Jiri Hon
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/triplex |
| git_branch: RELEASE_3_16 |
| git_last_commit: 41843cf |
| git_last_commit_date: 2022-11-01 11:08:11 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the triplex package: - Please 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 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 2098/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| triplex 1.38.0 (landing page) Jiri Hon
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: triplex |
| Version: 1.38.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:triplex.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings triplex_1.38.0.tar.gz |
| StartedAt: 2023-04-11 00:40:45 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:42:43 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 117.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: triplex.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:triplex.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings triplex_1.38.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/triplex.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘triplex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘triplex’ version ‘1.38.0’
* 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-3.16-bioc/meat/triplex.Rcheck/00install.out’ for details.
* 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 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 ‘nlm’
triplex.3D: no visible global function definition for ‘rgl.bg’
triplex.3D: no visible global function definition for ‘rgl.spheres’
Undefined global functions or variables:
installed.packages nlm optimize rgl.bg rgl.quads rgl.spheres
rgl.triangles
Consider adding
importFrom("stats", "nlm", "optimize")
importFrom("utils", "installed.packages")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘triplex.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/triplex.Rcheck/00check.log’
for details.
triplex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL triplex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘triplex’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_triplex.c -o R_init_triplex.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c align.c -o align.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_interface.c -o align_interface.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c dl_list.c -o dl_list.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c interval.c -o interval.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c libtriplex.c -o libtriplex.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c progress.c -o progress.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c search.c -o search.o gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -c search_interface.c -o search_interface.o gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/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 | 0.143 | 0.000 | 0.143 | |
| ins | 0.009 | 0.004 | 0.013 | |
| lend | 0.012 | 0.000 | 0.012 | |
| lstart | 0.004 | 0.008 | 0.012 | |
| lwidth | 0.009 | 0.004 | 0.013 | |
| pvalue | 0.013 | 0.000 | 0.013 | |
| triplex-package | 0.077 | 0.000 | 0.077 | |
| triplex.3D | 0.011 | 0.000 | 0.011 | |
| triplex.alignment | 0.026 | 0.000 | 0.026 | |
| triplex.diagram | 0.036 | 0.000 | 0.036 | |
| triplex.group.table | 0.001 | 0.000 | 0.001 | |
| triplex.score.table | 0 | 0 | 0 | |
| triplex.search | 0.088 | 0.000 | 0.088 | |