Jiri Hon
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/triplex |
| git_branch: devel |
| git_last_commit: 7c99430 |
| git_last_commit_date: 2025-04-15 10:23:57 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:08 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 2260/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| triplex 1.49.0 (landing page) Jiri Hon
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the triplex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/triplex.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: triplex |
| Version: 1.49.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:triplex.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings triplex_1.49.0.tar.gz |
| StartedAt: 2025-10-17 14:42:15 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 14:44:07 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 112.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: triplex.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:triplex.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings triplex_1.49.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/triplex.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘triplex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘triplex’ version ‘1.49.0’
* 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 ‘triplex’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’
See ‘/home/biocbuild/bbs-3.22-bioc/meat/triplex.Rcheck/00install.out’ for details.
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 ... OK
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘triplex’ for: ‘type’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rgl’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘IRanges:::new_Views’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
countBend: no visible global function definition for ‘optimize’
drawBase: no visible global function definition for ‘rgl.triangles’
join: no visible global function definition for ‘rgl.quads’
joinRect: no visible global function definition for ‘rgl.quads’
triplex.3D: no visible global function definition for
‘installed.packages’
triplex.3D: no visible global function definition for ‘type’
triplex.3D: no visible global function definition for ‘nlm’
triplex.3D: no visible global function definition for ‘rgl.bg’
triplex.3D: no visible global function definition for ‘rgl.spheres’
triplex.diagram: no visible global function definition for ‘type’
triplex.input: no visible global function definition for ‘type’
coerce,TriplexViews-DNAStringSet: no visible global function definition
for ‘type’
coerce,TriplexViews-GRanges: no visible global function definition for
‘type’
Undefined global functions or variables:
installed.packages nlm optimize rgl.bg rgl.quads rgl.spheres
rgl.triangles type
Consider adding
importFrom("stats", "nlm", "optimize")
importFrom("utils", "installed.packages")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) TriplexViews-class.Rd:68-71: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:76-80: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:81-84: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:85-88: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:89-92: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:93-96: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:97-100: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:101-104: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
TriplexViews-class.Rd: DNAString, XStringViews
triplex-package.Rd: DNAString
triplex.3D.Rd: DNAStringSet
triplex.alignment.Rd: DNAStringSet
triplex.diagram.Rd: DNAStringSet
triplex.search.Rd: DNAString, XStringViews
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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: 2 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/triplex.Rcheck/00check.log’
for details.
triplex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL triplex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘triplex’ ... ** this is package ‘triplex’ version ‘1.49.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_triplex.c -o R_init_triplex.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c align.c -o align.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c align_interface.c -o align_interface.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c dl_list.c -o dl_list.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c interval.c -o interval.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c libtriplex.c -o libtriplex.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c progress.c -o progress.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c search.c -o search.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c search_interface.c -o search_interface.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-triplex/00new/triplex/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ ** testing if installed package keeps a record of temporary installation path * DONE (triplex)
triplex.Rcheck/triplex-Ex.timings
| name | user | system | elapsed | |
| TriplexViews-class | 0.216 | 0.004 | 0.221 | |
| ins | 0.018 | 0.000 | 0.018 | |
| lend | 0.018 | 0.000 | 0.018 | |
| lstart | 0.008 | 0.008 | 0.016 | |
| lwidth | 0.018 | 0.000 | 0.018 | |
| pvalue | 0.015 | 0.000 | 0.016 | |
| triplex-package | 0.080 | 0.004 | 0.085 | |
| triplex.3D | 0.014 | 0.000 | 0.014 | |
| triplex.alignment | 0.048 | 0.000 | 0.048 | |
| triplex.diagram | 0.047 | 0.000 | 0.048 | |
| triplex.group.table | 0 | 0 | 0 | |
| triplex.score.table | 0 | 0 | 0 | |
| triplex.search | 0.129 | 0.000 | 0.129 | |