Jiri Hon
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/triplex |
| git_branch: RELEASE_3_17 |
| git_last_commit: fd58eba |
| git_last_commit_date: 2023-04-25 10:26:57 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 2146/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| triplex 1.40.0 (landing page) Jiri Hon
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the triplex package: - 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: triplex |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:triplex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings triplex_1.40.0.tar.gz |
| StartedAt: 2023-10-19 08:29:56 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 08:32:57 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 181.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: triplex.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:triplex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings triplex_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/triplex.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘triplex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘triplex’ version ‘1.40.0’
* 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/triplex.Rcheck/00install.out’ for details.
* 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 ... 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 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 ... 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 ... 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/triplex.Rcheck/00check.log’
for details.
triplex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL triplex ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘triplex’ ... ** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_triplex.c -o R_init_triplex.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align.c -o align.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align_interface.c -o align_interface.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dl_list.c -o dl_list.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interval.c -o interval.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libtriplex.c -o libtriplex.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progress.c -o progress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c search.c -o search.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c search_interface.c -o search_interface.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 | 0.198 | 0.015 | 0.376 | |
| ins | 0.019 | 0.002 | 0.040 | |
| lend | 0.016 | 0.002 | 0.030 | |
| lstart | 0.016 | 0.002 | 0.029 | |
| lwidth | 0.018 | 0.002 | 0.036 | |
| pvalue | 0.016 | 0.001 | 0.031 | |
| triplex-package | 0.094 | 0.007 | 0.181 | |
| triplex.3D | 0.014 | 0.000 | 0.027 | |
| triplex.alignment | 0.032 | 0.001 | 0.060 | |
| triplex.diagram | 0.044 | 0.002 | 0.085 | |
| triplex.group.table | 0.000 | 0.001 | 0.000 | |
| triplex.score.table | 0.000 | 0.000 | 0.001 | |
| triplex.search | 0.124 | 0.004 | 0.237 | |