Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:04 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 GenomicRanges package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/GenomicRanges.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 756/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicRanges 1.46.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GenomicRanges |
Version: 1.46.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicRanges_1.46.1.tar.gz |
StartedAt: 2022-04-12 13:39:11 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 13:45:34 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 382.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicRanges.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicRanges_1.46.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GenomicRanges.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicRanges/DESCRIPTION’ ... OK * this is package ‘GenomicRanges’ version ‘1.46.1’ * 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 ‘GenomicRanges’ 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genomicvars 61.545 7.752 69.385 GPos-class 48.921 2.459 51.434 setops-methods 7.257 0.023 7.281 inter-range-methods 4.764 0.293 5.099 makeGRangesFromDataFrame 1.310 0.082 10.754 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/GenomicRanges.Rcheck/00check.log’ for details.
GenomicRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicRanges ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include -fPIC -Wall -g -O2 -c transcript_utils.c -o transcript_utils.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > 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, 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: S4Vectors Attaching package: 'S4Vectors' 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 -- Tue Apr 12 13:45:22 2022 *********************************************** Number of test functions: 73 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicRanges RUnit Tests - 73 test functions, 0 errors, 0 failures Number of test functions: 73 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 89.458 0.655 90.487
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
name | user | system | elapsed | |
GNCList-class | 0.569 | 0.055 | 0.623 | |
GPos-class | 48.921 | 2.459 | 51.434 | |
GRanges-class | 1.774 | 0.052 | 1.829 | |
GRangesFactor-class | 1.695 | 0.140 | 1.839 | |
GRangesList-class | 1.005 | 0.033 | 1.041 | |
GenomicRanges-comparison | 0.421 | 0.007 | 0.429 | |
absoluteRanges | 1.837 | 0.176 | 2.109 | |
constraint | 1.685 | 0.029 | 1.717 | |
coverage-methods | 0.508 | 0.004 | 0.515 | |
findOverlaps-methods | 2.165 | 0.017 | 2.184 | |
genomic-range-squeezers | 0.000 | 0.000 | 0.001 | |
genomicvars | 61.545 | 7.752 | 69.385 | |
inter-range-methods | 4.764 | 0.293 | 5.099 | |
intra-range-methods | 1.329 | 0.025 | 1.361 | |
makeGRangesFromDataFrame | 1.310 | 0.082 | 10.754 | |
makeGRangesListFromDataFrame | 0.243 | 0.006 | 0.248 | |
nearest-methods | 3.137 | 0.023 | 3.162 | |
phicoef | 0.002 | 0.001 | 0.002 | |
setops-methods | 7.257 | 0.023 | 7.281 | |
strand-utils | 0.176 | 0.007 | 0.183 | |
tile-methods | 0.209 | 0.001 | 0.211 | |
tileGenome | 0.697 | 0.016 | 0.714 | |