| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1384/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NewWave 1.10.0 (landing page) Federico Agostinis
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the NewWave 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: NewWave |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NewWave.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NewWave_1.10.0.tar.gz |
| StartedAt: 2023-10-18 11:28:06 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 11:34:10 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 363.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NewWave.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NewWave.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NewWave_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NewWave.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NewWave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NewWave’ version ‘1.10.0’
* 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 ‘NewWave’ 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 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: OK
NewWave.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NewWave ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘NewWave’ ... ** using staged installation ** R ** 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 (NewWave)
NewWave.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(NewWave)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> Sys.setenv("R_TESTS" = "")
> test_check("NewWave")
Time of setup
user system elapsed
0.013 0.010 0.618
Time of initialization
user system elapsed
0.003 0.001 0.080
Time of dispersion optimization
user system elapsed
0.001 0.000 0.001
Time of right optimization
user system elapsed
0.001 0.000 0.204
Time of left optimization
user system elapsed
0.000 0.000 0.026
Time of dispersion optimization
user system elapsed
0.002 0.001 0.002
Time of right optimization
user system elapsed
0.000 0.000 0.023
Time of left optimization
user system elapsed
0.001 0.000 0.021
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 53 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_design.R:5:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 53 ]
>
> proc.time()
user system elapsed
11.630 0.955 73.420
NewWave.Rcheck/NewWave-Ex.timings
| name | user | system | elapsed | |
| newAIC | 0.006 | 0.001 | 0.011 | |
| newAlpha | 0.001 | 0.000 | 0.002 | |
| newBIC | 0.022 | 0.001 | 0.037 | |
| newBeta | 0.001 | 0.000 | 0.002 | |
| newEpsilon_W | 0.001 | 0.000 | 0.001 | |
| newEpsilon_alpha | 0.002 | 0.000 | 0.003 | |
| newEpsilon_beta | 0.002 | 0.000 | 0.005 | |
| newEpsilon_gamma | 0.001 | 0.000 | 0.002 | |
| newEpsilon_zeta | 0.002 | 0.000 | 0.003 | |
| newFit | 0.767 | 0.051 | 4.403 | |
| newGamma | 0.002 | 0.000 | 0.006 | |
| newLogMu | 0.002 | 0.001 | 0.004 | |
| newMu | 0.002 | 0.001 | 0.005 | |
| newPhi | 0.002 | 0.001 | 0.005 | |
| newSim | 0.003 | 0.004 | 0.010 | |
| newTheta | 0.001 | 0.000 | 0.001 | |
| newV | 0.002 | 0.000 | 0.002 | |
| newW | 0.002 | 0.000 | 0.002 | |
| newWave | 0.402 | 0.027 | 2.315 | |
| newX | 0.001 | 0.000 | 0.001 | |
| newZeta | 0.002 | 0.000 | 0.003 | |
| newloglik | 0.002 | 0.001 | 0.003 | |
| newmodel | 0.001 | 0.001 | 0.002 | |
| newpenalty | 0.002 | 0.000 | 0.003 | |
| numberFactors | 0.002 | 0.000 | 0.006 | |
| numberFeatures | 0.003 | 0.000 | 0.004 | |
| numberParams | 0.002 | 0.001 | 0.007 | |
| numberSamples | 0.003 | 0.001 | 0.006 | |