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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sitadela.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings sitadela_1.12.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/sitadela.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sitadela/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sitadela' version '1.12.0'
* 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 'sitadela' 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 code 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 whether startup messages can be suppressed ... NOTE
sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'sitadela-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnotation
> ### Title: Annotation downloader
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
> mm10Genes <- getAnnotation("mm10","gene")
Using Ensembl host https://jan2024.archive.ensembl.org
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
    ▆
 1. └─sitadela::getAnnotation("mm10", "gene")
 2.   └─sitadela:::getEnsemblAnnotation(org, type, ver, tv)
 3.     └─biomaRt::useEnsembl(biomart = dat, host = host, dataset = .getDataset(org))
 4.       └─biomaRt:::.listMarts(...)
 5.         └─biomaRt:::bmRequest(...)
 6.           └─httr2::req_perform(request)
 7.             └─httr2:::handle_resp(req, resp, error_call = error_call)
 8.               └─httr2:::resp_abort(resp, req, body, call = error_call)
 9.                 └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test_sitadela_ensembl_rare: Error in checkTrue(is.null(f1)) : Test not TRUE
  
  
  Test files with failing tests
  
     test_sitadela.R 
       test_sitadela_ensembl_often 
       test_sitadela_ensembl_rare 
  
  
  Error in BiocGenerics:::testPackage("sitadela") : 
    unit tests failed for package sitadela
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/sitadela.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL sitadela
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'sitadela' ...
** using staged installation
** R
** 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
sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory
** testing if installed package can be loaded from final location
sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory
** testing if installed package keeps a record of temporary installation path
* DONE (sitadela)

R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> BiocGenerics:::testPackage("sitadela")
sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory
Scheduling 1 tests
==================================================


Running test 1 of 1 scheduled
Testing level gene from mm10 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 failed with error:
Failed to perform HTTP request.
Testing finished!

Summary
==================================================

Succesful tests: 0 out of 1
Failed tests   : 1 out of 1
 
Check the output for failure details
Timing stopped at: 2.17 0.66 602.8
Error in checkTrue(is.null(f1)) : Test not TRUE

Scheduling 1 tests
==================================================


Running test 1 of 1 scheduled
Testing level gene from danrer11 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 failed with error:
HTTP 500 Internal Server Error.
Testing finished!

Summary
==================================================

Succesful tests: 0 out of 1
Failed tests   : 1 out of 1
 
Check the output for failure details
Timing stopped at: 0.9 0.12 302.3
Error in checkTrue(is.null(f1)) : Test not TRUE

Scheduling 2 tests
==================================================

Running test 1 of 2 scheduled
Opening sitadela SQLite database F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp08UWQy\filea2143f8e7409
  Importing GTF F:/biocbuild/bbs-3.19-bioc/R/library/sitadela/dummy.gtf.gz as GTF to make id map
  Making id map
  Importing GTF F:/biocbuild/bbs-3.19-bioc/R/library/sitadela/dummy.gtf.gz as TxDb
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Retrieving gene annotation for dummy from dummy_db version 1 from F:/biocbuild/bbs-3.19-bioc/R/library/sitadela/dummy.gtf.gz
Retrieving transcript annotation for dummy from dummy_db version 1
Retrieving summarized transcript annotation for dummy from dummy_db version 1
Retrieving 3' UTR annotation for dummy from dummy_db version 1
Retrieving summarized 3' UTR annotation per gene for dummy from dummy_db version 1
Retrieving summarized 3' UTR annotation per transcript for dummy from dummy_db version 1
Retrieving exon annotation for dummy from dummy_db version 1
Retrieving summarized exon annotation for dummy from dummy_db version 1
Retrieving extended exon annotation for dummy from dummy_db version 1
Retrieving summarized transcript exon annotation for dummy from dummy_db version 1
Test 1 successful!

Running test 2 of 2 scheduled
Test 2 successful!
Deleting temporary database F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp08UWQy\filea2143f8e7409
Scheduling 2 tests
==================================================

Running test 1 of 2 scheduled

********************************************************
This is sitadela 1.12.0 genomic region annotation builder
********************************************************
sitadela database found at F:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmp08UWQy directory

========================================================
2024-05-22 07:04:28 - Try 1
========================================================

Opening sitadela SQLite database F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp08UWQy\filea214294941e3
Retrieving genome information for dm6 from ensembl
Retrieving gene annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Retrieving transcript annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Merging transcripts for dm6 from ensembl version 102
Retrieving 3' UTR annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Merging gene 3' UTRs for dm6 from ensembl version 102
Merging transcript 3' UTRs for dm6 from ensembl version 102
Retrieving exon annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Retrieving extended exon annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Merging exons for dm6 from ensembl version 102
Merging exons for dm6 from ensembl version 102

-------------------------------------------------------
Building process complete!
-------------------------------------------------------

Test 1 successful!

Running test 2 of 2 scheduled
Test 2 successful!
Deleting temporary database F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp08UWQy\filea214294941e3
Loading required package: RMySQL
Loading required package: DBI
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!


RUNIT TEST PROTOCOL -- Wed May 22 07:05:05 2024 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
sitadela RUnit Tests - 8 test functions, 0 errors, 2 failures
FAILURE in test_sitadela_ensembl_often: Error in checkTrue(is.null(f1)) : Test not TRUE

FAILURE in test_sitadela_ensembl_rare: Error in checkTrue(is.null(f1)) : Test not TRUE


Test files with failing tests

   test_sitadela.R 
     test_sitadela_ensembl_often 
     test_sitadela_ensembl_rare 


Error in BiocGenerics:::testPackage("sitadela") : 
  unit tests failed for package sitadela
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted