Hervé Pagès
| Snapshot Date: 2024-05-29 11:04:14 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/GenomicRanges |
| git_branch: devel |
| git_last_commit: d8c95f2 |
| git_last_commit_date: 2024-04-30 14:34:23 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-30 12:36:53 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 810/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicRanges 1.57.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 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: 1.57.0 |
| 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_1.57.0.tar.gz |
| StartedAt: 2024-05-30 01:26:21 -0400 (Thu, 30 May 2024) |
| EndedAt: 2024-05-30 01:35:28 -0400 (Thu, 30 May 2024) |
| EllapsedTime: 546.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.57.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicRanges.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.57.0’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... NOTE
checkRd: (-1) intra-range-methods.Rd:85-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:89-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:98-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:106-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:119-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:148-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:154-162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) intra-range-methods.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:92-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:99-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:106-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:112-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:120-146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:147-149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:150-155: Lost braces in \itemize; meant \describe ?
* 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 77.496 10.000 95.842
GPos-class 59.439 3.561 72.362
setops-methods 7.688 0.097 9.152
inter-range-methods 6.019 0.480 7.125
nearest-methods 5.241 0.305 6.786
findOverlaps-methods 4.434 0.053 5.022
makeGRangesFromDataFrame 1.567 0.100 8.440
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transcript_utils.c -o transcript_utils.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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, 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 -- Thu May 30 01:35:05 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
112.435 1.340 128.495
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 1.298 | 0.067 | 1.563 | |
| GPos-class | 59.439 | 3.561 | 72.362 | |
| GRanges-class | 2.068 | 0.117 | 2.568 | |
| GRangesFactor-class | 1.967 | 0.181 | 2.563 | |
| GRangesList-class | 1.094 | 0.024 | 1.337 | |
| GenomicRanges-comparison | 0.563 | 0.018 | 0.683 | |
| absoluteRanges | 2.367 | 0.133 | 2.961 | |
| constraint | 2.146 | 0.051 | 2.563 | |
| coverage-methods | 0.642 | 0.006 | 0.693 | |
| findOverlaps-methods | 4.434 | 0.053 | 5.022 | |
| genomic-range-squeezers | 0.000 | 0.001 | 0.001 | |
| genomicvars | 77.496 | 10.000 | 95.842 | |
| inter-range-methods | 6.019 | 0.480 | 7.125 | |
| intra-range-methods | 1.475 | 0.254 | 2.042 | |
| makeGRangesFromDataFrame | 1.567 | 0.100 | 8.440 | |
| makeGRangesListFromDataFrame | 0.226 | 0.006 | 0.239 | |
| nearest-methods | 5.241 | 0.305 | 6.786 | |
| phicoef | 0.002 | 0.002 | 0.004 | |
| setops-methods | 7.688 | 0.097 | 9.152 | |
| strand-utils | 0.246 | 0.013 | 0.306 | |
| subtract-methods | 0.589 | 0.008 | 0.732 | |
| tile-methods | 0.243 | 0.003 | 0.287 | |
| tileGenome | 0.735 | 0.029 | 0.904 | |