| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-06-03 14:37:15 -0400 (Sat, 03 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" | 4623 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" | 4374 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" | 4332 |
| 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 798/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.2.0 (landing page) Robersy Sanchez
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomAutomorphism |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2023-06-03 02:37:14 -0400 (Sat, 03 Jun 2023) |
| EndedAt: 2023-06-03 02:43:52 -0400 (Sat, 03 Jun 2023) |
| EllapsedTime: 397.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
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### 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_1.2.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GenomAutomorphism.Rcheck'
* using R version 4.3.0 RC (2023-04-13 r84269 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomAutomorphism/DESCRIPTION' ... OK
* this is package 'GenomAutomorphism' version '1.2.0'
* 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 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 ... 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 4.66 0.44 35.25
aminoacid_dist 3.31 0.11 52.78
autZ64 1.75 0.27 10.60
aut3D 1.50 0.26 11.21
autZ125 1.42 0.30 10.89
autZ5 0.97 0.33 10.37
codon_dist_matrix 0.06 0.00 6.22
* 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 NOTE
See
'F:/biocbuild/bbs-3.17-bioc/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 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 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow"
Copyright (C) 2023 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
0.18 0.03 0.23
GenomAutomorphism.Rcheck/tests/testthat.Rout
R version 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow"
Copyright (C) 2023 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 31 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
21.34 4.71 82.37
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.36 | 0.00 | 0.36 | |
| AutomorphismList | 2.02 | 0.28 | 2.35 | |
| CodonSeq | 0.50 | 0.60 | 1.11 | |
| aa_mutmat | 0.02 | 0.00 | 0.03 | |
| aaindex2 | 0.01 | 0.00 | 0.01 | |
| aaindex3 | 0.02 | 0.00 | 0.02 | |
| aminoacid_dist | 3.31 | 0.11 | 52.78 | |
| as.AutomorphismList | 0.42 | 0.03 | 0.45 | |
| aut3D | 1.50 | 0.26 | 11.21 | |
| autZ125 | 1.42 | 0.30 | 10.89 | |
| autZ5 | 0.97 | 0.33 | 10.37 | |
| autZ64 | 1.75 | 0.27 | 10.60 | |
| autm | 0.09 | 0.28 | 0.39 | |
| automorphismByRanges | 0.17 | 0.25 | 0.42 | |
| automorphism_bycoef | 0.17 | 0.26 | 0.44 | |
| automorphisms | 4.66 | 0.44 | 35.25 | |
| base2codon | 0.20 | 0.28 | 0.49 | |
| base2int | 0.00 | 0.02 | 0.01 | |
| base_coord | 0.25 | 0.23 | 0.49 | |
| cdm_z64 | 0.02 | 0.00 | 0.01 | |
| codon_coord | 0.92 | 0.31 | 1.23 | |
| codon_dist | 0.41 | 0.47 | 0.88 | |
| codon_dist_matrix | 0.06 | 0.00 | 6.22 | |
| conserved_regions | 0.63 | 0.69 | 1.33 | |
| extract-methods | 0.35 | 0.00 | 0.36 | |
| getAutomorphisms | 0.22 | 0.26 | 0.48 | |
| get_coord | 0.60 | 0.25 | 0.85 | |
| get_mutscore | 0.09 | 0.02 | 0.11 | |
| matrices | 0.53 | 0.29 | 0.82 | |
| mod | 0 | 0 | 0 | |
| modeq | 0 | 0 | 0 | |
| modlineq | 0 | 0 | 0 | |
| mut_type | 0 | 0 | 0 | |
| reexports | 0.24 | 0.50 | 0.74 | |
| seqranges | 0.64 | 0.25 | 0.89 | |
| slapply | 0 | 0 | 0 | |
| sortByChromAndStart | 0.08 | 0.00 | 0.08 | |
| str2chr | 0.01 | 0.00 | 0.01 | |
| str2dig | 0 | 0 | 0 | |
| translation | 1.11 | 0.47 | 1.58 | |