| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:15 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 812/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.5.0 (landing page) Robersy Sanchez
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-03-02 04:28:01 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 04:42:13 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 852.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.5.0’
* 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 6.653 0.283 130.100
aminoacid_dist 4.191 1.311 20.376
AutomorphismList 4.806 0.109 5.730
autZ64 2.468 0.107 46.878
aut3D 2.144 0.192 42.636
autZ125 2.086 0.101 43.761
autZ5 1.402 0.084 43.123
codon_dist_matrix 0.069 0.014 16.180
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.19-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/4.4-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
0.351 0.114 0.515
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 0 | WARN 7 | SKIP 0 | PASS 31 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
31.554 1.874 147.477
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.981 | 0.032 | 1.162 | |
| AutomorphismList | 4.806 | 0.109 | 5.730 | |
| CodonSeq | 0.851 | 0.020 | 1.024 | |
| aa_mutmat | 0.044 | 0.015 | 0.065 | |
| aaindex2 | 0.012 | 0.002 | 0.018 | |
| aaindex3 | 0.009 | 0.002 | 0.011 | |
| aminoacid_dist | 4.191 | 1.311 | 20.376 | |
| as.AutomorphismList | 1.197 | 0.092 | 1.465 | |
| aut3D | 2.144 | 0.192 | 42.636 | |
| autZ125 | 2.086 | 0.101 | 43.761 | |
| autZ5 | 1.402 | 0.084 | 43.123 | |
| autZ64 | 2.468 | 0.107 | 46.878 | |
| autm | 0.137 | 0.009 | 0.159 | |
| automorphismByRanges | 0.278 | 0.011 | 0.344 | |
| automorphism_bycoef | 0.233 | 0.013 | 0.302 | |
| automorphisms | 6.653 | 0.283 | 130.100 | |
| base2codon | 0.134 | 0.007 | 0.145 | |
| base2int | 0.003 | 0.002 | 0.008 | |
| base_coord | 0.365 | 0.015 | 0.425 | |
| cdm_z64 | 0.048 | 0.004 | 0.058 | |
| codon_coord | 1.161 | 0.029 | 1.338 | |
| codon_dist | 0.648 | 0.017 | 0.769 | |
| codon_dist_matrix | 0.069 | 0.014 | 16.180 | |
| conserved_regions | 0.946 | 0.064 | 1.152 | |
| extract-methods | 1.060 | 0.029 | 1.260 | |
| getAutomorphisms | 0.429 | 0.025 | 0.534 | |
| get_coord | 0.830 | 0.029 | 0.984 | |
| get_mutscore | 0.274 | 0.005 | 0.331 | |
| matrices | 0.778 | 0.015 | 0.928 | |
| mod | 0.003 | 0.003 | 0.006 | |
| modeq | 0.002 | 0.001 | 0.003 | |
| modlineq | 0.005 | 0.005 | 0.011 | |
| mut_type | 0.004 | 0.001 | 0.005 | |
| reexports | 0.244 | 0.014 | 0.296 | |
| seqranges | 0.878 | 0.013 | 1.029 | |
| slapply | 0.005 | 0.001 | 0.008 | |
| sortByChromAndStart | 0.142 | 0.002 | 0.171 | |
| str2chr | 0.001 | 0.002 | 0.003 | |
| str2dig | 0.000 | 0.002 | 0.003 | |
| translation | 1.083 | 0.016 | 1.268 | |