| Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:43 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 | ||||
| Package 1794/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAmodR.ML 1.18.0 (landing page) Felix G.M. Ernst
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the RNAmodR.ML package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RNAmodR.ML |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.ML.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR.ML_1.18.0.tar.gz |
| StartedAt: 2024-05-07 00:25:44 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 00:28:28 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 164.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAmodR.ML.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.ML.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR.ML_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/RNAmodR.ML.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAmodR.ML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR.ML’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RNAmodR.ML’ 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 code 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'get_D_score'
* 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 ... NOTE
checkRd: (-1) RNAmodR.ML-example.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RNAmodR.ML-example.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/RNAmodR.ML.Rcheck/00check.log’
for details.
RNAmodR.ML.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAmodR.ML ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘RNAmodR.ML’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (RNAmodR.ML)
RNAmodR.ML.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(RNAmodR.ML)
Loading required package: RNAmodR
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'RNAmodR'
The following object is masked from 'package:testthat':
compare
>
> test_check("RNAmodR.ML")
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de593990a6_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de60774fae_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de6083cca8_2525'
Error in x$.self$finalize() : attempt to apply non-function
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de593990a6_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de60774fae_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de6083cca8_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de593990a6_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de593990a6_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de60774fae_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de60774fae_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de6083cca8_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/31de6083cca8_2525'
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 21 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 21 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
22.801 1.773 23.215
RNAmodR.ML.Rcheck/RNAmodR.ML-Ex.timings
| name | user | system | elapsed | |
| ModifierML-class | 0.003 | 0.000 | 0.004 | |
| ModifierMLModel-class | 0.002 | 0.000 | 0.003 | |
| ModifierMLranger-class | 0.002 | 0.000 | 0.002 | |
| RNAmodR.ML-example | 0.001 | 0.001 | 0.001 | |
| trainingData | 1.090 | 0.034 | 1.127 | |