Multiple platform build/check report for BioC 3.13 - CHECK results for glmSparseNet on tokay2

Package: glmSparseNet

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:glmSparseNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings glmSparseNet_1.10.0.tar.gz

StartedAt: 2021-10-14 23:52:43 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 23:58:36 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 353.3 seconds

RetCode: 0

Status: OK

CheckDir: glmSparseNet.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:glmSparseNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings glmSparseNet_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/glmSparseNet.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'glmSparseNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmSparseNet' 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
biomart.load 13.34   0.29   17.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
biomart.load 10.47   0.13   14.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/glmSparseNet_1.10.0.tar.gz && rm -rf glmSparseNet.buildbin-libdir && mkdir glmSparseNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=glmSparseNet.buildbin-libdir glmSparseNet_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL glmSparseNet_1.10.0.zip && rm glmSparseNet_1.10.0.tar.gz glmSparseNet_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 45  745k   45  337k    0     0  1016k      0 --:--:-- --:--:-- --:--:-- 1016k
100  745k  100  745k    0     0   611k      0  0:00:01  0:00:01 --:--:--  612k

install for i386

* installing *source* package 'glmSparseNet' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'glmSparseNet'
    finding HTML links ... done
    biomart.load                            html  
    buildLambda                             html  
    buildStringNetwork                      html  
    calculate.combined.score                html  
    curl.workaround                         html  
    cv.glmDegree                            html  
    cv.glmHub                               html  
    cv.glmOrphan                            html  
    cv.glmSparseNet                         html  
    degreeCor                               html  
    degreeCov                               html  
    degreeSparsebn                          html  
    dot-calcPenalty                         html  
    dot-degreeGeneric                       html  
    dot-glmSparseNetPrivate                 html  
    dot-networkGenericParallel              html  
    dot-networkWorker                       html  
    downloadFileLocal                       html  
    ensemblGeneNames                        html  
    geneNames                               html  
    glmDegree                               html  
    glmHub                                  html  
    glmOrphan                               html  
    glmSparseNet                            html  
    hallmarks                               html  
    heuristicScale                          html  
    hubHeuristic                            html  
    networkCorParallel                      html  
    networkCovParallel                      html  
    networkOptions                          html  
    orphanHeuristic                         html  
    protein2EnsemblGeneNames                html  
    separate2GroupsCox                      html  
    string.network.700.cache                html  
    stringDBhomoSapiens                     html  
** 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

install for x64

* installing *source* package 'glmSparseNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'glmSparseNet' as glmSparseNet_1.10.0.zip
* DONE (glmSparseNet)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'glmSparseNet' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 4.1-2
> 
> test_check("glmSparseNet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
  26.51    1.42   33.40


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 4.1-2
> 
> test_check("glmSparseNet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
  25.62    0.93   47.71

name	user	system	elapsed
biomart.load	13.34	0.29	17.12
buildLambda	0	0	0
buildStringNetwork	0	0	0
curl.workaround	0	0	0
cv.glmDegree	0.14	0.00	0.14
cv.glmHub	0.05	0.00	0.05
cv.glmOrphan	0.04	0.00	0.04
cv.glmSparseNet	2.60	0.49	3.39
degreeCor	0.01	0.01	0.03
degreeCov	0	0	0
degreeSparsebn	1.25	0.00	1.40
dot-calcPenalty	0.72	0.00	0.71
downloadFileLocal	0.00	0.00	0.57
ensemblGeneNames	0	0	0
geneNames	0.86	0.02	1.11
glmDegree	0.02	0.00	0.01
glmHub	0	0	0
glmOrphan	0.01	0.00	0.02
glmSparseNet	1.50	0.06	1.56
hallmarks	0	0	0
heuristicScale	0	0	0
hubHeuristic	0	0	0
networkCorParallel	0.02	0.02	0.03
networkCovParallel	0.01	0.00	0.02
networkOptions	0	0	0
orphanHeuristic	0	0	0
protein2EnsemblGeneNames	0.74	0.01	0.93
separate2GroupsCox	2.61	0.11	2.72
string.network.700.cache	0.70	0.14	0.85
stringDBhomoSapiens	0	0	0

name	user	system	elapsed
biomart.load	10.47	0.13	14.08
buildLambda	0	0	0
buildStringNetwork	0	0	0
curl.workaround	0	0	0
cv.glmDegree	0.15	0.00	0.15
cv.glmHub	0.05	0.00	0.05
cv.glmOrphan	0.05	0.00	0.05
cv.glmSparseNet	2.85	0.09	2.95
degreeCor	0.04	0.00	0.03
degreeCov	0	0	0
degreeSparsebn	1.32	0.00	4.28
dot-calcPenalty	0.74	0.02	0.75
downloadFileLocal	0.00	0.00	0.31
ensemblGeneNames	0	0	0
geneNames	0.83	0.00	0.97
glmDegree	0	0	0
glmHub	0.02	0.00	0.02
glmOrphan	0	0	0
glmSparseNet	1.51	0.00	1.51
hallmarks	0	0	0
heuristicScale	0	0	0
hubHeuristic	0	0	0
networkCorParallel	0.02	0.02	0.04
networkCovParallel	0	0	0
networkOptions	0	0	0
orphanHeuristic	0	0	0
protein2EnsemblGeneNames	0.79	0.01	0.94
separate2GroupsCox	2.53	0.13	2.66
string.network.700.cache	0.90	0.09	1.00
stringDBhomoSapiens	0	0	0

CHECK results for glmSparseNet on tokay2

Summary

Command output

Installation output

Tests output

Example timings