Nirav V Malani
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/hiReadsProcessor |
| Branch: RELEASE_3_6 |
| Last Commit: 9486aab |
| Last Changed Date: 2017-10-30 12:40:25 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:12 -0400 (Thu, 12 Apr 2018).
| Package 656/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hiReadsProcessor 1.14.0 Nirav V Malani
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... | ||||||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| Package: hiReadsProcessor |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.14.0.tar.gz |
| StartedAt: 2018-04-12 05:02:59 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 05:07:14 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 255.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hiReadsProcessor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/hiReadsProcessor.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK * this is package ‘hiReadsProcessor’ version ‘1.14.0’ * 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.6-bioc/meat/hiReadsProcessor.Rcheck/00check.log’ for details.
hiReadsProcessor.Rcheck/00install.out
* installing *source* package ‘hiReadsProcessor’ ... ** R ** data ** inst ** preparing 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 | 0.278 | 0.009 | 0.291 | |
| addListNameToReads | 0.922 | 0.041 | 0.975 | |
| annotateSites | 0 | 0 | 0 | |
| blatSeqs | 0.001 | 0.000 | 0.000 | |
| chunkize | 0.050 | 0.001 | 0.051 | |
| clusterSites | 0.864 | 0.007 | 0.895 | |
| crossOverCheck | 0.432 | 0.003 | 0.449 | |
| dereplicateReads | 0.089 | 0.000 | 0.090 | |
| doRCtest | 0.208 | 0.054 | 0.319 | |
| extractFeature | 0.262 | 0.043 | 0.310 | |
| extractSeqs | 0.510 | 0.034 | 0.558 | |
| findAndTrimSeq | 1.565 | 0.097 | 1.702 | |
| findBarcodes | 0.445 | 0.001 | 0.456 | |
| findIntegrations | 0.000 | 0.000 | 0.001 | |
| findLTRs | 0.001 | 0.000 | 0.001 | |
| findLinkers | 0.000 | 0.000 | 0.001 | |
| findPrimers | 0.000 | 0.000 | 0.001 | |
| findVector | 0.001 | 0.001 | 0.004 | |
| getIntegrationSites | 1.039 | 0.008 | 1.063 | |
| getSectorsForSamples | 0.102 | 0.003 | 0.109 | |
| getSonicAbund | 0.792 | 0.059 | 0.876 | |
| isuSites | 2.639 | 0.034 | 2.724 | |
| otuSites | 2.627 | 0.008 | 2.686 | |
| pairUpAlignments | 0 | 0 | 0 | |
| pairwiseAlignSeqs | 1.911 | 0.407 | 2.440 | |
| primerIDAlignSeqs | 1.803 | 0.200 | 2.076 | |
| pslCols | 0.001 | 0.000 | 0.001 | |
| pslToRangedObject | 0.110 | 0.005 | 0.115 | |
| read.BAMasPSL | 0.001 | 0.001 | 0.001 | |
| read.SeqFolder | 0.105 | 0.001 | 0.108 | |
| read.blast8 | 0.001 | 0.000 | 0.000 | |
| read.psl | 0 | 0 | 0 | |
| read.sampleInfo | 0.346 | 0.013 | 0.362 | |
| read.seqsFromSector | 0 | 0 | 0 | |
| removeReadsWithNs | 0.017 | 0.000 | 0.017 | |
| replicateReads | 0.046 | 0.001 | 0.047 | |
| sampleSummary | 0.567 | 0.013 | 0.595 | |
| splitByBarcode | 0.051 | 0.001 | 0.052 | |
| splitSeqsToFiles | 0.190 | 0.003 | 0.198 | |
| startgfServer | 0.000 | 0.000 | 0.001 | |
| trimSeqs | 0.017 | 0.000 | 0.018 | |
| vpairwiseAlignSeqs | 1.340 | 0.332 | 1.762 | |
| write.listedDNAStringSet | 0 | 0 | 0 | |
| write.psl | 0.022 | 0.004 | 0.032 | |