| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:35:06 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GenomicRanges package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 720/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicRanges 1.42.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomicRanges |
| Version: 1.42.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicRanges_1.42.0.tar.gz |
| StartedAt: 2021-05-06 02:07:28 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:12:41 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 312.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicRanges_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GenomicRanges.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.42.0’
* 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 ‘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 52.477 5.869 58.447
GPos-class 40.194 1.869 45.928
setops-methods 5.197 0.154 5.361
makeGRangesFromDataFrame 0.710 0.022 9.203
* 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-3.12-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.
GenomicRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomicRanges ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()
RUNIT TEST PROTOCOL -- Thu May 6 02:12:27 2021
***********************************************
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
66.001 0.474 66.581
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 0.685 | 0.035 | 0.721 | |
| GPos-class | 40.194 | 1.869 | 45.928 | |
| GRanges-class | 1.310 | 0.090 | 1.424 | |
| GRangesFactor-class | 0.670 | 0.038 | 0.709 | |
| GRangesList-class | 0.668 | 0.009 | 0.678 | |
| GenomicRanges-comparison | 0.320 | 0.006 | 0.326 | |
| absoluteRanges | 1.547 | 0.065 | 1.617 | |
| constraint | 1.302 | 0.020 | 1.334 | |
| coverage-methods | 0.407 | 0.002 | 0.409 | |
| findOverlaps-methods | 1.633 | 0.015 | 1.661 | |
| genomic-range-squeezers | 0 | 0 | 0 | |
| genomicvars | 52.477 | 5.869 | 58.447 | |
| inter-range-methods | 3.227 | 0.143 | 3.375 | |
| intra-range-methods | 0.697 | 0.071 | 0.769 | |
| makeGRangesFromDataFrame | 0.710 | 0.022 | 9.203 | |
| makeGRangesListFromDataFrame | 0.127 | 0.002 | 0.130 | |
| nearest-methods | 2.066 | 0.008 | 2.076 | |
| phicoef | 0.002 | 0.000 | 0.002 | |
| setops-methods | 5.197 | 0.154 | 5.361 | |
| strand-utils | 0.133 | 0.004 | 0.138 | |
| tile-methods | 0.114 | 0.001 | 0.117 | |
| tileGenome | 0.435 | 0.011 | 0.447 | |