations: no visible global function definition for ‘fasta.info’ findIntegrations : <anonymous>: no visible global function definition for ‘IRanges’ findVector : <anonymous>: no visible global function definition for ‘IRanges’ pairUpAlignments : <anonymous>: no visible binding for global variable ‘queryHits’ pairwiseAlignSeqs: no visible global function definition for ‘IRangesList’ pairwiseAlignSeqs: no visible global function definition for ‘IRanges’ primerIDAlignSeqs: no visible global function definition for ‘IRanges’ primerIDAlignSeqs: no visible global function definition for ‘IRangesList’ pslToRangedObject: no visible global function definition for ‘IRanges’ read.BAMasPSL: no visible global function definition for ‘ScanBamParam’ read.BAMasPSL: no visible global function definition for ‘scanBamFlag’ read.BAMasPSL: no visible global function definition for ‘DataFrame’ read.SeqFolder: no visible global function definition for ‘SimpleList’ read.psl: no visible global function definition for ‘mclapply’ read.psl : <anonymous>: no visible binding for global variable ‘matches’ read.psl : <anonymous>: no visible binding for global variable ‘misMatches’ read.psl : <anonymous>: no visible binding for global variable ‘qBaseInsert’ read.psl : <anonymous>: no visible binding for global variable ‘tBaseInsert’ read.psl: no visible binding for global variable ‘matches’ read.psl: no visible binding for global variable ‘misMatches’ read.psl: no visible binding for global variable ‘qBaseInsert’ read.psl: no visible binding for global variable ‘tBaseInsert’ read.sampleInfo: no visible global function definition for ‘SimpleList’ splitSeqsToFiles: no visible global function definition for ‘fasta.info’ vpairwiseAlignSeqs: no visible global function definition for ‘Rle’ vpairwiseAlignSeqs: no visible global function definition for ‘runLength’ vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’ vpairwiseAlignSeqs: no visible global function definition for ‘runValue’ Undefined global functions or variables: DataFrame IRanges IRangesList Rle ScanBamParam SimpleList breakInChunks clusteredValue clusteredValue.freq detectCores fasta.info matches mclapply metadata metadata<- misMatches qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 ‘/home/biocbuild/bbs-3.14-bioc/meat/hiReadsProcessor.Rcheck/00check.log’ for details.
hiReadsProcessor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL hiReadsProcessor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘hiReadsProcessor’ ... ** 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 (hiReadsProcessor)
hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings
| name | user | system | elapsed | |
| addFeature | 0.161 | 0.004 | 0.165 | |
| addListNameToReads | 0.878 | 0.012 | 0.890 | |
| annotateSites | 0 | 0 | 0 | |
| blatSeqs | 0 | 0 | 0 | |
| chunkize | 0.024 | 0.000 | 0.024 | |
| clusterSites | 0.241 | 0.000 | 0.241 | |
| crossOverCheck | 0.084 | 0.000 | 0.084 | |
| dereplicateReads | 0.04 | 0.00 | 0.04 | |
| doRCtest | 1.519 | 0.043 | 1.605 | |
| extractFeature | 0.153 | 0.094 | 0.124 | |
| extractSeqs | 0.333 | 0.020 | 0.353 | |
| findAndTrimSeq | 1.081 | 0.104 | 1.185 | |
| findBarcodes | 0.957 | 0.000 | 0.956 | |
| findIntegrations | 0 | 0 | 0 | |
| findLTRs | 0 | 0 | 0 | |
| findLinkers | 0 | 0 | 0 | |
| findPrimers | 0 | 0 | 0 | |
| findVector | 0.001 | 0.000 | 0.000 | |
| getIntegrationSites | 2.282 | 0.000 | 2.282 | |
| getSectorsForSamples | 0.079 | 0.004 | 0.083 | |
| getSonicAbund | 0.335 | 0.156 | 0.457 | |
| isuSites | 3.801 | 0.112 | 3.914 | |
| otuSites | 4.339 | 0.056 | 4.395 | |
| pairUpAlignments | 0 | 0 | 0 | |
| pairwiseAlignSeqs | 2.349 | 0.519 | 2.667 | |
| primerIDAlignSeqs | 3.841 | 0.252 | 4.057 | |
| pslCols | 0.001 | 0.000 | 0.000 | |
| pslToRangedObject | 0.548 | 0.008 | 0.556 | |
| read.BAMasPSL | 0 | 0 | 0 | |
| read.SeqFolder | 0.909 | 0.088 | 0.998 | |
| read.blast8 | 0.000 | 0.000 | 0.001 | |
| read.psl | 0 | 0 | 0 | |
| read.sampleInfo | 0.878 | 0.028 | 0.909 | |
| read.seqsFromSector | 0 | 0 | 0 | |
| removeReadsWithNs | 0.02 | 0.00 | 0.02 | |
| replicateReads | 0.048 | 0.000 | 0.048 | |
| sampleSummary | 0.891 | 0.032 | 0.923 | |
| splitByBarcode | 0.039 | 0.000 | 0.040 | |
| splitSeqsToFiles | 0.164 | 0.000 | 0.164 | |
| startgfServer | 0 | 0 | 0 | |
| trimSeqs | 0.022 | 0.000 | 0.022 | |
| vpairwiseAlignSeqs | 2.068 | 0.756 | 2.587 | |
| write.listedDNAStringSet | 0 | 0 | 0 | |
| write.psl | 0.023 | 0.000 | 0.024 | |