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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 800/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.7.0  (landing page)
Robersy Sanchez
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: devel
git_last_commit: 2ab18e5
git_last_commit_date: 2024-05-05 14:06:42 -0400 (Sun, 05 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for GenomAutomorphism on palomino6

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: 1.7.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.7.0.tar.gz
StartedAt: 2024-07-16 00:18:04 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 00:22:13 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 249.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomAutomorphism.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/GenomAutomorphism.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomAutomorphism/DESCRIPTION' ... OK
* this is package 'GenomAutomorphism' version '1.7.0'
* 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 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
aminoacid_dist    3.41   0.25   51.85
codon_dist_matrix 0.05   0.03    5.36
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/GenomAutomorphism.Rcheck/00check.log'
for details.


Installation output

GenomAutomorphism.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GenomAutomorphism
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   0.17    0.03    0.20 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  16.06    2.81   35.34 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.310.010.33
AutomorphismList1.830.182.00
CodonMatrix0.170.000.18
CodonSeq0.290.290.57
GRangesMatrixSeq0.170.030.21
ListCodonMatrix0.180.000.18
MatrixSeq0.10.00.1
aa_phychem_index0.060.040.09
aaindex10.020.020.03
aaindex20.000.010.01
aaindex30.010.000.02
aln0.060.140.20
aminoacid_dist 3.41 0.2551.85
as.AutomorphismList0.340.030.37
aut3D1.180.111.28
autZ1252.430.112.55
autZ50.550.140.69
autZ641.300.101.39
autby_coef0.190.010.20
autm0.040.140.19
autm_3d0.060.050.11
autm_z1250.080.170.25
automorphismByRanges0.100.140.24
automorphism_bycoef0.100.120.22
automorphisms3.780.083.86
base2codon0.040.140.19
base2int000
base_methods0.450.050.50
brca1_aln0.050.000.04
brca1_aln20.050.000.05
brca1_autm0.230.050.28
cdm_z640.300.180.48
codon_coord0.980.131.11
codon_dist0.220.300.52
codon_dist_matrix0.050.035.36
codon_matrix0.490.010.52
conserved_regions0.280.380.66
covid_aln0.050.140.18
covid_autm0.070.170.25
cyc_aln0.140.080.22
cyc_autm0.10.20.3
dna_phyche0.000.020.02
dna_phychem000
extract-methods0.330.010.34
getAutomorphisms0.140.160.30
get_coord0.580.090.67
get_mutscore0.140.020.15
matrices0.530.120.66
mod000
modeq000
modlineq000
mut_type0.010.000.02
peptide_phychem_index0.100.000.09
reexports0.120.270.39
seqranges0.530.140.67
slapply000
sortByChromAndStart0.050.000.05
str2chr000
str2dig000
translation0.890.221.11