| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:03 -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 848/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| glmSparseNet 1.18.0 (landing page) André Veríssimo
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the glmSparseNet 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: glmSparseNet |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings glmSparseNet_1.18.0.tar.gz |
| StartedAt: 2023-10-17 22:43:02 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 22:49:10 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 367.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: glmSparseNet.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings glmSparseNet_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/glmSparseNet.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 ‘glmSparseNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmSparseNet’ 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 ‘glmSparseNet’ 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 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
biomart.load 3.92 0.276 14.868
* 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
glmSparseNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL glmSparseNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘glmSparseNet’ ... ** 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 (glmSparseNet)
glmSparseNet.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(glmSparseNet)
Loading required package: Matrix
Loading required package: MultiAssayExperiment
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 objects are masked from 'package:Matrix':
expand, unname
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
Loading required package: glmnet
Loaded glmnet 4.1-7
>
> test_check("glmSparseNet")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 82 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-run_cache.R:57:1', 'test-run_cache.R:80:1'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 82 ]
>
> proc.time()
user system elapsed
23.284 7.134 48.755
glmSparseNet.Rcheck/glmSparseNet-Ex.timings
| name | user | system | elapsed | |
| balanced.cv.folds | 0.005 | 0.002 | 0.011 | |
| base.dir | 0.001 | 0.000 | 0.001 | |
| biomart.load | 3.920 | 0.276 | 14.868 | |
| build.function.digest | 0.001 | 0.001 | 0.000 | |
| buildLambda | 0.002 | 0.002 | 0.006 | |
| buildStringNetwork | 0.000 | 0.000 | 0.001 | |
| cache.compression | 0 | 0 | 0 | |
| calculate.result | 0.001 | 0.001 | 0.002 | |
| create.directory.for.cache | 0.001 | 0.001 | 0.001 | |
| curl.workaround | 0 | 0 | 0 | |
| cv.glmDegree | 0.173 | 0.008 | 0.249 | |
| cv.glmHub | 0.637 | 0.009 | 0.853 | |
| cv.glmOrphan | 0.042 | 0.001 | 0.060 | |
| cv.glmSparseNet | 2.713 | 0.077 | 3.857 | |
| degreeCor | 0.018 | 0.007 | 0.034 | |
| degreeCov | 0.004 | 0.002 | 0.009 | |
| digest.cache | 0.001 | 0.000 | 0.000 | |
| dot-calcPenalty | 0.274 | 0.019 | 0.445 | |
| downloadFileLocal | 0.022 | 0.027 | 0.350 | |
| ensemblGeneNames | 0.401 | 0.031 | 0.803 | |
| geneNames | 0.383 | 0.029 | 0.755 | |
| glmDegree | 0.007 | 0.002 | 0.013 | |
| glmHub | 0.006 | 0.002 | 0.013 | |
| glmOrphan | 0.006 | 0.002 | 0.013 | |
| glmSparseNet | 1.381 | 0.028 | 2.156 | |
| hallmarks | 0.112 | 0.170 | 3.262 | |
| heuristicScale | 0 | 0 | 0 | |
| hubHeuristic | 0 | 0 | 0 | |
| my.colors | 0 | 0 | 0 | |
| my.symbols | 0.000 | 0.001 | 0.000 | |
| networkCorParallel | 0.031 | 0.008 | 0.058 | |
| networkCovParallel | 0.008 | 0.002 | 0.015 | |
| networkOptions | 0 | 0 | 0 | |
| orphanHeuristic | 0.001 | 0.000 | 0.000 | |
| protein2EnsemblGeneNames | 0.384 | 0.028 | 0.759 | |
| run.cache-function-method | 0.006 | 0.005 | 0.016 | |
| run.cache | 0.005 | 0.002 | 0.011 | |
| save.run.cache | 0.000 | 0.001 | 0.002 | |
| separate2GroupsCox | 3.010 | 0.083 | 4.708 | |
| show.message | 0 | 0 | 0 | |
| stringDBhomoSapiens | 0 | 0 | 0 | |
| write.readme | 0 | 0 | 0 | |