Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:13 -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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To the developers/maintainers of the metagene2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagene2.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 1135/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metagene2 1.15.0 (landing page) Eric Fournier
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: metagene2 |
Version: 1.15.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagene2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metagene2_1.15.0.tar.gz |
StartedAt: 2023-02-07 07:27:11 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 07:34:40 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 449.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: metagene2.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagene2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metagene2_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metagene2.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 ‘metagene2/DESCRIPTION’ ... OK * this is package ‘metagene2’ version ‘1.15.0’ * 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 ‘metagene2’ 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 ... WARNING checkRd: (5) Bam_Handler.Rd:20: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:40: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:44: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:48: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:52: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:56: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:59-60: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:69-70: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:451: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:456: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:461: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:466: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:475: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:480: \item in \describe must have non-empty label checkRd: (5) metagene2.Rd:485: \item in \describe must have non-empty label * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_metagene 6.923 0.012 6.946 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname region_name is missing from the new metadata. Recreating it. Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘metagene2.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING See ‘/home/biocbuild/bbs-3.17-bioc/meat/metagene2.Rcheck/00check.log’ for details.
metagene2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metagene2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘metagene2’ ... ** using staged installation ** R ** 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 (metagene2)
metagene2.Rcheck/tests/runTests.Rout.fail
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. > ## Run all tests in the metagene package > BiocGenerics:::testPackage("metagene2") 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname region_name is missing from the new metadata. Recreating it. Killed
metagene2.Rcheck/metagene2-Ex.timings
name | user | system | elapsed | |
Bam_Handler | 0.089 | 0.008 | 0.100 | |
as_is_region_order | 2.890 | 0.148 | 3.051 | |
coverage_order | 2.297 | 0.012 | 2.310 | |
get_demo_bam_files | 0.001 | 0.000 | 0.000 | |
get_demo_design | 0.001 | 0.000 | 0.001 | |
get_demo_metagene | 1.885 | 0.036 | 1.921 | |
get_demo_region_filenames | 0.109 | 0.000 | 0.109 | |
get_demo_regions | 0.11 | 0.00 | 0.11 | |
get_demo_rna_bam_files | 0.000 | 0.000 | 0.001 | |
get_demo_rna_regions | 0.111 | 0.000 | 0.113 | |
metagene2 | 1.917 | 0.020 | 1.938 | |
metagene2_heatmap | 4.352 | 0.040 | 4.405 | |
plot_metagene | 6.923 | 0.012 | 6.946 | |