| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:58 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (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 825/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.6.0 (landing page) Robersy Sanchez
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomAutomorphism_1.6.0.tar.gz |
| StartedAt: 2024-05-31 04:01:40 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 04:05:47 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 247.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomAutomorphism_1.6.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 4.598 0.993 5.077
automorphisms 4.554 0.824 4.818
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)
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: x86_64-pc-linux-gnu
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
0.162 0.028 0.178
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
20.225 1.867 21.830
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.404 | 0.020 | 0.425 | |
| AutomorphismList | 2.306 | 0.092 | 2.398 | |
| CodonMatrix | 0.157 | 0.020 | 0.177 | |
| CodonSeq | 0.346 | 0.012 | 0.358 | |
| GRangesMatrixSeq | 0.170 | 0.032 | 0.202 | |
| ListCodonMatrix | 0.218 | 0.000 | 0.218 | |
| MatrixSeq | 0.102 | 0.000 | 0.102 | |
| aa_phychem_index | 0.092 | 0.004 | 0.096 | |
| aaindex1 | 0.034 | 0.000 | 0.034 | |
| aaindex2 | 0.015 | 0.000 | 0.015 | |
| aaindex3 | 0.01 | 0.00 | 0.01 | |
| aln | 0.053 | 0.004 | 0.057 | |
| aminoacid_dist | 4.598 | 0.993 | 5.077 | |
| as.AutomorphismList | 0.583 | 0.107 | 0.550 | |
| aut3D | 1.337 | 0.325 | 1.445 | |
| autZ125 | 2.428 | 0.789 | 2.463 | |
| autZ5 | 1.003 | 0.261 | 1.099 | |
| autZ64 | 1.682 | 0.281 | 1.763 | |
| autby_coef | 0.283 | 0.016 | 0.299 | |
| autm | 0.055 | 0.000 | 0.055 | |
| autm_3d | 0.076 | 0.004 | 0.080 | |
| autm_z125 | 0.067 | 0.000 | 0.067 | |
| automorphismByRanges | 0.117 | 0.024 | 0.142 | |
| automorphism_bycoef | 0.109 | 0.003 | 0.113 | |
| automorphisms | 4.554 | 0.824 | 4.818 | |
| base2codon | 0.047 | 0.003 | 0.050 | |
| base2int | 0.007 | 0.000 | 0.007 | |
| base_methods | 0.383 | 0.032 | 0.415 | |
| brca1_aln | 0.057 | 0.008 | 0.064 | |
| brca1_aln2 | 0.063 | 0.004 | 0.066 | |
| brca1_autm | 0.409 | 0.008 | 0.416 | |
| cdm_z64 | 0.178 | 0.553 | 0.731 | |
| codon_coord | 0.85 | 0.16 | 1.01 | |
| codon_dist | 0.253 | 0.000 | 0.252 | |
| codon_dist_matrix | 0.050 | 0.029 | 2.049 | |
| codon_matrix | 2.323 | 0.329 | 0.652 | |
| conserved_regions | 0.389 | 0.009 | 0.398 | |
| covid_aln | 0.059 | 0.000 | 0.060 | |
| covid_autm | 0.066 | 0.000 | 0.066 | |
| cyc_aln | 0.083 | 0.000 | 0.083 | |
| cyc_autm | 0.107 | 0.003 | 0.112 | |
| dna_phyche | 0.002 | 0.004 | 0.006 | |
| dna_phychem | 0.001 | 0.002 | 0.003 | |
| extract-methods | 0.452 | 0.045 | 0.498 | |
| getAutomorphisms | 0.173 | 0.011 | 0.185 | |
| get_coord | 0.545 | 0.096 | 0.642 | |
| get_mutscore | 0.153 | 0.000 | 0.153 | |
| matrices | 0.441 | 0.003 | 0.446 | |
| mod | 0.000 | 0.002 | 0.002 | |
| modeq | 0.000 | 0.001 | 0.001 | |
| modlineq | 0.000 | 0.003 | 0.003 | |
| mut_type | 0.000 | 0.002 | 0.001 | |
| peptide_phychem_index | 0.101 | 0.009 | 0.110 | |
| reexports | 0.093 | 0.000 | 0.093 | |
| seqranges | 0.540 | 0.048 | 0.588 | |
| slapply | 0.002 | 0.000 | 0.002 | |
| sortByChromAndStart | 0.055 | 0.000 | 0.055 | |
| str2chr | 0.000 | 0.000 | 0.001 | |
| str2dig | 0.000 | 0.000 | 0.001 | |
| translation | 0.817 | 0.008 | 0.825 | |