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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 815/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.8.0  (landing page)
Robersy Sanchez
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: RELEASE_3_20
git_last_commit: 708be70
git_last_commit_date: 2024-10-29 11:13:18 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-12-20 20:23:56 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 20:30:50 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 413.9 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ 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 ‘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     7.290  0.173  63.109
aminoacid_dist    3.559  0.980  10.936
autZ64            2.525  0.066  21.618
aut3D             2.223  0.171  22.215
autZ125           2.234  0.053  17.434
autZ5             1.581  0.055  20.386
codon_dist_matrix 0.046  0.013   7.010
* 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-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 
  0.226   0.070   0.289 

GenomAutomorphism.Rcheck/tests/testthat.Rout.fail


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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
AutomorphismByCoef0.4770.0110.489
AutomorphismList2.8110.0392.850
CodonMatrix0.1960.0060.202
CodonSeq0.4240.0230.447
GRangesMatrixSeq0.2350.0190.254
ListCodonMatrix0.2550.0070.262
MatrixSeq0.1420.0050.147
aa_phychem_index0.1360.0110.147
aaindex10.0470.0020.050
aaindex20.0210.0020.022
aaindex30.0140.0020.016
aln0.0760.0030.080
aminoacid_dist 3.559 0.98010.936
as.AutomorphismList0.5930.0660.658
aut3D 2.223 0.17122.215
autZ125 2.234 0.05317.434
autZ5 1.581 0.05520.386
autZ64 2.525 0.06621.618
autby_coef0.3190.0070.326
autm0.0740.0060.080
autm_3d0.1250.0050.131
autm_z1250.1030.0040.107
automorphismByRanges0.1640.0110.175
automorphism_bycoef0.1300.0110.141
automorphisms 7.290 0.17363.109
base2codon0.0640.0060.083
base2int0.0060.0010.007
base_methods0.3020.0190.321
brca1_aln0.0350.0040.039
brca1_aln20.0380.0030.043
brca1_autm0.2380.0040.243
cdm_z640.1050.2150.323
codon_coord1.0080.0111.022
codon_dist0.3510.0070.358
codon_dist_matrix0.0460.0137.010
codon_matrix0.5590.0110.569
conserved_regions0.4180.0090.426
covid_aln0.0840.0040.089
covid_autm0.1120.0050.118
cyc_aln0.1050.0050.111
cyc_autm0.1960.0070.204
dna_phyche0.0060.0020.008
dna_phychem0.0030.0000.003
extract-methods0.5370.0100.547
getAutomorphisms0.2040.0110.215
get_coord0.6560.0090.665
get_mutscore0.2070.0080.214
matrices0.6350.0140.659
mod0.0020.0010.002
modeq0.0010.0000.001
modlineq0.0020.0020.003
mut_type0.0020.0000.001
peptide_phychem_index0.1560.0080.166
reexports0.1570.0080.164
seqranges0.6550.0070.663
slapply0.0020.0000.003
sortByChromAndStart0.060.000.06
str2chr0.0000.0010.001
str2dig0.0000.0010.001
translation1.0360.0081.044