| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-04-29 11:40:51 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 1.5.0 (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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-04-29 06:24:47 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 06:28:46 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 239.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.5.0.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 ‘1.5.0’
* 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 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 ... NOTE
checkRd: (-1) mut_type.Rd:20: Lost braces; missing escapes or markup?
20 | number of hydrogen bonds (on DNA/RNA double helix): strong S={C,G} (three
| ^
checkRd: (-1) mut_type.Rd:21: Lost braces; missing escapes or markup?
21 | hydrogen bonds) and weak W={A,U} (two hydrogen bonds). According to the
| ^
checkRd: (-1) mut_type.Rd:22: Lost braces; missing escapes or markup?
22 | chemical type: purines R={A, G} and pyrimidines Y={C,U}. 3). According to
| ^
checkRd: (-1) mut_type.Rd:22: Lost braces; missing escapes or markup?
22 | chemical type: purines R={A, G} and pyrimidines Y={C,U}. 3). According to
| ^
checkRd: (-1) mut_type.Rd:23: Lost braces; missing escapes or markup?
23 | the presence of amino or keto groups on the base rings: amino M={C,A} and
| ^
checkRd: (-1) mut_type.Rd:24: Lost braces; missing escapes or markup?
24 | keto K={G,U}. So, each mutational event can be classified as according to
| ^
* 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
aminoacid_dist 6.264 1.318 6.950
automorphisms 4.934 1.094 5.324
* 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: 2 NOTEs
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 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 4.4.0 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
0.192 0.039 0.215
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 7 | SKIP 0 | PASS 31 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
25.156 2.831 27.644
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.595 | 0.004 | 0.600 | |
| AutomorphismList | 3.103 | 0.016 | 3.125 | |
| CodonSeq | 0.584 | 0.004 | 0.589 | |
| aa_mutmat | 0.021 | 0.000 | 0.021 | |
| aaindex2 | 0.007 | 0.000 | 0.007 | |
| aaindex3 | 0.005 | 0.000 | 0.005 | |
| aminoacid_dist | 6.264 | 1.318 | 6.950 | |
| as.AutomorphismList | 0.803 | 0.206 | 0.749 | |
| aut3D | 1.433 | 0.353 | 1.520 | |
| autZ125 | 2.946 | 0.851 | 2.760 | |
| autZ5 | 0.826 | 0.358 | 0.950 | |
| autZ64 | 1.860 | 0.376 | 1.997 | |
| autm | 0.074 | 0.008 | 0.081 | |
| automorphismByRanges | 0.164 | 0.016 | 0.180 | |
| automorphism_bycoef | 0.150 | 0.016 | 0.166 | |
| automorphisms | 4.934 | 1.094 | 5.324 | |
| base2codon | 0.092 | 0.012 | 0.104 | |
| base2int | 0.003 | 0.000 | 0.002 | |
| base_coord | 0.261 | 0.047 | 0.309 | |
| cdm_z64 | 0.03 | 0.00 | 0.03 | |
| codon_coord | 1.121 | 0.099 | 1.224 | |
| codon_dist | 0.385 | 0.000 | 0.385 | |
| codon_dist_matrix | 0.029 | 0.047 | 2.788 | |
| conserved_regions | 3.099 | 0.291 | 0.639 | |
| extract-methods | 0.636 | 0.020 | 0.656 | |
| getAutomorphisms | 0.269 | 0.000 | 0.269 | |
| get_coord | 0.693 | 0.104 | 0.798 | |
| get_mutscore | 0.146 | 0.000 | 0.146 | |
| matrices | 0.667 | 0.004 | 0.672 | |
| mod | 0.002 | 0.000 | 0.003 | |
| modeq | 0.001 | 0.000 | 0.001 | |
| modlineq | 0.003 | 0.000 | 0.003 | |
| mut_type | 0.000 | 0.003 | 0.002 | |
| reexports | 0.131 | 0.001 | 0.132 | |
| seqranges | 0.757 | 0.000 | 0.759 | |
| slapply | 0.003 | 0.000 | 0.003 | |
| sortByChromAndStart | 0.089 | 0.000 | 0.089 | |
| str2chr | 0.001 | 0.000 | 0.001 | |
| str2dig | 0.001 | 0.000 | 0.001 | |
| translation | 1.095 | 0.035 | 1.133 | |