##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sitadela.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sitadela_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/sitadela.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-14 00:21:36 UTC
* using option ‘--no-vignettes’
* checking for file ‘sitadela/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sitadela’ version ‘1.19.0’
* 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 ‘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 /Users/biocbuild/Library/Application Support/org.R-project.R/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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getSeqInfo.Rd: Seqinfo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: testFuns
> ### Title: Query and database build testing functions
> ### Aliases: testEnsembl testEnsemblSimple testUcsc testUcscAll testUcscUtr
> ###   testUcscUtrAll testCustomGtf testKnownBuild testCustomBuild
> 
> ### ** Examples
> 
>     # Test a dummy GTF file
>     gtf <- file.path(system.file(package="sitadela"),
+         "dummy.gtf.gz")
>     chromInfo <- data.frame(length=c(1000L,2000L,1500L),
+         row.names=c("A","B","C"))
>     metadata=list(
+         organism="dummy",
+         source="dummy_db",
+         version=1,
+         chromInfo=chromInfo
+     )
>     
>     testResult <- testCustomBuild(gtf,metadata)
Scheduling 2 tests
==================================================

Running test 1 of 2 scheduled
Opening sitadela SQLite database /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7VlFBd/file1245d67ad7107
  Importing GTF /Library/Frameworks/R.framework/Versions/4.6/Resources/library/sitadela/dummy.gtf.gz as GTF to make id map
  Making id map
  Importing GTF /Library/Frameworks/R.framework/Versions/4.6/Resources/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 /Library/Frameworks/R.framework/Versions/4.6/Resources/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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7VlFBd/file1245d67ad7107
>     # For this case, just testResult <- testCustomBuild()
>     # would also work
>     
>     # More real tests
>     if (require(RMySQL))
+         f <- testUcsc("hg19","refseq","gene",TRUE)
Loading required package: RMySQL
Loading required package: DBI
Scheduling 1 tests
==================================================

==========> Now testing hg19
Connecting to UCSC database hg19...

Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it
Calls: testUcsc -> dbConnect -> dbConnect -> .local -> .Call
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:
  
  
  Test files with failing tests
  
     test_sitadela.R 
       test_sitadela_ensembl_rare 
       test_sitadela_known 
       test_sitadela_ucsc_often 
       test_sitadela_ucsc_rare 
       test_sitadela_ucsc_versioned 
  
  
  Error in BiocGenerics:::testPackage("sitadela") : 
    unit tests failed for package sitadela
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/sitadela.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sitadela
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘sitadela’ ...
** this is package ‘sitadela’ version ‘1.19.0’
** 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 /Users/biocbuild/Library/Application Support/org.R-project.R/R/sitadela directory
** testing if installed package can be loaded from final location
sitadela database found at /Users/biocbuild/Library/Application Support/org.R-project.R/R/sitadela directory
** testing if installed package keeps a record of temporary installation path
* DONE (sitadela)

R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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 /Users/biocbuild/Library/Application Support/org.R-project.R/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 successful!
Created 57089 features
Sample data:
                   chromosome   start     end            gene_id gc_content
ENSMUSG00000102693       chr1 3143476 3144545 ENSMUSG00000102693      34.21
ENSMUSG00000064842       chr1 3172239 3172348 ENSMUSG00000064842      36.36
ENSMUSG00000051951       chr1 3276124 3741721 ENSMUSG00000051951      38.51
ENSMUSG00000102851       chr1 3322980 3323459 ENSMUSG00000102851      39.79
ENSMUSG00000103377       chr1 3435954 3438772 ENSMUSG00000103377      40.79
ENSMUSG00000104017       chr1 3445779 3448011 ENSMUSG00000104017      36.99
                   strand     gene_name              biotype
ENSMUSG00000102693      + 4933401J01Rik                  TEC
ENSMUSG00000064842      +       Gm26206                snRNA
ENSMUSG00000051951      -          Xkr4       protein_coding
ENSMUSG00000102851      +       Gm18956 processed_pseudogene
ENSMUSG00000103377      -       Gm37180                  TEC
ENSMUSG00000104017      -       Gm37363                  TEC
Testing finished!

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

Succesful tests: 1 out of 1
Failed tests   : 0 out of 1
 
Scheduling 1 tests
==================================================


Running test 1 of 1 scheduled
Testing level transcript from mm10 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 successful!
Created 149039 features
Sample data:
                   chromosome   start     end      transcript_id
ENSMUST00000193812       chr1 3143476 3144545 ENSMUST00000193812
ENSMUST00000082908       chr1 3172239 3172348 ENSMUST00000082908
ENSMUST00000162897       chr1 3276124 3286567 ENSMUST00000162897
ENSMUST00000159265       chr1 3276746 3285855 ENSMUST00000159265
ENSMUST00000070533       chr1 3284705 3741721 ENSMUST00000070533
ENSMUST00000192857       chr1 3322980 3323459 ENSMUST00000192857
                              gene_id strand     gene_name              biotype
ENSMUST00000193812 ENSMUSG00000102693      + 4933401J01Rik                  TEC
ENSMUST00000082908 ENSMUSG00000064842      +       Gm26206                snRNA
ENSMUST00000162897 ENSMUSG00000051951      -          Xkr4       protein_coding
ENSMUST00000159265 ENSMUSG00000051951      -          Xkr4       protein_coding
ENSMUST00000070533 ENSMUSG00000051951      -          Xkr4       protein_coding
ENSMUST00000192857 ENSMUSG00000102851      +       Gm18956 processed_pseudogene
Testing finished!

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

Succesful tests: 1 out of 1
Failed tests   : 0 out of 1
 
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: 0.242 0.02 131.2
Error in checkTrue(is.null(f1)) : Test not TRUE

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

Running test 1 of 2 scheduled
Opening sitadela SQLite database /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp8cm4dv/file12d0b65e5d6ba
  Importing GTF /Library/Frameworks/R.framework/Versions/4.6/Resources/library/sitadela/dummy.gtf.gz as GTF to make id map
  Making id map
  Importing GTF /Library/Frameworks/R.framework/Versions/4.6/Resources/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 /Library/Frameworks/R.framework/Versions/4.6/Resources/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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp8cm4dv/file12d0b65e5d6ba
Scheduling 2 tests
==================================================

Running test 1 of 2 scheduled

********************************************************
This is sitadela 1.19.0 genomic region annotation builder
********************************************************
sitadela database found at /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp8cm4dv directory

========================================================
2026-03-13 20:30:53 - Try 1
========================================================

Opening sitadela SQLite database /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp8cm4dv/file12d0b54748199
Retrieving genome information for dm6 from ensembl
Retrieving gene annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Possible connection failure! Marking...
Caught error: HTTP 500 Internal Server Error.
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
Possible connection failure! Marking...
Caught error: HTTP 500 Internal Server Error.
Retrieving extended exon annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Possible connection failure! Marking...
Caught error: HTTP 500 Internal Server Error.
Test 1 failed with error:
Exon annotation for dm6 from ensembl version 102 is required in order to build predefined merged exon regions for RNA-Seq (exon) coverage calculations.
Please rerun the addAnnotation function with appropriate parameters.

Running test 2 of 2 scheduled
Test 2 successful!
Deleting temporary database /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp8cm4dv/file12d0b54748199
Timing stopped at: 3.592 0.231 516.5
Error in checkTrue(all(testResult)) : Test not TRUE

Loading required package: RMySQL
Loading required package: DBI
Scheduling 1 tests
==================================================

==========> Now testing hg19
Connecting to UCSC database hg19...

Timing stopped at: 0.047 0.003 0.32
Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it

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

==========> Now testing dm3
Connecting to UCSC database dm3...

Timing stopped at: 0.008 0 0.159
Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it

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

==========> Now testing hg19
Connecting to UCSC database hg19...

Timing stopped at: 0.001 0.001 0.149
Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it



RUNIT TEST PROTOCOL -- Fri Mar 13 20:39:31 2026 
*********************************************** 
Number of test functions: 8 
Number of errors: 3 
Number of failures: 2 

 
1 Test Suite : 
sitadela RUnit Tests - 8 test functions, 3 errors, 2 failures
FAILURE in test_sitadela_ensembl_rare: Error in checkTrue(is.null(f1)) : Test not TRUE

FAILURE in test_sitadela_known: Error in checkTrue(all(testResult)) : Test not TRUE

ERROR in test_sitadela_ucsc_often: Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it

ERROR in test_sitadela_ucsc_rare: Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it

ERROR in test_sitadela_ucsc_versioned: Error in .local(drv, ...) : 
  Failed to connect to database: Error: TLS/SSL error: SSL is required, but the server does not support it


Test files with failing tests

   test_sitadela.R 
     test_sitadela_ensembl_rare 
     test_sitadela_known 
     test_sitadela_ucsc_often 
     test_sitadela_ucsc_rare 
     test_sitadela_ucsc_versioned 


Error in BiocGenerics:::testPackage("sitadela") : 
  unit tests failed for package sitadela
Execution halted