| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:53 -0400 (Thu, 09 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" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GenomAutomorphism |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GenomAutomorphism_1.6.0.tar.gz |
| StartedAt: 2024-05-09 07:42:18 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 07:46:23 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 245.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GenomAutomorphism_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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
automorphisms 6.162 1.291 6.690
aminoacid_dist 6.100 1.137 6.591
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.203 0.028 0.214
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
27.591 2.303 29.571
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.599 | 0.000 | 0.600 | |
| AutomorphismList | 3.057 | 0.559 | 3.622 | |
| CodonMatrix | 0.285 | 0.076 | 0.361 | |
| CodonSeq | 0.528 | 0.036 | 0.565 | |
| GRangesMatrixSeq | 0.240 | 0.012 | 0.253 | |
| ListCodonMatrix | 0.335 | 0.024 | 0.359 | |
| MatrixSeq | 0.121 | 0.008 | 0.129 | |
| aa_phychem_index | 0.089 | 0.008 | 0.097 | |
| aaindex1 | 0.032 | 0.004 | 0.036 | |
| aaindex2 | 0.015 | 0.000 | 0.015 | |
| aaindex3 | 0.01 | 0.00 | 0.01 | |
| aln | 0.067 | 0.004 | 0.072 | |
| aminoacid_dist | 6.100 | 1.137 | 6.591 | |
| as.AutomorphismList | 0.795 | 0.205 | 0.721 | |
| aut3D | 1.700 | 0.393 | 1.835 | |
| autZ125 | 3.127 | 0.911 | 3.082 | |
| autZ5 | 1.190 | 0.335 | 1.296 | |
| autZ64 | 2.197 | 0.362 | 2.313 | |
| autby_coef | 0.397 | 0.008 | 0.406 | |
| autm | 0.073 | 0.004 | 0.078 | |
| autm_3d | 0.110 | 0.004 | 0.114 | |
| autm_z125 | 0.095 | 0.012 | 0.107 | |
| automorphismByRanges | 0.156 | 0.024 | 0.181 | |
| automorphism_bycoef | 0.141 | 0.028 | 0.169 | |
| automorphisms | 6.162 | 1.291 | 6.690 | |
| base2codon | 0.121 | 0.004 | 0.124 | |
| base2int | 0.015 | 0.000 | 0.016 | |
| base_methods | 0.632 | 0.088 | 0.721 | |
| brca1_aln | 0.079 | 0.007 | 0.087 | |
| brca1_aln2 | 0.081 | 0.000 | 0.081 | |
| brca1_autm | 0.518 | 0.016 | 0.535 | |
| cdm_z64 | 0.131 | 0.079 | 0.211 | |
| codon_coord | 1.095 | 0.212 | 1.309 | |
| codon_dist | 0.420 | 0.004 | 0.424 | |
| codon_dist_matrix | 0.057 | 0.020 | 2.932 | |
| codon_matrix | 3.492 | 0.360 | 0.958 | |
| conserved_regions | 0.575 | 0.044 | 0.620 | |
| covid_aln | 0.082 | 0.000 | 0.083 | |
| covid_autm | 0.091 | 0.000 | 0.091 | |
| cyc_aln | 0.121 | 0.000 | 0.121 | |
| cyc_autm | 0.186 | 0.000 | 0.187 | |
| dna_phyche | 0.004 | 0.004 | 0.008 | |
| dna_phychem | 0.003 | 0.000 | 0.003 | |
| extract-methods | 0.615 | 0.016 | 0.632 | |
| getAutomorphisms | 0.243 | 0.012 | 0.256 | |
| get_coord | 0.657 | 0.147 | 0.807 | |
| get_mutscore | 0.194 | 0.004 | 0.198 | |
| matrices | 0.610 | 0.000 | 0.611 | |
| mod | 0.002 | 0.000 | 0.002 | |
| modeq | 0.001 | 0.000 | 0.001 | |
| modlineq | 0.003 | 0.000 | 0.002 | |
| mut_type | 0.002 | 0.000 | 0.002 | |
| peptide_phychem_index | 0.125 | 0.003 | 0.129 | |
| reexports | 0.116 | 0.000 | 0.117 | |
| seqranges | 0.679 | 0.036 | 0.715 | |
| slapply | 0.003 | 0.000 | 0.002 | |
| sortByChromAndStart | 0.083 | 0.000 | 0.083 | |
| str2chr | 0 | 0 | 0 | |
| str2dig | 0.000 | 0.000 | 0.001 | |
| translation | 0.962 | 0.012 | 0.974 | |