| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-27 02:34:34 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 767/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.1.2 (landing page) Robersy Sanchez
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: GenomAutomorphism |
| Version: 1.1.2 |
| 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/library --timings GenomAutomorphism_1.1.2.tar.gz |
| StartedAt: 2023-02-24 11:27:12 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 11:32:37 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 325.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 1 |
##############################################################################
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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/library --timings GenomAutomorphism_1.1.2.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomAutomorphism.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.1.2’
* 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 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 'names<-' and siglist 'AutomorphismList'
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 5.843 1.128 6.313
automorphisms 4.633 1.191 5.077
* 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 WARNING
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/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.207 0.023 0.217
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 29 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
24.953 2.533 27.094
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.588 | 0.016 | 0.604 | |
| AutomorphismList | 3.144 | 0.088 | 3.232 | |
| CodonSeq | 0.533 | 0.008 | 0.542 | |
| aa_mutmat | 0.022 | 0.000 | 0.023 | |
| aaindex2 | 0.008 | 0.000 | 0.008 | |
| aaindex3 | 0.001 | 0.004 | 0.005 | |
| aminoacid_dist | 5.843 | 1.128 | 6.313 | |
| as.AutomorphismList | 0.806 | 0.220 | 0.760 | |
| aut3D | 1.320 | 0.385 | 1.445 | |
| autZ125 | 2.764 | 0.957 | 2.708 | |
| autZ5 | 0.805 | 0.317 | 0.891 | |
| autZ64 | 1.688 | 0.395 | 1.835 | |
| autm | 0.068 | 0.008 | 0.076 | |
| automorphismByRanges | 0.156 | 0.008 | 0.164 | |
| automorphism_bycoef | 0.142 | 0.020 | 0.162 | |
| automorphisms | 4.633 | 1.191 | 5.077 | |
| base2codon | 0.084 | 0.007 | 0.090 | |
| base2int | 0.001 | 0.000 | 0.003 | |
| base_coord | 0.230 | 0.032 | 0.262 | |
| cdm_z64 | 0.03 | 0.00 | 0.03 | |
| codon_coord | 1.091 | 0.100 | 1.191 | |
| codon_dist | 0.379 | 0.000 | 0.380 | |
| codon_dist_matrix | 0.044 | 0.040 | 2.756 | |
| conserved_regions | 3.015 | 0.312 | 0.608 | |
| extract-methods | 0.622 | 0.044 | 0.666 | |
| getAutomorphisms | 0.235 | 0.040 | 0.275 | |
| get_coord | 0.656 | 0.116 | 0.772 | |
| get_mutscore | 0.133 | 0.000 | 0.133 | |
| matrices | 0.596 | 0.004 | 0.600 | |
| modeq | 0.001 | 0.000 | 0.002 | |
| mut_type | 0.003 | 0.000 | 0.003 | |
| reexports | 0.120 | 0.004 | 0.124 | |
| seqranges | 0.659 | 0.000 | 0.659 | |
| slapply | 0.003 | 0.000 | 0.003 | |
| sortByChromAndStart | 0.081 | 0.000 | 0.081 | |
| str2chr | 0 | 0 | 0 | |
| str2dig | 0 | 0 | 0 | |
| translation | 0.954 | 0.002 | 0.955 | |