Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:09 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
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 1149/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metagene2 1.14.0 (landing page) Eric Fournier
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: metagene2 |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:metagene2.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings metagene2_1.14.0.tar.gz |
StartedAt: 2023-04-10 21:49:12 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:55:33 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 381.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metagene2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:metagene2.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings metagene2_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/metagene2.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘metagene2/DESCRIPTION’ ... OK * this is package ‘metagene2’ version ‘1.14.0’ * 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 loading without being on the library search path ... 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 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 5.72 0.052 5.773 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: OK
metagene2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL metagene2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-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. region_name is missing from the new metadata. Recreating it. region_name is missing from the new metadata. Recreating it. Replace region_metadata with metadata which would result in a different region split. All caches at the 'split_regions' step will be invalidated, and split_by will be reset to its default value. RUNIT TEST PROTOCOL -- Mon Apr 10 21:54:07 2023 *********************************************** Number of test functions: 128 Number of errors: 0 Number of failures: 0 1 Test Suite : metagene2 RUnit Tests - 128 test functions, 0 errors, 0 failures Number of test functions: 128 Number of errors: 0 Number of failures: 0 Warning messages: 1: In checkIdentical(obs, warning(exp)) : Some bam files have discrepancies in their seqnames. This could be caused by chromosome names present only in a subset of the bam files (i.e.: chrY in some bam files, but absent in others. This could also be caused by discrepancies in the seqlevels style (i.e.: UCSC:chr1 versus NCBI:1) 2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 100 out-of-bound ranges located on sequence chr1. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 200 out-of-bound ranges located on sequence chr1. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 600 out-of-bound ranges located on sequence chr1. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > #BiocGenerics:::testPackage("metagene2", pattern="^test_demo.*\\.R$") > > proc.time() user system elapsed 77.690 2.155 79.039
metagene2.Rcheck/metagene2-Ex.timings
name | user | system | elapsed | |
Bam_Handler | 1.063 | 0.092 | 1.157 | |
as_is_region_order | 2.110 | 0.081 | 2.194 | |
coverage_order | 1.625 | 0.016 | 1.641 | |
get_demo_bam_files | 0.001 | 0.000 | 0.000 | |
get_demo_design | 0.001 | 0.000 | 0.000 | |
get_demo_metagene | 1.312 | 0.016 | 1.328 | |
get_demo_region_filenames | 0.067 | 0.008 | 0.074 | |
get_demo_regions | 0.079 | 0.004 | 0.082 | |
get_demo_rna_bam_files | 0.000 | 0.000 | 0.001 | |
get_demo_rna_regions | 0.078 | 0.004 | 0.083 | |
metagene2 | 1.305 | 0.040 | 1.346 | |
metagene2_heatmap | 3.572 | 0.172 | 3.745 | |
plot_metagene | 5.720 | 0.052 | 5.773 | |