Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:06 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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Package 829/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
goseq 1.51.0 (landing page) Matthew Young
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: goseq |
Version: 1.51.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:goseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings goseq_1.51.0.tar.gz |
StartedAt: 2023-02-07 03:28:43 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 03:36:33 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 469.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: goseq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:goseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings goseq_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/goseq.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘goseq/DESCRIPTION’ ... OK * this is package ‘goseq’ version ‘1.51.0’ * 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 ... ERROR Running examples in ‘goseq-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getlength > ### Title: Retrieves Gene length data > ### Aliases: getlength > > ### ** Examples > > genes <- c("ENSG00000124208", "ENSG00000182463", "ENSG00000124201", "ENSG00000124205", "ENSG00000124207") > getlength(genes,'hg19','ensGene') Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘goseq.Rnw’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘goseq.Rnw’ ... 140 TRUE 141 TRUE 10 FALSE 11 TRUE > supportedOrganisms()[supportedOrganisms()$Genome == + "hg19", ] Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘goseq.Rnw’ using Sweave Loading required package: BiasedUrn Loading required package: geneLenDataBase Loading required package: limma Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object is masked from ‘package:limma’: plotMA The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:geneLenDataBase’: unfactor The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading hg19 length data... Warning in pcls(G) : initial point very close to some inequality constraints Fetching GO annotations... Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Killed * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/goseq.Rcheck/00check.log’ for details.
goseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL goseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 0.021 | 0.000 | 0.021 | |
getgo | 17.241 | 0.655 | 18.337 | |