Hervé Pagès
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/GenomicRanges |
| git_branch: RELEASE_3_17 |
| git_last_commit: 9e58f81 |
| git_last_commit_date: 2023-10-06 16:38:35 -0400 (Fri, 06 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:23 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 812/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicRanges 1.52.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.52.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenomicRanges_1.52.1.tar.gz |
| StartedAt: 2023-10-15 21:36:05 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 21:45:19 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 554.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenomicRanges_1.52.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.52.1’
* 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
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 ... WARNING
checkRd: (5) GRanges-class.Rd:115-165: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:173-176: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:177-182: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:183-187: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:188-191: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:192-195: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:196-199: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:200-204: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:209-218: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:219-223: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:224-228: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:229-238: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:239-245: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:246-251: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:252-257: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:258-263: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:264-267: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:268-276: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:284-299: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:300-307: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:308-322: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:323-332: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:333-342: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:343-349: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:356-361: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:368-371: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:372-376: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:377-380: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:381-394: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:409-415: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:421-427: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:433-445: \item in \describe must have non-empty label
checkRd: (5) GRanges-class.Rd:453-466: \item in \describe must have non-empty label
* 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 44.846 5.780 50.627
GPos-class 37.883 5.509 43.392
makeGRangesFromDataFrame 0.661 0.041 8.500
* 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 ...
‘GenomicRangesIntroduction.Rmd’ using ‘UTF-8’... OK
‘ExtendingGenomicRanges.Rnw’ using ‘UTF-8’... OK
‘GRanges_and_GRangesList_slides.Rnw’ using ‘UTF-8’... OK
‘GenomicRangesHOWTOs.Rnw’ using ‘UTF-8’... OK
‘Ten_things_slides.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.
GenomicRanges.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicRanges
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘GenomicRanges’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:143:45: warning: ‘end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
143 | return on_minus_strand ? end - tloc : start + tloc;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:31: note: ‘end’ was declared here
120 | int nexons, j, start, end, width;
| ^~~
transcript_utils.c:143:45: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
143 | return on_minus_strand ? end - tloc : start + tloc;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:24: note: ‘start’ was declared here
120 | int nexons, j, start, end, width;
| ^~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.
> 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, sort, 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 -- Sun Oct 15 21:39:58 2023
***********************************************
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
41.628 0.643 42.269
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 0.295 | 0.064 | 0.358 | |
| GPos-class | 37.883 | 5.509 | 43.392 | |
| GRanges-class | 0.793 | 0.016 | 0.809 | |
| GRangesFactor-class | 0.409 | 0.004 | 0.413 | |
| GRangesList-class | 0.426 | 0.000 | 0.426 | |
| GenomicRanges-comparison | 0.202 | 0.012 | 0.214 | |
| absoluteRanges | 0.975 | 0.048 | 1.024 | |
| constraint | 0.811 | 0.024 | 0.835 | |
| coverage-methods | 0.236 | 0.004 | 0.240 | |
| findOverlaps-methods | 1.684 | 0.032 | 1.717 | |
| genomic-range-squeezers | 0.001 | 0.000 | 0.001 | |
| genomicvars | 44.846 | 5.780 | 50.627 | |
| inter-range-methods | 2.228 | 0.036 | 2.265 | |
| intra-range-methods | 0.530 | 0.004 | 0.533 | |
| makeGRangesFromDataFrame | 0.661 | 0.041 | 8.500 | |
| makeGRangesListFromDataFrame | 0.080 | 0.015 | 0.095 | |
| nearest-methods | 1.465 | 0.149 | 1.614 | |
| phicoef | 0.001 | 0.000 | 0.001 | |
| setops-methods | 2.985 | 0.324 | 3.309 | |
| strand-utils | 0.096 | 0.016 | 0.112 | |
| subtract-methods | 0.230 | 0.015 | 0.245 | |
| tile-methods | 0.109 | 0.024 | 0.133 | |
| tileGenome | 0.281 | 0.020 | 0.301 | |