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This page was generated on 2025-09-20 12:03 -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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSA2dist_1.13.0.tar.gz
StartedAt: 2025-09-20 02:01:14 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 02:05:21 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 247.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MSA2dist.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSA2dist_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MSA2dist.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
* 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 loading without being on the library search path ... 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 6.158  0.893  10.891
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MSA2dist.Rcheck/00check.log’
for details.


Installation output

MSA2dist.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MSA2dist
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MSA2dist’ ...
** this is package ‘MSA2dist’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c GY94.cpp -o GY94.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c KaKs.cpp -o KaKs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c LPB93.cpp -o LPB93.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c LWL85.cpp -o LWL85.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c MSMA.cpp -o MSMA.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c MYN.cpp -o MYN.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c NG86.cpp -o NG86.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c YN00.cpp -o YN00.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c base.cpp -o base.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_KaKs.cpp -o rcpp_KaKs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_distSTRING.cpp -o rcpp_distSTRING.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppThread/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 80.215  11.751  95.889 

Example timings

MSA2dist.Rcheck/MSA2dist-Ex.timings

nameusersystemelapsed
AAMatrix-data0.0030.0000.002
GENETIC_CODE_TCAG0.0030.0010.003
aa2selfscore0.2590.0000.259
aabin2aastring0.0360.0000.036
aastring2aabin0.2300.0020.233
aastring2aln0.1310.0000.131
aastring2dist0.9140.0510.964
addmask2string0.5990.0430.643
addpop2string0.1920.0240.216
addpos2string0.0840.0190.103
addregion2string0.5130.0270.540
aln2aastring0.1360.0020.137
aln2dnastring0.0190.0010.020
cds2aa0.6070.0270.634
cds2codonaln0.3990.0010.400
cdsstring2codonaln0.2020.0000.202
codon2numberAMBIG0.0000.0000.001
codon2numberTCAG0.0000.0000.001
codonmat2pnps0.0370.0020.039
codonmat2xy 6.158 0.89310.891
compareCodons0.0520.0030.055
dnabin2dnastring0.0320.0040.036
dnastring2aln0.0140.0030.017
dnastring2codonmat0.0490.0160.065
dnastring2dist0.2120.0950.310
dnastring2dnabin0.0150.0030.018
dnastring2kaks1.4820.7432.065
getmask0.2420.0340.276
getpos0.0720.0110.082
globalDeletion0.0180.0040.023
globalDeletionAA0.1960.0080.204
granthamMatrix0.0000.0010.001
hiv-data0.0280.0000.028
indices2kaks1.4250.5761.872
iupac-data0.0610.0070.067
iupacMatrix0.0010.0000.001
makePostalignedSeqs1.1220.1231.246
pal2nal0.9180.0921.010
popinteger0.1850.0100.194
popnames0.1700.0130.183
rcpp_KaKs0.0440.0000.045
rcpp_distSTRING0.0280.0030.032
rcpp_pairwiseDeletionAA0.1550.0170.176
rcpp_pairwiseDeletionDNA0.0200.0030.024
region0.1950.0480.243
regionused0.1640.0070.170
string2region0.4720.0240.495
subString0.0190.0000.020
uptriidx0.0000.0000.001