Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:42 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 |
To the developers/maintainers of the RSVSim package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/RSVSim.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 1665/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RSVSim 1.34.0 (landing page) Christoph Bartenhagen
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: RSVSim |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RSVSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RSVSim_1.34.0.tar.gz |
StartedAt: 2022-04-12 17:55:07 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 17:59:46 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 278.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RSVSim.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RSVSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RSVSim_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/RSVSim.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RSVSim/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RSVSim’ version ‘1.34.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RSVSim’ 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 ... NOTE 'library' or 'require' calls in package code: ‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Hsapiens.UCSC.hg19.masked’ ‘MASS’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .drawPos: no visible global function definition for ‘seqlevels’ .drawPos: no visible global function definition for ‘queryHits’ .getHG19: no visible binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’ .getHG19: no visible binding for global variable ‘Hsapiens’ .getHG19: no visible global function definition for ‘as’ .getSVSizes: no visible global function definition for ‘rbeta’ .loadFromBSGenome_TandemRepeats: no visible binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’ .loadFromBSGenome_TandemRepeats: no visible global function definition for ‘seqlevels<-’ .loadFromBSGenome_TandemRepeats: no visible global function definition for ‘as’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘browserSession’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘genome<-’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘ucscTableQuery’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘txtProgressBar’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘range<-’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘getTable’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘setTxtProgressBar’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘data’ .loadFromUCSC_SegDups: no visible global function definition for ‘browserSession’ .loadFromUCSC_SegDups: no visible global function definition for ‘genome<-’ .loadFromUCSC_SegDups: no visible global function definition for ‘getTable’ .loadFromUCSC_SegDups: no visible global function definition for ‘ucscTableQuery’ .readRepeatMaskerOutput: no visible global function definition for ‘read.table’ .readRepeatMaskerOutput: no visible global function definition for ‘data’ .simInsertionPositions: no visible global function definition for ‘txtProgressBar’ .simInsertionPositions: no visible global function definition for ‘seqlevels’ .simInsertionPositions: no visible global function definition for ‘setTxtProgressBar’ .simPositions: no visible global function definition for ‘txtProgressBar’ .simPositions: no visible global function definition for ‘setTxtProgressBar’ .simTranslocationPositions: no visible global function definition for ‘txtProgressBar’ .simTranslocationPositions: no visible global function definition for ‘seqlevels’ .simTranslocationPositions: no visible global function definition for ‘setTxtProgressBar’ .subtractIntervals: no visible global function definition for ‘seqlevels<-’ .testSVSim: no visible global function definition for ‘metadata’ compareSV,character-character: no visible global function definition for ‘read.table’ compareSV,character-data.frame: no visible global function definition for ‘read.table’ estimateSVSizes,numeric-numeric-ANY-ANY-missing: no visible global function definition for ‘fitdistr’ simulateSV,ANY: no visible global function definition for ‘data’ simulateSV,ANY: no visible global function definition for ‘txtProgressBar’ simulateSV,ANY: no visible global function definition for ‘setTxtProgressBar’ simulateSV,ANY: no visible global function definition for ‘write.table’ simulateSV,ANY: no visible global function definition for ‘metadata<-’ Undefined global functions or variables: BSgenome.Hsapiens.UCSC.hg19.masked Hsapiens as browserSession data fitdistr genome<- getTable metadata metadata<- queryHits range<- rbeta read.table seqlevels seqlevels<- setTxtProgressBar txtProgressBar ucscTableQuery write.table Consider adding importFrom("methods", "as") importFrom("stats", "rbeta") importFrom("utils", "data", "read.table", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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 simulateSV 14.773 0.078 14.864 compareSVs 6.887 0.156 7.051 * 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-3.14-bioc/meat/RSVSim.Rcheck/00check.log’ for details.
RSVSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RSVSim ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘RSVSim’ ... ** using staged installation ** R ** data ** 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 (RSVSim)
RSVSim.Rcheck/RSVSim-Ex.timings
name | user | system | elapsed | |
compareSVs | 6.887 | 0.156 | 7.051 | |
estimateSVSizes | 0.360 | 0.019 | 0.380 | |
segmentalDuplications | 0.263 | 0.008 | 0.310 | |
simulateSV | 14.773 | 0.078 | 14.864 | |
weightsMechanisms | 0.005 | 0.003 | 0.007 | |
weightsRepeats | 0.004 | 0.003 | 0.007 | |