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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/library --timings glmSparseNet_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/glmSparseNet.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmSparseNet’ version ‘1.17.0’
* 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 ... ERROR
Running examples in ‘glmSparseNet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biomart.load
> ### Title: Common call to biomaRt to avoid repetitive code
> ### Aliases: biomart.load
> 
> ### ** Examples
> 
> glmSparseNet:::biomart.load(
+     attributes = c("external_gene_name","ensembl_gene_id"), 
+     filters = "external_gene_name", 
+     values = c('MOB1A','RFLNB', 'SPIC', 'TP53'),
+     use.cache = TRUE,
+     verbose = FALSE
+ )
Warning in curl.workaround({ :
  There was an problem, calling the function with ssl_verifypeer to FALSE

	 error: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10001 milliseconds with 0 bytes received
Warning in force(expr) : restarting interrupted promise evaluation
* Hostname www.ensembl.org was found in DNS cache
*   Trying 193.62.193.83:443...
* Connected to www.ensembl.org (193.62.193.83) port 443 (#1)
* found 374 certificates in /etc/ssl/certs
* GnuTLS ciphers: NORMAL:-ARCFOUR-128:-CTYPE-ALL:+CTYPE-X509:-VERS-SSL3.0
* ALPN, offering h2
* ALPN, offering http/1.1
* SSL connection using TLS1.2 / ECDHE_RSA_AES_128_GCM_SHA256
*   server certificate verification SKIPPED
*   server certificate status verification SKIPPED
*   common name: *.ensembl.org (matched)
*   server certificate expiration date OK
*   server certificate activation date OK
*   certificate public key: RSA
*   certificate version: #3
*   subject: CN=*.ensembl.org
*   start date: Tue, 26 Apr 2022 20:10:48 GMT
*   expire date: Sun, 28 May 2023 20:10:48 GMT
*   issuer: C=US,ST=Arizona,L=Scottsdale,O=GoDaddy.com\, Inc.,OU=http://certs.godaddy.com/repository/,CN=Go Daddy Secure Certificate Authority - G2
* ALPN, server did not agree to a protocol
> GET /info/website/archives/index.html?redirect=no HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.81.0 r-curl/5.0.0 httr/1.4.4
Accept-Encoding: deflate, gzip, br, zstd
Cookie: ENSEMBL_HINX_SESSION=1a221bd5eeb51ea80eed80e46430dbe00d6a66f092e03c1e0c2e4167; redirect_mirror=no
Accept: application/json, text/xml, application/xml, */*

* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 07 Feb 2023 03:13:54 GMT
< Content-Type: text/html; charset=utf-8
< Content-Length: 9171
< Connection: keep-alive
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Vary: Accept-Encoding
< Content-Encoding: gzip
< X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk
< 
* Connection #1 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab2e823810 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#1) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#1)
> GET /biomart/martservice?type=registry&requestid=biomaRt HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.81.0 r-curl/5.0.0 httr/1.4.4
Accept-Encoding: deflate, gzip, br, zstd
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain

* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 07 Feb 2023 03:13:59 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
< 
* Connection #1 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab2e823810 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#1) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#1)
> GET /biomart/martservice?redirect=no&type=datasets&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.81.0 r-curl/5.0.0 httr/1.4.4
Accept-Encoding: deflate, gzip, br, zstd
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain

* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 07 Feb 2023 03:14:05 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
< 
* Connection #1 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab2e823810 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#1) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#1)
> GET /biomart/martservice?redirect=no&type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.81.0 r-curl/5.0.0 httr/1.4.4
Accept-Encoding: deflate, gzip, br, zstd
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain

* Operation timed out after 10001 milliseconds with 0 bytes received
* Closing connection 1
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:443] Operation timed out after 10001 milliseconds with 0 bytes received
Calls: <Anonymous> ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* 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 ...

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL glmSparseNet
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 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 4.1-6
> 
> test_check("glmSparseNet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 84 ]
> 
> proc.time()
   user  system elapsed 
 27.287   7.444  38.120