Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2146/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
triplex 1.40.0  (landing page)
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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for triplex on kjohnson2


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.

raw results


Summary

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

Command output

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### Running 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
###
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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.



Installation output

triplex.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL triplex
###
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* 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)

Tests output


Example timings

triplex.Rcheck/triplex-Ex.timings

nameusersystemelapsed
TriplexViews-class0.1980.0150.376
ins0.0190.0020.040
lend0.0160.0020.030
lstart0.0160.0020.029
lwidth0.0180.0020.036
pvalue0.0160.0010.031
triplex-package0.0940.0070.181
triplex.3D0.0140.0000.027
triplex.alignment0.0320.0010.060
triplex.diagram0.0440.0020.085
triplex.group.table0.0000.0010.000
triplex.score.table0.0000.0000.001
triplex.search0.1240.0040.237