Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:31 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 765/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomAutomorphism 1.1.2 (landing page) Robersy Sanchez
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
Package: GenomAutomorphism |
Version: 1.1.2 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.1.2.tar.gz |
StartedAt: 2022-12-29 00:03:42 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 00:09:34 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 352.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomAutomorphism.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomAutomorphism.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 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 automorphisms 3.98 0.25 31.26 aminoacid_dist 2.74 0.14 46.61 autZ64 1.50 0.23 10.57 aut3D 1.29 0.27 10.15 autZ125 1.19 0.23 11.12 autZ5 1.00 0.16 9.75 codon_dist_matrix 0.05 0.01 5.35 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomAutomorphism.Rcheck/00check.log' for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library 'F:/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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 0.17 0.03 0.18
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 17.85 3.79 73.54
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
name | user | system | elapsed | |
AutomorphismByCoef | 0.33 | 0.01 | 0.34 | |
AutomorphismList | 1.98 | 0.28 | 2.27 | |
CodonSeq | 0.45 | 0.41 | 0.86 | |
aa_mutmat | 0.00 | 0.02 | 0.02 | |
aaindex2 | 0.01 | 0.00 | 0.01 | |
aaindex3 | 0 | 0 | 0 | |
aminoacid_dist | 2.74 | 0.14 | 46.61 | |
as.AutomorphismList | 0.40 | 0.01 | 0.43 | |
aut3D | 1.29 | 0.27 | 10.15 | |
autZ125 | 1.19 | 0.23 | 11.12 | |
autZ5 | 1.00 | 0.16 | 9.75 | |
autZ64 | 1.50 | 0.23 | 10.57 | |
autm | 0.11 | 0.24 | 0.34 | |
automorphismByRanges | 0.15 | 0.25 | 0.41 | |
automorphism_bycoef | 0.21 | 0.16 | 0.36 | |
automorphisms | 3.98 | 0.25 | 31.26 | |
base2codon | 0.19 | 0.28 | 0.47 | |
base2int | 0 | 0 | 0 | |
base_coord | 0.27 | 0.18 | 0.45 | |
cdm_z64 | 0.01 | 0.00 | 0.02 | |
codon_coord | 0.83 | 0.19 | 1.01 | |
codon_dist | 0.31 | 0.49 | 0.80 | |
codon_dist_matrix | 0.05 | 0.01 | 5.35 | |
conserved_regions | 0.51 | 0.62 | 1.14 | |
extract-methods | 0.44 | 0.00 | 0.44 | |
getAutomorphisms | 0.25 | 0.24 | 0.48 | |
get_coord | 0.50 | 0.23 | 0.74 | |
get_mutscore | 0.10 | 0.00 | 0.09 | |
matrices | 0.51 | 0.24 | 0.75 | |
modeq | 0 | 0 | 0 | |
mut_type | 0.02 | 0.00 | 0.02 | |
reexports | 0.28 | 0.54 | 0.83 | |
seqranges | 0.67 | 0.24 | 0.90 | |
slapply | 0 | 0 | 0 | |
sortByChromAndStart | 0.06 | 0.00 | 0.06 | |
str2chr | 0 | 0 | 0 | |
str2dig | 0 | 0 | 0 | |
translation | 0.92 | 0.33 | 1.25 | |