| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-23 01:34:02 -0000 (Thu, 23 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
| 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 | ||||
|
To the developers/maintainers of the glmSparseNet package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 815/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| glmSparseNet 1.17.0 (landing page) André Veríssimo
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: glmSparseNet |
| Version: 1.17.0 |
| 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/library --timings glmSparseNet_1.17.0.tar.gz |
| StartedAt: 2023-02-22 05:50:35 -0000 (Wed, 22 Feb 2023) |
| EndedAt: 2023-02-22 06:07:06 -0000 (Wed, 22 Feb 2023) |
| EllapsedTime: 991.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: glmSparseNet.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* 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 89756 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=a0b7e0ee1b7961290c0c7e0a6444c8000fad3c9a681e36fd41bb482f; redirect_mirror=no
Accept: application/json, text/xml, application/xml, */*
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:54:32 GMT
< Content-Type: text/html; charset=utf-8
< Content-Length: 9154
< 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-p1m2-35.ebi.ac.uk
<
* Connection #1 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab0773a2a0 [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: Wed, 22 Feb 2023 05:54:35 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: 0xaaab0773a2a0 [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
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:54:39 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Operation timed out after 10001 milliseconds with 68094 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 68094 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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
x[2]: "ENSP00000299272"
y[2]: "ENSG00000166211"
x[3]: "ENSP00000331915"
y[3]: "ENSG00000183688"
x[4]: "ENSP00000361021"
y[4]: "ENSG00000171862"
x[5]: "ENSP00000269305"
y[5]: "ENSG00000141510"
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 82 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/glmSparseNet.Rcheck/00check.log’
for details.
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/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.fail
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")
* 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=cb2de0602b9f19920e9770b76444c8420d363267a20fccf5a6487647; redirect_mirror=no
Accept: application/json, text/xml, application/xml, */*
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:55:29 GMT
< Content-Type: text/html; charset=utf-8
< Content-Length: 9151
< 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-p1m2-31.ebi.ac.uk
<
* Connection #1 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab2304ea80 [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: Wed, 22 Feb 2023 05:55:32 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: 0xaaab2304ea80 [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
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:55:33 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Operation timed out after 10000 milliseconds with 239971 bytes received
* Closing connection 1
* 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 (#3)
* 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 re-using session ID
* 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=cb2de0602b9f19920e9770b76444c8420d363267a20fccf5a6487647; redirect_mirror=no
Accept: application/json, text/xml, application/xml, */*
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:56:00 GMT
< Content-Type: text/html; charset=utf-8
< Content-Length: 9155
< 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-p1m2-32.ebi.ac.uk
<
* Connection #3 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab1005a290 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#3) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#3)
> 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: Wed, 22 Feb 2023 05:56:01 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Connection #3 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab1005a290 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#3) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#3)
> 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
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:56:02 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Connection #3 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0xaaab1005a290 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#3) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#3)
> GET /biomart/martservice?redirect=no&type=filters&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
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Wed, 22 Feb 2023 05:56:07 GMT
< Server: Apache
< X-Frame-Options: SAMEORIGIN
< Content-Security-Policy: frame-ancestors 'self'
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Operation timed out after 10000 milliseconds with 509094 bytes received
* Closing connection 3
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 82 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-external_apis.R:19'): gene name query ────────────────────────
res$external_gene_name not equal to target[res$ensembl_gene_id, "gene.name"].
5/5 mismatches
x[1]: "ENSG00000114978"
y[1]: "MOB1A"
x[2]: "ENSG00000166211"
y[2]: "SPIC"
x[3]: "ENSG00000183688"
y[3]: "RFLNB"
x[4]: "ENSG00000171862"
y[4]: "PTEN"
x[5]: "ENSG00000141510"
y[5]: "TP53"
── Failure ('test-external_apis.R:37'): protein query ──────────────────────────
res$ensembl_gene_id not equal to target[res$ensembl_peptide_id, "gene.name"].
5/5 mismatches
x[1]: "ENSP00000379364"
y[1]: "ENSG00000114978"
x[2]: "ENSP00000299272"
y[2]: "ENSG00000166211"
x[3]: "ENSP00000331915"
y[3]: "ENSG00000183688"
x[4]: "ENSP00000361021"
y[4]: "ENSG00000171862"
x[5]: "ENSP00000269305"
y[5]: "ENSG00000141510"
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 82 ]
Error: Test failures
Execution halted
glmSparseNet.Rcheck/glmSparseNet-Ex.timings
| name | user | system | elapsed | |
| balanced.cv.folds | 0.006 | 0.000 | 0.006 | |
| base.dir | 0.000 | 0.000 | 0.001 | |