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This page was generated on 2023-10-16 11:35:24 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 848/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
glmSparseNet 1.18.0  (landing page)
André Veríssimo
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/glmSparseNet
git_branch: RELEASE_3_17
git_last_commit: fa0321e
git_last_commit_date: 2023-04-25 11:04:37 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for glmSparseNet on nebbiolo1


To the developers/maintainers of the glmSparseNet package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/glmSparseNet.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: glmSparseNet
Version: 1.18.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings glmSparseNet_1.18.0.tar.gz
StartedAt: 2023-10-15 21:43:23 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 21:52:01 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 517.6 seconds
RetCode: 0
Status:   OK  
CheckDir: glmSparseNet.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings glmSparseNet_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/glmSparseNet.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 3.314  0.224   6.749
hallmarks    0.024  0.004   5.953
* 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 ...
  ‘example_brca_logistic.Rmd’ using ‘UTF-8’... OK
  ‘example_brca_protein-protein-interactions_survival.Rmd’ using ‘UTF-8’... OK
  ‘example_brca_survival.Rmd’ using ‘UTF-8’... OK
  ‘example_prad_survival.Rmd’ using ‘UTF-8’... OK
  ‘example_skcm_survival.Rmd’ using ‘UTF-8’... OK
  ‘separate2GroupsCox.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

glmSparseNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL glmSparseNet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)

Tests output

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: x86_64-pc-linux-gnu (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 4.1-8
> 
> test_check("glmSparseNet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 84 ]
> 
> proc.time()
   user  system elapsed 
 18.036   6.014  24.003 

Example timings

glmSparseNet.Rcheck/glmSparseNet-Ex.timings

nameusersystemelapsed
balanced.cv.folds0.0060.0010.007
base.dir0.0000.0000.001
biomart.load3.3140.2246.749
build.function.digest000
buildLambda0.0000.0040.004
buildStringNetwork000
cache.compression0.0010.0000.000
calculate.result0.0010.0000.001
create.directory.for.cache0.0000.0010.000
curl.workaround000
cv.glmDegree0.1180.0260.144
cv.glmHub0.0380.0000.038
cv.glmOrphan0.0340.0040.038
cv.glmSparseNet1.9510.1842.135
degreeCor0.0140.0030.016
degreeCov0.0070.0000.007
digest.cache0.0010.0000.001
dot-calcPenalty0.2250.0310.256
downloadFileLocal0.0850.0060.516
ensemblGeneNames0.3010.0320.462
geneNames0.2610.0160.410
glmDegree0.0040.0030.007
glmHub0.0030.0030.006
glmOrphan0.0060.0000.006
glmSparseNet1.0070.0481.055
hallmarks0.0240.0045.953
heuristicScale0.0010.0000.001
hubHeuristic000
my.colors0.0000.0010.000
my.symbols0.0000.0010.000
networkCorParallel0.0260.0010.027
networkCovParallel0.0080.0000.008
networkOptions0.0010.0000.001
orphanHeuristic000
protein2EnsemblGeneNames0.3140.0330.480
run.cache-function-method0.0010.0040.005
run.cache0.0010.0020.004
save.run.cache000
separate2GroupsCox2.3270.2162.544
show.message000
stringDBhomoSapiens000
write.readme0.0000.0010.000