| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-04 11:37:23 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 815/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.4.0 (landing page) Robersy Sanchez
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| 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: 2024-03-03 20:48:36 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:56:00 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 444.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
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 5.268 0.203 66.066
aminoacid_dist 3.448 1.276 11.901
autZ64 1.948 0.089 21.906
autZ125 1.788 0.102 23.561
aut3D 1.731 0.135 22.617
autZ5 1.086 0.077 21.393
codon_dist_matrix 0.046 0.012 7.518
* 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.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)
GenomAutomorphism.Rcheck/tests/spelling.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 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
0.225 0.086 0.299
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 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
22.409 1.303 78.929
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.574 | 0.017 | 0.596 | |
| AutomorphismList | 2.880 | 0.053 | 2.959 | |
| CodonSeq | 0.508 | 0.015 | 0.528 | |
| aa_mutmat | 0.026 | 0.006 | 0.033 | |
| aaindex2 | 0.008 | 0.001 | 0.009 | |
| aaindex3 | 0.005 | 0.001 | 0.006 | |
| aminoacid_dist | 3.448 | 1.276 | 11.901 | |
| as.AutomorphismList | 0.686 | 0.046 | 0.742 | |
| aut3D | 1.731 | 0.135 | 22.617 | |
| autZ125 | 1.788 | 0.102 | 23.561 | |
| autZ5 | 1.086 | 0.077 | 21.393 | |
| autZ64 | 1.948 | 0.089 | 21.906 | |
| autm | 0.077 | 0.030 | 0.128 | |
| automorphismByRanges | 0.140 | 0.005 | 0.146 | |
| automorphism_bycoef | 0.146 | 0.007 | 0.155 | |
| automorphisms | 5.268 | 0.203 | 66.066 | |
| base2codon | 0.119 | 0.019 | 0.154 | |
| base2int | 0.002 | 0.001 | 0.004 | |
| base_coord | 0.245 | 0.012 | 0.260 | |
| cdm_z64 | 0.027 | 0.002 | 0.029 | |
| codon_coord | 0.950 | 0.026 | 0.996 | |
| codon_dist | 0.369 | 0.012 | 0.385 | |
| codon_dist_matrix | 0.046 | 0.012 | 7.518 | |
| conserved_regions | 0.520 | 0.040 | 0.565 | |
| extract-methods | 0.545 | 0.012 | 0.560 | |
| getAutomorphisms | 0.233 | 0.014 | 0.249 | |
| get_coord | 0.548 | 0.012 | 0.563 | |
| get_mutscore | 0.110 | 0.003 | 0.114 | |
| matrices | 0.578 | 0.016 | 0.598 | |
| mod | 0.002 | 0.001 | 0.002 | |
| modeq | 0.001 | 0.001 | 0.001 | |
| modlineq | 0.003 | 0.003 | 0.006 | |
| mut_type | 0.002 | 0.001 | 0.002 | |
| reexports | 0.112 | 0.008 | 0.120 | |
| seqranges | 0.601 | 0.010 | 0.615 | |
| slapply | 0.003 | 0.000 | 0.004 | |
| sortByChromAndStart | 0.070 | 0.000 | 0.071 | |
| str2chr | 0.000 | 0.001 | 0.001 | |
| str2dig | 0.000 | 0.001 | 0.001 | |
| translation | 0.895 | 0.015 | 0.915 | |