| Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-22 11:05:10 -0400 (Wed, 22 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4508 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4293 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4290 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 783/2189 | 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 |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | 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: 2023-03-21 20:42:43 -0400 (Tue, 21 Mar 2023) |
| EndedAt: 2023-03-21 20:46:57 -0400 (Tue, 21 Mar 2023) |
| EllapsedTime: 253.8 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) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 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
automorphisms 4.955 0.995 5.336
aminoacid_dist 4.887 0.815 5.187
* 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) (2023-03-16 r83996) -- "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
0.146 0.031 0.167
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-16 r83996) -- "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
19.743 1.855 21.437
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.409 | 0.012 | 0.421 | |
| AutomorphismList | 2.296 | 0.088 | 2.384 | |
| CodonSeq | 0.358 | 0.016 | 0.374 | |
| aa_mutmat | 0.024 | 0.000 | 0.024 | |
| aaindex2 | 0.004 | 0.004 | 0.008 | |
| aaindex3 | 0.006 | 0.000 | 0.005 | |
| aminoacid_dist | 4.887 | 0.815 | 5.187 | |
| as.AutomorphismList | 0.597 | 0.144 | 0.526 | |
| aut3D | 1.256 | 0.383 | 1.428 | |
| autZ125 | 2.630 | 0.848 | 2.545 | |
| autZ5 | 0.851 | 0.287 | 0.936 | |
| autZ64 | 1.985 | 0.344 | 2.064 | |
| autm | 0.060 | 0.004 | 0.064 | |
| automorphismByRanges | 0.139 | 0.004 | 0.143 | |
| automorphism_bycoef | 0.137 | 0.004 | 0.142 | |
| automorphisms | 4.955 | 0.995 | 5.336 | |
| base2codon | 0.061 | 0.004 | 0.065 | |
| base2int | 0.002 | 0.000 | 0.002 | |
| base_coord | 0.172 | 0.020 | 0.192 | |
| cdm_z64 | 0.023 | 0.000 | 0.024 | |
| codon_coord | 1.127 | 0.115 | 1.242 | |
| codon_dist | 0.295 | 0.020 | 0.315 | |
| codon_dist_matrix | 0.040 | 0.032 | 2.070 | |
| conserved_regions | 2.210 | 0.288 | 0.460 | |
| extract-methods | 0.458 | 0.040 | 0.498 | |
| getAutomorphisms | 0.192 | 0.020 | 0.212 | |
| get_coord | 0.716 | 0.072 | 0.788 | |
| get_mutscore | 0.102 | 0.000 | 0.102 | |
| matrices | 0.606 | 0.008 | 0.614 | |
| mod | 0.002 | 0.000 | 0.002 | |
| modeq | 0.001 | 0.000 | 0.001 | |
| modlineq | 0.000 | 0.003 | 0.003 | |
| mut_type | 0.002 | 0.000 | 0.002 | |
| reexports | 0.097 | 0.000 | 0.097 | |
| seqranges | 0.655 | 0.000 | 0.655 | |
| slapply | 0.003 | 0.000 | 0.003 | |
| sortByChromAndStart | 0.058 | 0.000 | 0.058 | |
| str2chr | 0.001 | 0.000 | 0.001 | |
| str2dig | 0.000 | 0.000 | 0.001 | |
| translation | 0.836 | 0.003 | 0.839 | |