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This page was generated on 2024-06-21 17:42 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 825/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.6.0  (landing page)
Robersy Sanchez
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: RELEASE_3_19
git_last_commit: 22d7b7a
git_last_commit_date: 2024-04-30 11:43:53 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for GenomAutomorphism on kjohnson1

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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2024-06-20 21:57:56 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 22:05:19 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 442.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenomAutomorphism.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.6.0’
* 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 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AutomorphismList,ANY'
  generic '[' and siglist 'ListCodonMatrix,ANY'
  generic '[' and siglist 'MatrixSeq,ANY'
  generic '[[' and siglist 'AutomorphismList'
  generic '[[' and siglist 'ListCodonMatrix'
  generic 'names<-' and siglist 'AutomorphismList'
  generic 'names<-' and siglist 'MatrixSeq'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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     7.884  0.178  67.596
aminoacid_dist    3.828  0.972  11.712
autZ64            2.841  0.065  23.373
aut3D             2.391  0.314  23.046
autZ125           2.537  0.060  18.780
autZ5             1.904  0.071  21.900
codon_dist_matrix 0.059  0.014   7.179
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(GenomAutomorphism)
  > 
  > test_check("GenomAutomorphism")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-aa_mutmat.R:7:6'): multiplication works ──────────────────────
  mat && aa is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.


Installation output

GenomAutomorphism.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘GenomAutomorphism’ ...
** using staged installation
** R
** data
** inst
** 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
** 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 4.4.0 (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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.140   0.043   0.186 

GenomAutomorphism.Rcheck/tests/testthat.Rout.fail


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(GenomAutomorphism)
> 
> test_check("GenomAutomorphism")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-aa_mutmat.R:7:6'): multiplication works ──────────────────────
mat && aa is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
Error: Test failures
Execution halted

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.4880.0110.501
AutomorphismList2.8490.0382.899
CodonMatrix0.2160.0030.219
CodonSeq0.4550.0160.473
GRangesMatrixSeq0.2500.0170.268
ListCodonMatrix0.2560.0050.261
MatrixSeq0.1400.0050.146
aa_phychem_index0.1380.0120.150
aaindex10.0480.0020.051
aaindex20.0220.0020.024
aaindex30.0130.0020.015
aln0.1000.0030.104
aminoacid_dist 3.828 0.97211.712
as.AutomorphismList0.6060.1230.732
aut3D 2.391 0.31423.046
autZ125 2.537 0.06018.780
autZ5 1.904 0.07121.900
autZ64 2.841 0.06523.373
autby_coef0.3300.0050.360
autm0.0920.0040.102
autm_3d0.1530.0060.164
autm_z1250.1250.0060.132
automorphismByRanges0.1680.0090.187
automorphism_bycoef0.1370.0080.151
automorphisms 7.884 0.17867.596
base2codon0.0630.0040.071
base2int0.0070.0020.009
base_methods0.4100.0250.442
brca1_aln0.0660.0040.072
brca1_aln20.0780.0060.085
brca1_autm0.4620.0050.467
cdm_z640.2210.4190.646
codon_coord1.2550.0121.280
codon_dist0.3320.0090.362
codon_dist_matrix0.0590.0147.179
codon_matrix0.6080.0170.628
conserved_regions0.4550.0080.466
covid_aln0.0920.0030.095
covid_autm0.1040.0040.110
cyc_aln0.1250.0040.130
cyc_autm0.2610.0040.266
dna_phyche0.0070.0010.008
dna_phychem0.0030.0000.004
extract-methods0.5260.0090.543
getAutomorphisms0.1000.0050.107
get_coord0.5880.0070.603
get_mutscore0.1240.0070.133
matrices0.6460.0060.657
mod0.0020.0010.003
modeq0.0010.0000.001
modlineq0.0020.0010.004
mut_type0.0020.0000.002
peptide_phychem_index0.1590.0080.168
reexports0.1640.0090.175
seqranges0.7070.0060.713
slapply0.0020.0000.003
sortByChromAndStart0.0620.0000.063
str2chr000
str2dig000
translation1.1300.0131.153