Kristian K Ullrich
| Snapshot Date: 2026-05-11 13:40 -0400 (Mon, 11 May 2026) |
| git_url: https://git.bioconductor.org/packages/MSA2dist |
| git_branch: RELEASE_3_23 |
| git_last_commit: 4f21e42 |
| git_last_commit_date: 2026-04-28 08:57:42 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-12 11:36 -0400 (Tue, 12 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4994 |
| 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 1407/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSA2dist 1.16.0 (landing page) Kristian K Ullrich
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for MSA2dist in R Universe. | ||||||||||||||
|
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. |
| Package: MSA2dist |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSA2dist_1.16.0.tar.gz |
| StartedAt: 2026-05-12 02:22:19 -0400 (Tue, 12 May 2026) |
| EndedAt: 2026-05-12 02:26:23 -0400 (Tue, 12 May 2026) |
| EllapsedTime: 244.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSA2dist.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSA2dist.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSA2dist_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MSA2dist.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-12 06:22:19 UTC
* checking for file ‘MSA2dist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSA2dist’ version ‘1.16.0’
* 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 ... NOTE
Found the following notes/warnings:
SystemRequirements specified C++11: support has been removed
See ‘/home/biocbuild/bbs-3.23-bioc/meat/MSA2dist.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... NOTE
Obsolete C++11 standard request will be ignored
* checking installed package size ... INFO
installed size is 5.7Mb
sub-directories of 1Mb or more:
libs 5.1Mb
* 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 ... INFO
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 5.729 0.801 10.506
* 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-3.23-bioc/meat/MSA2dist.Rcheck/00check.log’
for details.
MSA2dist.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MSA2dist
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘MSA2dist’ ...
** this is package ‘MSA2dist’ version ‘1.16.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
from RcppExports.cpp:5:
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’
27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: ‘#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’
35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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++20 -shared -L/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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)
MSA2dist.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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
82.315 12.078 98.643
MSA2dist.Rcheck/MSA2dist-Ex.timings
| name | user | system | elapsed | |
| AAMatrix-data | 0.003 | 0.000 | 0.003 | |
| GENETIC_CODE_TCAG | 0.004 | 0.001 | 0.005 | |
| aa2selfscore | 0.235 | 0.002 | 0.237 | |
| aabin2aastring | 0.033 | 0.001 | 0.035 | |
| aastring2aabin | 0.210 | 0.005 | 0.215 | |
| aastring2aln | 0.130 | 0.000 | 0.131 | |
| aastring2dist | 0.946 | 0.066 | 1.014 | |
| addmask2string | 0.207 | 0.019 | 0.226 | |
| addpop2string | 0.599 | 0.047 | 0.646 | |
| addpos2string | 0.086 | 0.013 | 0.099 | |
| addregion2string | 0.214 | 0.020 | 0.234 | |
| aln2aastring | 0.147 | 0.005 | 0.152 | |
| aln2dnastring | 0.02 | 0.00 | 0.02 | |
| cds2aa | 0.593 | 0.016 | 0.609 | |
| cds2codonaln | 0.391 | 0.000 | 0.391 | |
| cdsstring2codonaln | 0.198 | 0.023 | 0.221 | |
| codon2numberAMBIG | 0.001 | 0.000 | 0.001 | |
| codon2numberTCAG | 0.001 | 0.000 | 0.002 | |
| codonmat2pnps | 0.038 | 0.003 | 0.040 | |
| codonmat2xy | 5.729 | 0.801 | 10.506 | |
| compareCodons | 0.045 | 0.003 | 0.048 | |
| dnabin2dnastring | 0.034 | 0.010 | 0.045 | |
| dnastring2aln | 0.013 | 0.002 | 0.014 | |
| dnastring2codonmat | 0.036 | 0.005 | 0.041 | |
| dnastring2dist | 0.158 | 0.035 | 0.192 | |
| dnastring2dnabin | 0.011 | 0.004 | 0.014 | |
| dnastring2kaks | 1.438 | 0.673 | 1.943 | |
| getmask | 0.229 | 0.027 | 0.255 | |
| getpos | 0.082 | 0.010 | 0.093 | |
| globalDeletion | 0.022 | 0.002 | 0.023 | |
| globalDeletionAA | 0.236 | 0.005 | 0.241 | |
| granthamMatrix | 0.000 | 0.004 | 0.004 | |
| hiv-data | 0.025 | 0.001 | 0.026 | |
| indices2kaks | 1.477 | 0.537 | 1.917 | |
| iupac-data | 0.077 | 0.020 | 0.096 | |
| iupacMatrix | 0.000 | 0.002 | 0.003 | |
| makePostalignedSeqs | 1.120 | 0.141 | 1.262 | |
| pal2nal | 0.877 | 0.199 | 1.077 | |
| popinteger | 0.189 | 0.011 | 0.201 | |
| popnames | 0.178 | 0.014 | 0.192 | |
| rcpp_KaKs | 0.043 | 0.001 | 0.044 | |
| rcpp_distSTRING | 0.028 | 0.003 | 0.031 | |
| rcpp_pairwiseDeletionAA | 0.149 | 0.014 | 0.164 | |
| rcpp_pairwiseDeletionDNA | 0.020 | 0.001 | 0.021 | |
| region | 0.195 | 0.006 | 0.201 | |
| regionused | 0.170 | 0.002 | 0.171 | |
| string2region | 0.468 | 0.014 | 0.483 | |
| subString | 0.017 | 0.002 | 0.018 | |
| uptriidx | 0.000 | 0.000 | 0.001 | |