| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:35 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 | ||||
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To the developers/maintainers of the GenomicRanges package: - Please 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 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 798/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicRanges 1.51.4 (landing page) Hervé Pagès
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: GenomicRanges |
| Version: 1.51.4 |
| 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_1.51.4.tar.gz |
| StartedAt: 2023-03-25 03:10:37 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 03:22:58 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 741.0 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_1.51.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.51.4’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ... 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 89.243 4.456 93.703
GPos-class 54.897 5.339 60.263
makeGRangesFromDataFrame 0.839 0.056 16.969
* 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicRanges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -c transcript_utils.c -o transcript_utils.o gcc -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 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 -- Sat Mar 25 03:16:10 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
56.780 0.452 57.226
GenomicRanges.Rcheck/GenomicRanges-Ex.timings
| name | user | system | elapsed | |
| GNCList-class | 0.648 | 0.028 | 0.676 | |
| GPos-class | 54.897 | 5.339 | 60.263 | |
| GRanges-class | 1.039 | 0.004 | 1.043 | |
| GRangesFactor-class | 0.526 | 0.004 | 0.531 | |
| GRangesList-class | 0.546 | 0.004 | 0.553 | |
| GenomicRanges-comparison | 0.292 | 0.004 | 0.297 | |
| absoluteRanges | 1.471 | 0.027 | 1.503 | |
| constraint | 1.131 | 0.000 | 1.131 | |
| coverage-methods | 0.334 | 0.004 | 0.338 | |
| findOverlaps-methods | 2.290 | 0.004 | 2.294 | |
| genomic-range-squeezers | 0 | 0 | 0 | |
| genomicvars | 89.243 | 4.456 | 93.703 | |
| inter-range-methods | 3.366 | 0.152 | 3.518 | |
| intra-range-methods | 0.689 | 0.016 | 0.704 | |
| makeGRangesFromDataFrame | 0.839 | 0.056 | 16.969 | |
| makeGRangesListFromDataFrame | 0.119 | 0.011 | 0.131 | |
| nearest-methods | 2.131 | 0.191 | 2.323 | |
| phicoef | 0.002 | 0.001 | 0.001 | |
| setops-methods | 4.304 | 0.335 | 4.640 | |
| strand-utils | 0.137 | 0.012 | 0.149 | |
| subtract-methods | 0.326 | 0.016 | 0.342 | |
| tile-methods | 0.126 | 0.004 | 0.130 | |
| tileGenome | 0.409 | 0.020 | 0.429 | |