Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 829/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicRanges 1.58.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicRanges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GenomicRanges |
Version: 1.58.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GenomicRanges_1.58.0.tar.gz |
StartedAt: 2024-12-20 00:18:33 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:28:44 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 610.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicRanges.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GenomicRanges_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GenomicRanges.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GenomicRanges/DESCRIPTION’ ... OK * this is package ‘GenomicRanges’ version ‘1.58.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘GenomicRanges’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: SIGNIFICANT USER-VISIBLE CHANGES Cannot process chunk/lines: DEPRECATED AND DEFUNCT * checking code 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 C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genomicvars 40.944 4.074 45.022 GPos-class 33.156 5.076 38.239 makeGRangesFromDataFrame 0.959 0.061 5.221 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/GenomicRanges.Rcheck/00check.log’ for details.
GenomicRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GenomicRanges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c transcript_utils.c -o transcript_utils.o In function ‘tloc2rloc’, inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26: transcript_utils.c:143:45: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c: In function ‘tlocs2rlocs’: transcript_utils.c:120:24: note: ‘start’ was declared here 120 | int nexons, j, start, end, width; | ^~~~~ In function ‘tloc2rloc’, inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26: transcript_utils.c:143:45: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c: In function ‘tlocs2rlocs’: transcript_utils.c:120:31: note: ‘end’ was declared here 120 | int nexons, j, start, end, width; | ^~~ gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-GenomicRanges/00new/GenomicRanges/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicRanges)
GenomicRanges.Rcheck/tests/run_unitTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > require("GenomicRanges") || stop("unable to load GenomicRanges package") Loading required package: GenomicRanges Loading required package: stats4 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb [1] TRUE > GenomicRanges:::.test() RUNIT TEST PROTOCOL -- Fri Dec 20 00:25:35 2024 *********************************************** Number of test functions: 74 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicRanges RUnit Tests - 74 test functions, 0 errors, 0 failures Number of test functions: 74 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 36.640 0.180 36.818
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
name | user | system | elapsed | |
GNCList-class | 0.558 | 0.005 | 0.563 | |
GPos-class | 33.156 | 5.076 | 38.239 | |
GRanges-class | 0.667 | 0.004 | 0.672 | |
GRangesFactor-class | 0.340 | 0.003 | 0.344 | |
GRangesList-class | 0.385 | 0.003 | 0.387 | |
GenomicRanges-comparison | 0.192 | 0.001 | 0.192 | |
absoluteRanges | 1.484 | 0.093 | 1.577 | |
constraint | 0.719 | 0.004 | 0.725 | |
coverage-methods | 0.221 | 0.000 | 0.222 | |
findOverlaps-methods | 1.515 | 0.005 | 1.521 | |
genomic-range-squeezers | 0 | 0 | 0 | |
genomicvars | 40.944 | 4.074 | 45.022 | |
inter-range-methods | 2.089 | 0.122 | 2.212 | |
intra-range-methods | 0.508 | 0.002 | 0.510 | |
makeGRangesFromDataFrame | 0.959 | 0.061 | 5.221 | |
makeGRangesListFromDataFrame | 0.095 | 0.001 | 0.095 | |
nearest-methods | 1.551 | 0.193 | 1.745 | |
phicoef | 0.001 | 0.000 | 0.001 | |
setops-methods | 2.790 | 0.215 | 3.006 | |
strand-utils | 0.087 | 0.004 | 0.090 | |
subtract-methods | 0.206 | 0.004 | 0.210 | |
tile-methods | 0.109 | 0.043 | 0.152 | |
tileGenome | 0.270 | 0.054 | 0.324 | |