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This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1339/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSA2dist 1.8.0  (landing page)
Kristian K Ullrich
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/MSA2dist
git_branch: RELEASE_3_19
git_last_commit: 92b6ecd
git_last_commit_date: 2024-04-30 11:39:56 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-06-10 22:56:49 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 23:02:03 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 314.4 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSA2dist.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSA2dist/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSA2dist’ version ‘1.8.0’
* 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.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 5.391  0.899   7.054
* 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-3.19-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/4.4-arm64/Resources/library’
* installing *source* package ‘MSA2dist’ ...
** 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.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)

Tests output

MSA2dist.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "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 
 77.738  15.709 121.865 

Example timings

MSA2dist.Rcheck/MSA2dist-Ex.timings

nameusersystemelapsed
AAMatrix-data0.0030.0010.006
GENETIC_CODE_TCAG0.0040.0020.007
aa2selfscore0.2770.0090.441
aabin2aastring0.0380.0040.068
aastring2aabin0.2080.0060.335
aastring2aln0.1670.0030.263
aastring2dist1.0630.0291.466
addmask2string0.2490.0110.399
addpop2string0.2630.0090.419
addpos2string0.0830.0020.085
addregion2string0.7850.0070.911
aln2aastring0.1460.0020.147
aln2dnastring0.0230.0020.033
cds2aa0.7030.0221.045
cds2codonaln0.4850.0090.709
cdsstring2codonaln0.2540.0050.326
codon2numberAMBIG0.0000.0010.003
codon2numberTCAG0.0010.0010.001
codonmat2pnps0.0380.0020.051
codonmat2xy5.3910.8997.054
compareCodons0.0650.0070.087
dnabin2dnastring0.0330.0050.054
dnastring2aln0.0160.0020.025
dnastring2codonmat0.0410.0040.068
dnastring2dist0.1780.0210.303
dnastring2dnabin0.0170.0010.023
dnastring2kaks1.6100.8783.069
getmask0.2410.0400.405
getpos0.1290.0170.147
globalDeletion0.0220.0020.024
granthamMatrix0.0000.0030.003
hiv-data0.0220.0010.024
indices2kaks1.3920.7283.430
iupac-data0.3850.1910.097
iupacMatrix0.0000.0020.003
makePostalignedSeqs1.3790.1481.798
pal2nal1.1080.1051.372
popinteger0.2060.0180.280
popnames0.1810.0080.189
rcpp_KaKs0.0360.0020.041
rcpp_distSTRING0.0250.0040.045
rcpp_pairwiseDeletionAA0.1700.0070.241
rcpp_pairwiseDeletionDNA0.0140.0030.028
region0.2320.0110.359
regionused0.1840.0040.235
string2region0.5000.0140.589
subString0.0180.0010.020
uptriidx0.0010.0000.001