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This page was generated on 2023-02-08 01:15:32 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the TimiRGeN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TimiRGeN.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 2037/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TimiRGeN 1.9.0 (landing page) Krutik Patel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: TimiRGeN |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TimiRGeN_1.9.0.tar.gz |
StartedAt: 2023-02-07 17:38:41 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 17:47:06 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 504.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: TimiRGeN.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TimiRGeN_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TimiRGeN.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 ‘TimiRGeN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TimiRGeN’ version ‘1.9.0’ * package encoding: UTF-8 * 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 ‘TimiRGeN’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 ... NOTE Note: found 3 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘TimiRGeN-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: enrichWiki > ### Title: enrichWiki > ### Aliases: enrichWiki > > ### ** Examples > > library(org.Mm.eg.db) Loading required package: AnnotationDbi > > MAE <- MultiAssayExperiment() > > metadata(MAE)[["e_list"]] <- e_list_mouse > > MAE <- dloadGmt(MAE, species = "Mus musculus") trying URL 'https://data.wikipathways.org/current/gmt/wikipathways-20230110-gmt-Mus_musculus.gmt' Content type 'unknown' length 84419 bytes (82 KB) ================================================== downloaded 82 KB > > MAE <- enrichWiki(MAE = MAE, method = 'c', ID_list = metadata(MAE)[[1]], + orgDB = org.Mm.eg.db, path_gene = assay(MAE, 1), + path_name = assay(MAE, 2), ID = "ENTREZID", + universe = assay(MAE, 1)[[2]]) Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘TimiRGeN_tutorial.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/TimiRGeN.Rcheck/00check.log’ for details.
TimiRGeN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TimiRGeN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘TimiRGeN’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (TimiRGeN)
TimiRGeN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #unit test check > library(testthat) > library(TimiRGeN) Loading required package: Mfuzz Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: e1071 Attaching package: 'DynDoc' The following object is masked from 'package:BiocGenerics': path Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars The following object is masked from 'package:Biobase': rowMedians Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb > test_check(package = "TimiRGeN") [ FAIL 0 | WARN 49 | SKIP 0 | PASS 124 ] [ FAIL 0 | WARN 49 | SKIP 0 | PASS 124 ] > > proc.time() user system elapsed 27.486 1.542 29.813
TimiRGeN.Rcheck/TimiRGeN-Ex.timings
name | user | system | elapsed | |
UUO_data | 0.007 | 0.000 | 0.008 | |
addIds | 5.782 | 0.326 | 17.941 | |
addPrefix | 0.683 | 0.052 | 0.737 | |
clusterCheck | 0.930 | 0.020 | 4.271 | |
clusterList | 5.852 | 0.191 | 17.499 | |
combineGenes | 0.402 | 0.004 | 0.407 | |
createClusters | 0.822 | 0.040 | 3.926 | |
createClusters2 | 0.744 | 0.036 | 0.780 | |
cytoMake | 0 | 0 | 0 | |
diffExpressRes | 5.101 | 0.154 | 16.563 | |
dloadGmt | 1.660 | 0.075 | 8.282 | |
dloadMirdb | 0 | 0 | 0 | |
dloadMirtarbase | 0.344 | 0.016 | 0.364 | |
dloadTargetscan | 0 | 0 | 0 | |
eNames | 5.240 | 0.145 | 8.760 | |
e_list_mouse | 0.002 | 0.000 | 0.002 | |