Nirav V Malani
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/hiReadsProcessor |
| Branch: RELEASE_3_8 |
| Last Commit: c231665 |
| Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:45 -0400 (Tue, 16 Apr 2019).
| Package 727/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hiReadsProcessor 1.18.0 Nirav V Malani
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: hiReadsProcessor |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.18.0.tar.gz |
| StartedAt: 2019-04-16 00:39:18 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:44:09 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 290.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hiReadsProcessor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/hiReadsProcessor.Rcheck’ * using R version 3.5.3 (2019-03-11) * 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 ‘1.18.0’ * 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-3.8-bioc/meat/hiReadsProcessor.Rcheck/00check.log’ for details.
hiReadsProcessor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL hiReadsProcessor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘hiReadsProcessor’ ... ** 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 * DONE (hiReadsProcessor)
hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings
| name | user | system | elapsed | |
| addFeature | 0.284 | 0.016 | 0.299 | |
| addListNameToReads | 0.400 | 0.004 | 0.401 | |
| annotateSites | 0 | 0 | 0 | |
| blatSeqs | 0 | 0 | 0 | |
| chunkize | 0.048 | 0.000 | 0.047 | |
| clusterSites | 0.496 | 0.012 | 0.509 | |
| crossOverCheck | 0.228 | 0.004 | 0.231 | |
| dereplicateReads | 0.036 | 0.000 | 0.037 | |
| doRCtest | 0.124 | 0.188 | 0.438 | |
| extractFeature | 0.240 | 0.076 | 0.258 | |
| extractSeqs | 1.360 | 0.108 | 1.471 | |
| findAndTrimSeq | 1.704 | 0.016 | 1.723 | |
| findBarcodes | 0.712 | 0.000 | 0.715 | |
| findIntegrations | 0 | 0 | 0 | |
| findLTRs | 0 | 0 | 0 | |
| findLinkers | 0.000 | 0.000 | 0.001 | |
| findPrimers | 0 | 0 | 0 | |
| findVector | 0 | 0 | 0 | |
| getIntegrationSites | 1.764 | 0.000 | 1.767 | |
| getSectorsForSamples | 0.144 | 0.000 | 0.145 | |
| getSonicAbund | 0.384 | 0.024 | 0.433 | |
| isuSites | 3.140 | 0.016 | 3.218 | |
| otuSites | 3.744 | 0.000 | 3.747 | |
| pairUpAlignments | 0 | 0 | 0 | |
| pairwiseAlignSeqs | 2.356 | 0.568 | 2.942 | |
| primerIDAlignSeqs | 3.088 | 0.304 | 3.365 | |
| pslCols | 0.000 | 0.000 | 0.001 | |
| pslToRangedObject | 0.264 | 0.000 | 0.265 | |
| read.BAMasPSL | 0.000 | 0.000 | 0.001 | |
| read.SeqFolder | 1.116 | 0.084 | 1.236 | |
| read.blast8 | 0 | 0 | 0 | |
| read.psl | 0 | 0 | 0 | |
| read.sampleInfo | 1.192 | 0.000 | 1.228 | |
| read.seqsFromSector | 0 | 0 | 0 | |
| removeReadsWithNs | 0.020 | 0.000 | 0.023 | |
| replicateReads | 0.036 | 0.000 | 0.034 | |
| sampleSummary | 0.684 | 0.000 | 0.698 | |
| splitByBarcode | 0.032 | 0.000 | 0.034 | |
| splitSeqsToFiles | 0.224 | 0.004 | 0.232 | |
| startgfServer | 0 | 0 | 0 | |
| trimSeqs | 0.036 | 0.004 | 0.037 | |
| vpairwiseAlignSeqs | 1.852 | 0.544 | 2.379 | |
| write.listedDNAStringSet | 0 | 0 | 0 | |
| write.psl | 0.040 | 0.004 | 0.041 | |