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This page was generated on 2025-09-20 12:06 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1358/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSA2dist 1.13.0  (landing page)
Kristian K Ullrich
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/MSA2dist
git_branch: devel
git_last_commit: 2328f45
git_last_commit_date: 2025-04-15 12:44:47 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MSA2dist on kjohnson3

To the developers/maintainers of the MSA2dist package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSA2dist.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.

raw results


Summary

Package: MSA2dist
Version: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-09-19 20:34:09 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 20:35:36 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MSA2dist.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MSA2dist.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSA2dist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSA2dist’ version ‘1.13.0’
* 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-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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
* 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-3.22-bioc/meat/MSA2dist.Rcheck/00check.log’
for details.


Installation output

MSA2dist.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSA2dist
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘MSA2dist’ ...
** this is package ‘MSA2dist’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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
installing to /Library/Frameworks/R.framework/Versions/4.5-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)

Tests output

MSA2dist.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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 177 ]
> 
> proc.time()
   user  system elapsed 
 28.681   6.902  35.545 

Example timings

MSA2dist.Rcheck/MSA2dist-Ex.timings

nameusersystemelapsed
AAMatrix-data0.0010.0000.001
GENETIC_CODE_TCAG0.0010.0000.002
aa2selfscore0.0800.0020.088
aabin2aastring0.0100.0010.010
aastring2aabin0.0780.0020.085
aastring2aln0.0460.0010.047
aastring2dist0.3160.0130.334
addmask2string0.0760.0030.082
addpop2string0.0800.0050.085
addpos2string0.0310.0010.032
addregion2string0.2150.0020.222
aln2aastring0.0460.0010.047
aln2dnastring0.0050.0000.005
cds2aa0.2010.0100.218
cds2codonaln0.1310.0030.138
cdsstring2codonaln0.0680.0020.079
codon2numberAMBIG0.0000.0000.001
codon2numberTCAG000
codonmat2pnps0.0130.0010.014
codonmat2xy1.8580.4151.873
compareCodons0.0200.0050.026
dnabin2dnastring0.0070.0030.010
dnastring2aln0.0030.0010.004
dnastring2codonmat0.0110.0010.012
dnastring2dist0.0600.0070.079
dnastring2dnabin0.0040.0010.004
dnastring2kaks0.5920.4190.904
getmask0.0710.0190.098
getpos0.0410.0140.055
globalDeletion0.0060.0010.006
globalDeletionAA0.0600.0020.071
granthamMatrix0.0010.0010.001
hiv-data0.0090.0010.010
indices2kaks0.4970.3930.889
iupac-data0.0260.0070.034
iupacMatrix0.0010.0000.001
makePostalignedSeqs0.3880.1000.495
pal2nal0.3080.0370.348
popinteger0.0700.0090.081
popnames0.0660.0020.070
rcpp_KaKs0.0160.0000.016
rcpp_distSTRING0.0110.0010.012
rcpp_pairwiseDeletionAA0.0560.0030.060
rcpp_pairwiseDeletionDNA0.0090.0010.010
region0.0690.0040.074
regionused0.0560.0010.059
string2region0.1620.0060.169
subString0.0060.0000.006
uptriidx000