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This page was generated on 2024-04-17 11:37:46 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 815/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.4.0  (landing page)
Robersy Sanchez
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: RELEASE_3_18
git_last_commit: 2c0069e
git_last_commit_date: 2023-10-24 11:43:17 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GenomAutomorphism on merida1


To the developers/maintainers of the GenomAutomorphism package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomAutomorphism.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: GenomAutomorphism
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomAutomorphism_1.4.0.tar.gz
StartedAt: 2024-04-16 03:13:53 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 03:26:50 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 777.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomAutomorphism.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomAutomorphism_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.4.0’
* 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 ‘GenomAutomorphism’ can be installed ... OK
* 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 R 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 ... NOTE
Package unavailable to check Rd xrefs: ‘mod’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
automorphisms     6.666  0.269 121.351
aminoacid_dist    4.288  1.289  19.167
AutomorphismList  4.860  0.090   5.285
autZ64            2.486  0.097  39.859
aut3D             2.179  0.208  42.706
autZ125           2.071  0.093  41.097
autZ5             1.425  0.078  39.911
codon_dist_matrix 0.072  0.013  14.254
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.



Installation output

GenomAutomorphism.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘GenomAutomorphism’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘mod’ in package ‘GenomAutomorphism’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomAutomorphism)

Tests output

GenomAutomorphism.Rcheck/tests/spelling.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.353   0.110   0.449 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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(GenomAutomorphism)
> 
> test_check("GenomAutomorphism")
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 31 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 32.403   1.810 137.179 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.9790.0341.101
AutomorphismList4.8600.0905.285
CodonSeq0.8440.0200.886
aa_mutmat0.0430.0150.058
aaindex20.0130.0020.016
aaindex30.0080.0020.010
aminoacid_dist 4.288 1.28919.167
as.AutomorphismList1.2500.0971.467
aut3D 2.179 0.20842.706
autZ125 2.071 0.09341.097
autZ5 1.425 0.07839.911
autZ64 2.486 0.09739.859
autm0.1420.0100.154
automorphismByRanges0.2820.0090.293
automorphism_bycoef0.2370.0080.247
automorphisms 6.666 0.269121.351
base2codon0.1310.0060.143
base2int0.0030.0030.006
base_coord0.3630.0130.395
cdm_z640.0490.0040.054
codon_coord1.2560.0211.302
codon_dist0.6350.0170.660
codon_dist_matrix 0.072 0.01314.254
conserved_regions0.9780.0701.083
extract-methods1.0630.0241.121
getAutomorphisms0.4190.0240.461
get_coord0.8290.0180.922
get_mutscore0.2640.0050.274
matrices0.7930.0200.848
mod0.0030.0010.005
modeq0.0020.0010.003
modlineq0.0060.0050.011
mut_type0.0040.0010.006
reexports0.2490.0130.274
seqranges0.8860.0140.939
slapply0.0040.0020.007
sortByChromAndStart0.1470.0020.154
str2chr0.0010.0020.002
str2dig0.0010.0010.002
translation1.0690.0131.117