| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:36 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 791/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.1.3 (landing page) Robersy Sanchez
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: GenomAutomorphism |
| Version: 1.1.3 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenomAutomorphism_1.1.3.tar.gz |
| StartedAt: 2023-04-12 06:28:02 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 06:32:19 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 256.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenomAutomorphism_1.1.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomAutomorphism.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.1.3’
* 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 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 ... 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 5.254 0.912 5.476
automorphisms 4.801 0.834 4.947
* 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 ...
‘GenomAutomorphism.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 0.025 0.236
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
21.401 1.758 22.893
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.425 | 0.004 | 0.429 | |
| AutomorphismList | 2.458 | 0.096 | 2.554 | |
| CodonSeq | 0.37 | 0.00 | 0.37 | |
| aa_mutmat | 0.014 | 0.007 | 0.022 | |
| aaindex2 | 0.003 | 0.004 | 0.008 | |
| aaindex3 | 0.005 | 0.000 | 0.005 | |
| aminoacid_dist | 5.254 | 0.912 | 5.476 | |
| as.AutomorphismList | 0.584 | 0.130 | 0.544 | |
| aut3D | 1.462 | 0.315 | 1.522 | |
| autZ125 | 3.049 | 0.930 | 2.897 | |
| autZ5 | 0.796 | 0.232 | 0.862 | |
| autZ64 | 1.986 | 0.272 | 2.008 | |
| autm | 0.057 | 0.004 | 0.061 | |
| automorphismByRanges | 0.121 | 0.004 | 0.124 | |
| automorphism_bycoef | 0.109 | 0.004 | 0.113 | |
| automorphisms | 4.801 | 0.834 | 4.947 | |
| base2codon | 0.077 | 0.000 | 0.077 | |
| base2int | 0.001 | 0.001 | 0.001 | |
| base_coord | 0.173 | 0.015 | 0.187 | |
| cdm_z64 | 0.018 | 0.004 | 0.023 | |
| codon_coord | 1.195 | 0.044 | 1.239 | |
| codon_dist | 0.324 | 0.000 | 0.324 | |
| codon_dist_matrix | 0.057 | 0.028 | 2.134 | |
| conserved_regions | 2.344 | 0.260 | 0.518 | |
| extract-methods | 0.461 | 0.012 | 0.472 | |
| getAutomorphisms | 0.196 | 0.008 | 0.203 | |
| get_coord | 0.639 | 0.044 | 0.683 | |
| get_mutscore | 0.104 | 0.000 | 0.104 | |
| matrices | 0.621 | 0.004 | 0.625 | |
| mod | 0.001 | 0.000 | 0.002 | |
| modeq | 0.001 | 0.000 | 0.001 | |
| modlineq | 0.003 | 0.000 | 0.003 | |
| mut_type | 0.002 | 0.000 | 0.002 | |
| reexports | 0.097 | 0.008 | 0.105 | |
| seqranges | 0.612 | 0.024 | 0.635 | |
| slapply | 0.003 | 0.000 | 0.003 | |
| sortByChromAndStart | 0.061 | 0.000 | 0.061 | |
| str2chr | 0.001 | 0.000 | 0.001 | |
| str2dig | 0 | 0 | 0 | |
| translation | 0.867 | 0.000 | 0.867 | |