Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:34:19 -0000 (Sun, 29 Jan 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" | 4021 |
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To the developers/maintainers of the topGO package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/topGO.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 2049/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
topGO 2.51.0 (landing page) Adrian Alexa
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: topGO |
Version: 2.51.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings topGO_2.51.0.tar.gz |
StartedAt: 2023-01-29 10:32:34 -0000 (Sun, 29 Jan 2023) |
EndedAt: 2023-01-29 10:37:36 -0000 (Sun, 29 Jan 2023) |
EllapsedTime: 301.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: topGO.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings topGO_2.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/topGO.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 ‘topGO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘topGO’ version ‘2.51.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi', 'SparseM' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘topGO’ can be installed ... 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 ... WARNING Error in library(topGO, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : there is no package called ‘topGO’ Execution halted It looks like this package has a loading problem when not on .libPaths: see the messages for details. * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Rgraphviz’ ‘multtest’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing object imported by a ':::' call: ‘globaltest:::globaltest’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GOplot: no visible global function definition for ‘getDefaultAttrs’ GOplot: no visible global function definition for ‘agopen’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getNodeCenter’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘pieGlyph’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getX’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getY’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getNodeLW’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘drawTxtLabel’ GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘txtLabel’ GOplot.counts : plotSigChart: no visible global function definition for ‘AgNode’ GOplot.counts : plotSigChart : <anonymous>: no visible global function definition for ‘name’ GOplot.counts : plotSigChart : <anonymous>: no visible global function definition for ‘getNodeCenter’ GOplot.counts : plotSigChart: no visible global function definition for ‘getNodeXY’ GOplot.counts : plotSigChart: no visible global function definition for ‘getY’ GOplot.counts: no visible global function definition for ‘getDefaultAttrs’ GOplot.counts: no visible global function definition for ‘agopen’ getPvalues: no visible global function definition for ‘mt.teststat’ getPvalues: no visible global function definition for ‘mt.rawp2adjp’ printDOT: no visible global function definition for ‘getDefaultAttrs’ printDOT: no visible global function definition for ‘toDot’ GOSumTest,classicScore: no visible binding for global variable ‘.PERMSUM.MAT’ GOSumTest,classicScore: no visible binding for global variable ‘.PERMSUM.LOOKUP’ initialize,classicExpr: no visible global function definition for ‘error’ scoresInTerm,topGOdata-missing: no visible global function definition for ‘scoreInNode’ Undefined global functions or variables: .PERMSUM.LOOKUP .PERMSUM.MAT AgNode agopen drawTxtLabel error getDefaultAttrs getNodeCenter getNodeLW getNodeXY getX getY mt.rawp2adjp mt.teststat name pieGlyph scoreInNode toDot txtLabel * 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 ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘topGO.Rnw’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘topGO.Rnw’ ... ( 7711 GO terms found. ) Build GO DAG topology .......... ( 11555 GO terms and 26037 relations. ) Annotating nodes ............... ( 3889 genes annotated to the GO terms. ) Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘topGO.Rnw’ using Sweave Loading required package: xtable Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ 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: graph 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")'. Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: SparseM Attaching package: ‘SparseM’ The following object is masked from ‘package:base’: backsolve groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: ‘topGO’ The following object is masked from ‘package:IRanges’: members Loading required package: org.Hs.eg.db Building most specific GOs ..... Warning in result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). ( 1676 GO terms found. ) Build GO DAG topology .......... ( 4372 GO terms and 9730 relations. ) Annotating nodes ............... ( 314 genes annotated to the GO terms. ) -- Classic Algorithm -- the algorithm is scoring 884 nontrivial nodes parameters: test statistic: fisher -- Classic Algorithm -- the algorithm is scoring 968 nontrivial nodes parameters: test statistic: ks score order: increasing -- Elim Algorithm -- the algorithm is scoring 968 nontrivial nodes parameters: test statistic: ks cutOff: 0.01 score order: increasing Level 16: 1 nodes to be scored (0 eliminated genes) Level 15: 1 nodes to be scored (0 eliminated genes) Level 14: 2 nodes to be scored (0 eliminated genes) Level 13: 9 nodes to be scored (25 eliminated genes) Level 12: 19 nodes to be scored (45 eliminated genes) Level 11: 30 nodes to be scored (45 eliminated genes) Level 10: 58 nodes to be scored (45 eliminated genes) Level 9: 84 nodes to be scored (55 eliminated genes) Level 8: 117 nodes to be scored (75 eliminated genes) Level 7: 149 nodes to be scored (149 eliminated genes) Level 6: 169 nodes to be scored (162 eliminated genes) Level 5: 162 nodes to be scored (174 eliminated genes) Level 4: 101 nodes to be scored (201 eliminated genes) Level 3: 50 nodes to be scored (214 eliminated genes) Level 2: 15 nodes to be scored (225 eliminated genes) Level 1: 1 nodes to be scored (225 eliminated genes) Loading required package: Rgraphviz Loading required package: grid Attaching package: ‘grid’ The following object is masked from ‘package:topGO’: depth Attaching package: ‘Rgraphviz’ The following objects are masked from ‘package:IRanges’: from, to The following objects are masked from ‘package:S4Vectors’: from, to Building most specific GOs ..... ( 109 GO terms found. ) Build GO DAG topology .......... ( 220 GO terms and 284 relations. ) Annotating nodes ............... ( 86 genes annotated to the GO terms. ) Loading required package: multtest Building most specific GOs ..... ( 7711 GO terms found. ) Build GO DAG topology .......... ( 11555 GO terms and 26037 relations. ) Annotating nodes ............... ( 3889 genes annotated to the GO terms. ) -- Classic Algorithm -- the algorithm is scoring 4045 nontrivial nodes parameters: test statistic: Fisher test -- Classic Algorithm -- the algorithm is scoring 5851 nontrivial nodes parameters: test statistic: KS tests score order: increasing Killed * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/topGO.Rcheck/00check.log’ for details.
topGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL topGO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘topGO’ ... ** 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 groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (topGO)