Kristian K Ullrich
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/MSA2dist |
| git_branch: devel |
| git_last_commit: 98bd32e |
| git_last_commit_date: 2024-04-30 11:39:56 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:15 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1297/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSA2dist 1.9.0 (landing page) Kristian K Ullrich
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the MSA2dist 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: MSA2dist |
| Version: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSA2dist_1.9.0.tar.gz |
| StartedAt: 2024-05-19 20:03:35 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 20:07:32 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 236.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSA2dist.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSA2dist_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/MSA2dist.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSA2dist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSA2dist’ version ‘1.9.0’
* 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 ‘MSA2dist’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
codonmat2xy 5.08 0.898 4.669
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/MSA2dist.Rcheck/00check.log’
for details.
MSA2dist.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSA2dist ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MSA2dist’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GY94.cpp -o GY94.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c KaKs.cpp -o KaKs.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LPB93.cpp -o LPB93.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LWL85.cpp -o LWL85.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MSMA.cpp -o MSMA.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MYN.cpp -o MYN.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NG86.cpp -o NG86.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c YN00.cpp -o YN00.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c base.cpp -o base.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_KaKs.cpp -o rcpp_KaKs.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_distSTRING.cpp -o rcpp_distSTRING.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppThread/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MSA2dist.so GY94.o KaKs.o LPB93.o LWL85.o MSMA.o MYN.o NG86.o RcppExports.o YN00.o base.o rcpp_KaKs.o rcpp_distSTRING.o rcpp_pairwiseDeletionAA.o rcpp_pairwiseDeletionDNA.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-MSA2dist/00new/MSA2dist/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (MSA2dist)
MSA2dist.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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.
> library(testthat)
> library(MSA2dist)
>
> test_check("MSA2dist")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 176 ]
>
> proc.time()
user system elapsed
82.075 15.374 96.215
MSA2dist.Rcheck/MSA2dist-Ex.timings
| name | user | system | elapsed | |
| AAMatrix-data | 0.003 | 0.002 | 0.004 | |
| GENETIC_CODE_TCAG | 0.005 | 0.003 | 0.007 | |
| aa2selfscore | 0.259 | 0.006 | 0.267 | |
| aabin2aastring | 0.033 | 0.002 | 0.035 | |
| aastring2aabin | 0.179 | 0.004 | 0.188 | |
| aastring2aln | 0.157 | 0.003 | 0.180 | |
| aastring2dist | 0.748 | 0.022 | 0.774 | |
| addmask2string | 0.118 | 0.007 | 0.127 | |
| addpop2string | 0.118 | 0.005 | 0.126 | |
| addpos2string | 0.077 | 0.002 | 0.080 | |
| addregion2string | 0.646 | 0.006 | 0.652 | |
| aln2aastring | 0.145 | 0.003 | 0.148 | |
| aln2dnastring | 0.018 | 0.000 | 0.020 | |
| cds2aa | 0.621 | 0.021 | 0.641 | |
| cds2codonaln | 0.417 | 0.011 | 0.428 | |
| cdsstring2codonaln | 0.225 | 0.004 | 0.229 | |
| codon2numberAMBIG | 0.001 | 0.001 | 0.001 | |
| codon2numberTCAG | 0.001 | 0.001 | 0.001 | |
| codonmat2pnps | 0.041 | 0.001 | 0.042 | |
| codonmat2xy | 5.080 | 0.898 | 4.669 | |
| compareCodons | 0.060 | 0.009 | 0.070 | |
| dnabin2dnastring | 0.023 | 0.004 | 0.027 | |
| dnastring2aln | 0.012 | 0.002 | 0.013 | |
| dnastring2codonmat | 0.033 | 0.003 | 0.037 | |
| dnastring2dist | 0.163 | 0.020 | 0.183 | |
| dnastring2dnabin | 0.012 | 0.000 | 0.013 | |
| dnastring2kaks | 1.118 | 0.693 | 1.923 | |
| getmask | 0.529 | 0.220 | 0.299 | |
| getpos | 0.145 | 0.029 | 0.174 | |
| globalDeletion | 0.018 | 0.002 | 0.020 | |
| granthamMatrix | 0.001 | 0.002 | 0.003 | |
| hiv-data | 0.030 | 0.001 | 0.031 | |
| indices2kaks | 1.254 | 0.828 | 2.319 | |
| iupac-data | 0.341 | 0.176 | 0.121 | |
| iupacMatrix | 0.000 | 0.001 | 0.002 | |
| makePostalignedSeqs | 1.170 | 0.175 | 1.345 | |
| pal2nal | 0.928 | 0.087 | 1.016 | |
| popinteger | 0.230 | 0.031 | 0.268 | |
| popnames | 0.215 | 0.009 | 0.224 | |
| rcpp_KaKs | 0.048 | 0.002 | 0.050 | |
| rcpp_distSTRING | 0.032 | 0.005 | 0.037 | |
| rcpp_pairwiseDeletionAA | 0.162 | 0.007 | 0.171 | |
| rcpp_pairwiseDeletionDNA | 0.015 | 0.003 | 0.018 | |
| region | 0.228 | 0.007 | 0.236 | |
| regionused | 0.170 | 0.003 | 0.174 | |
| string2region | 0.490 | 0.013 | 0.503 | |
| subString | 0.018 | 0.001 | 0.018 | |
| uptriidx | 0.001 | 0.001 | 0.001 | |