Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the goseq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/goseq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 790/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
goseq 1.44.0 (landing page) Matthew Young
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: goseq |
Version: 1.44.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:goseq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings goseq_1.44.0.tar.gz |
StartedAt: 2021-10-14 10:03:42 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:07:56 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 254.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: goseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:goseq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings goseq_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/goseq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘goseq/DESCRIPTION’ ... OK * this is package ‘goseq’ version ‘1.44.0’ * 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 ‘goseq’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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' call to ‘rtracklayer’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getlength: no visible global function definition for ‘installed.packages’ getlength: no visible global function definition for ‘tail’ getlength: no visible global function definition for ‘transcriptLengths’ getlength: no visible global function definition for ‘browserSession’ getlength: no visible global function definition for ‘genome<-’ getlength: no visible global function definition for ‘ucscTableQuery’ getlength: no visible global function definition for ‘getTable’ makespline: no visible global function definition for ‘show’ supportedOrganisms: no visible global function definition for ‘ucscGenomes’ Undefined global functions or variables: browserSession genome<- getTable installed.packages show tail transcriptLengths ucscGenomes ucscTableQuery Consider adding importFrom("methods", "show") importFrom("utils", "installed.packages", "tail") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed goseq 31.840 1.063 37.433 getgo 10.504 0.739 11.244 nullp 5.084 0.315 5.404 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/goseq.Rcheck/00check.log’ for details.
goseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL goseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘goseq’ ... ** 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 (goseq)
goseq.Rcheck/goseq-Ex.timings
name | user | system | elapsed | |
genes | 0.015 | 0.003 | 0.018 | |
getgo | 10.504 | 0.739 | 11.244 | |
getlength | 4.120 | 0.480 | 4.604 | |
goseq | 31.840 | 1.063 | 37.433 | |
makespline | 0.049 | 0.000 | 0.050 | |
nullp | 5.084 | 0.315 | 5.404 | |
plotPWF | 4.645 | 0.248 | 4.896 | |
supportedOrganisms | 0.409 | 0.020 | 3.665 | |