##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:sitadela.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings sitadela_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/sitadela.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-07 08:35:02 UTC
* checking for file ‘sitadela/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sitadela’ version ‘1.21.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
sitadela database found at /home/biocbuild/.local/share/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: getAnnotation
> ### Title: Annotation downloader
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
> mm39Genes <- getAnnotation("mm39","gene")
Using Ensembl host https://www.ensembl.org
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─sitadela::getAnnotation("mm39", "gene")
  2.   └─sitadela:::getEnsemblAnnotation(org, type, ver, tv)
  3.     └─biomaRt::useEnsembl(biomart = dat, host = host, dataset = .getDataset(org))
  4.       └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
  5.         └─biomaRt:::checkDataset(dataset = dataset, mart = mart)
  6.           └─biomaRt:::.listDatasets(mart, sort = FALSE)
  7.             └─biomaRt:::bmRequest(...)
  8.               └─httr2::req_perform(request)
  9.                 └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.                   └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 11.                     ├─rlang::catch_cnd(...)
 12.                     │ ├─rlang::eval_bare(...)
 13.                     │ ├─base::tryCatch(...)
 14.                     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15.                     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16.                     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17.                     │ └─base::force(expr)
 18.                     └─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:
  1 Test Suite : 
  sitadela RUnit Tests - 6 test functions, 0 errors, 1 failure
  FAILURE in test_sitadela_ensembl_often: Error in checkTrue(is.null(f1)) : Test not TRUE
  
  
  Test files with failing tests
  
     test_sitadela.R 
       test_sitadela_ensembl_often 
  
  
  Error in BiocGenerics:::testPackage("sitadela") : 
    unit tests failed for package sitadela
  In addition: There were 16 warnings (use warnings() to see them)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/sitadela.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL sitadela
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘sitadela’ ...
** this is package ‘sitadela’ version ‘1.21.0’
** 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 /home/biocbuild/.local/share/R/sitadela directory
** testing if installed package can be loaded from final location
sitadela database found at /home/biocbuild/.local/share/R/sitadela directory
** testing if installed package keeps a record of temporary installation path
* DONE (sitadela)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 /home/biocbuild/.local/share/R/sitadela directory
Scheduling 1 tests
==================================================


Running test 1 of 1 scheduled
Testing level gene from mm39 from latest version
Using Ensembl host https://www.ensembl.org
Test 1 failed with error:
biomaRt error: looks like we're connecting to incompatible version of BioMart.
Testing finished!

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

Succesful tests: 0 out of 1
Failed tests   : 1 out of 1
 
Check the output for failure details
Timing stopped at: 1.21 0.147 30.97
Error in checkTrue(is.null(f1)) : Test not TRUE

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

Running test 1 of 2 scheduled
Opening sitadela SQLite database /tmp/RtmpDHeIdr/file1bcd5418fb4b53
  Importing GTF /home/biocbuild/bbs-3.24-bioc/R/site-library/sitadela/dummy.gtf.gz as GTF to make id map
  Making id map
  Importing GTF /home/biocbuild/bbs-3.24-bioc/R/site-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 /home/biocbuild/bbs-3.24-bioc/R/site-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 /tmp/RtmpDHeIdr/file1bcd5418fb4b53
Loading required package: RMySQL
Loading required package: DBI
Scheduling 1 tests
==================================================

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

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : transcript
Query is: SELECT refFlat.chrom AS `chromosome`, refFlat.txStart AS `start`, refFlat.txEnd AS `end`, refFlat.name AS `transcript_id`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, ensemblSource.source AS `biotype` FROM `refFlat` INNER JOIN `knownToRefSeq` ON refFlat.name=knownToRefSeq.value INNER JOIN `knownCanonical` ON knownToRefSeq.name=knownCanonical.transcript  INNER JOIN `knownToEnsembl` ON knownCanonical.transcript=knownToEnsembl.name INNER JOIN `ensemblSource` ON knownToEnsembl.value=ensemblSource.name ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 0 features
Sample data:
[1] chromosome    start         end           transcript_id strand       
[6] gene_name     biotype      
<0 rows> (or 0-length row.names)
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

==========> Now testing mm10
Connecting to UCSC database mm10...

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : gene
Query is: SELECT  refFlat.chrom AS `chromosome`, refFlat.txStart AS `start`, refFlat.txEnd AS `end`, refFlat.name AS `gene_id`, 0 AS `gc_content`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, 'NA' AS `biotype` FROM `refFlat` INNER JOIN `knownToRefSeq` ON refFlat.name=knownToRefSeq.value INNER JOIN `knownCanonical` ON knownToRefSeq.name=knownCanonical.transcript  GROUP BY refFlat.name ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 23491 features
Sample data:
  chromosome   start     end      gene_id gc_content strand gene_name biotype
1       chr1 3214481 3671498 NM_001011874          0      -      Xkr4      NA
2       chr1 4119865 4360303 NM_001370921          0      -       Rp1      NA
3       chr1 4490927 4497354    NM_011441          0      -     Sox17      NA
4       chr1 4773199 4785726 NM_001177658          0      -    Mrpl15      NA
5       chr1 4807822 4846735    NM_008866          0      +    Lypla1      NA
6       chr1 4857693 4897909    NM_011541          0      +     Tcea1      NA
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

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

---------------------------------------------------
Running test 1 of 1 scheduled
Source: ucsc
Type  : transcript
Query is: SELECT knownGene.chrom AS `chromosome`, knownGene.txStart AS `start`, knownGene.txEnd AS `end`, knownGene.name AS `transcript_id`, knownGene.strand AS `strand`, `geneName` AS `gene_name`, `source` AS `biotype` FROM `knownGene` INNER JOIN `knownToRefSeq` ON knownGene.name=knownToRefSeq.name INNER JOIN `knownToEnsembl` ON knownGene.name=knownToEnsembl.name INNER JOIN `ensemblSource` ON knownToEnsembl.value=ensemblSource.name INNER JOIN `refFlat` ON knownToRefSeq.value=refFlat.name GROUP BY `transcript_id` ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 0 features
Sample data:
[1] chromosome    start         end           transcript_id strand       
[6] gene_name     biotype      
<0 rows> (or 0-length row.names)
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

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

---------------------------------------------------
Running test 1 of 1 scheduled
Source: ucsc
Type  : gene
Query is: SELECT flyBaseCanonical.chrom AS `chromosome`, `chromStart` AS `start`, `chromEnd` AS `end`, `transcript` AS `gene_id`, 0 AS `gc_content`, flyBaseGene.strand AS `strand`, `geneName` AS `gene_name`, `source` AS `biotype` FROM `flyBaseCanonical` INNER JOIN `flyBaseGene` ON flyBaseCanonical.transcript=flyBaseGene.name INNER JOIN `flyBaseToRefSeq` ON flyBaseCanonical.transcript=flyBaseToRefSeq.name INNER JOIN `refFlat` ON flyBaseToRefSeq.value=refFlat.name INNER JOIN `ensemblToGeneName` ON ensemblToGeneName.value=refFlat.geneName INNER JOIN `ensemblSource` ON ensemblToGeneName.name=ensemblSource.name GROUP BY `gene_id` ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 10792 features
Sample data:
  chromosome start   end    gene_id gc_content strand gene_name        biotype
1      chr2L  9835 18583  CG2671-RC          0      -    l(2)gl protein_coding
2      chr2L 21918 25151  CG2657-RB          0      -     Ir21a protein_coding
3      chr2L 25401 59242 CG31973-RB          0      -      Cda5 protein_coding
4      chr2L 67043 71390 CG11371-RB          0      +       dbr protein_coding
5      chr2L 72387 76203 CG11372-RA          0      +  galectin protein_coding
6      chr2L 76445 77639 CG11374-RB          0      +   CG11374 protein_coding
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

==========> Now testing equCab3
Connecting to UCSC database equCab3...

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : gene
Query is: SELECT `chromosome`,`start`,`end`,`gene_id`, `gc_content`,`strand`,`gene_name`,`biotype` FROM (SELECT MAX(`txEnd` - `txStart`) AS `width`, refFlat.chrom AS `chromosome`, `txStart` AS `start`, `txEnd` AS `end`, refFlat.name AS `gene_id`, 0 AS `gc_content`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, ensemblSource.source AS `biotype` FROM `refFlat` INNER JOIN `ensemblToGeneName` ON refFlat.geneName=ensemblToGeneName.value INNER JOIN `ensemblSource` ON ensemblToGeneName.name=ensemblSource.name  GROUP BY `gene_name` ORDER BY `chromosome`,`start`) AS tmp
Test 1 successful!
Fetched 1007 features
Sample data:
  chromosome    start      end      gene_id gc_content strand gene_name
1       chr1   131450   143029 NM_001111303          0      -    CYP2E1
2       chr1 11323857 11426445 NM_001163863          0      +     FGFR2
3       chr1 15653377 15670230 NM_001163949          0      -     PNLIP
4       chr1 20910562 20943976 NM_001308957          0      -      SMC3
5       chr1 27056246 27100149 NM_001309513          0      -    PDCD11
6       chr1 27571464 27577548 NM_001082523          0      +   CYP17A1
         biotype
1 protein_coding
2 protein_coding
3 protein_coding
4 protein_coding
5 protein_coding
6 protein_coding
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

==========> Now testing danRer11
Connecting to UCSC database danRer11...

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : transcript
Query is: SELECT refFlat.chrom AS `chromosome`, refFlat.txStart AS `start`, refFlat.txEnd AS `end`, refFlat.name AS `transcript_id`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, ensemblSource.source AS `biotype` FROM `refFlat` INNER JOIN `ensemblToGeneName` ON refFlat.geneName=ensemblToGeneName.value INNER JOIN `ensemblSource` ON ensemblToGeneName.name=ensemblSource.name  GROUP BY `transcript_id` ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 15068 features
Sample data:
  chromosome start   end transcript_id strand gene_name        biotype
1       chr1  6641 11878     NM_173235      -     rpl24 protein_coding
2       chr1 11966 16373     NM_198371      +     cep97 protein_coding
3       chr1 27687 34330  NM_001017766      +       eed protein_coding
4       chr1 36733 39191  NM_001017577      +   hikeshi protein_coding
5       chr1 39324 44525     NM_199632      -   tmem39a protein_coding
6       chr1 44838 49831     NM_200393      -    ildr1a protein_coding
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

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

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : gene
Query is: SELECT refFlat.chrom AS `chromosome`, refFlat.txStart AS `start`, refFlat.txEnd AS `end`, CONCAT(refFlat.name,'.',hgFixed.gbCdnaInfo.version) AS `gene_id`, 0 AS `gc_content`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, ensemblSource.source AS `biotype` FROM `refFlat` INNER JOIN `knownToRefSeq` ON refFlat.name=knownToRefSeq.value INNER JOIN `knownCanonical` ON knownToRefSeq.name=knownCanonical.transcript INNER JOIN hgFixed.gbCdnaInfo ON refFlat.name=hgFixed.gbCdnaInfo.acc INNER JOIN `knownToEnsembl` ON knownCanonical.transcript=knownToEnsembl.name INNER JOIN `ensemblSource` ON knownToEnsembl.value=ensemblSource.name GROUP BY refFlat.name ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 0 features
Sample data:
[1] chromosome start      end        gene_id    gc_content strand     gene_name 
[8] biotype   
<0 rows> (or 0-length row.names)
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

==========> Now testing mm10
Connecting to UCSC database mm10...

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : gene
Query is: SELECT  refFlat.chrom AS `chromosome`, refFlat.txStart AS `start`, refFlat.txEnd AS `end`, CONCAT(refFlat.name,'.',hgFixed.gbCdnaInfo.version) AS `gene_id`, 0 AS `gc_content`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, 'NA' AS `biotype` FROM `refFlat` INNER JOIN `knownToRefSeq` ON refFlat.name=knownToRefSeq.value INNER JOIN `knownCanonical` ON knownToRefSeq.name=knownCanonical.transcript INNER JOIN hgFixed.gbCdnaInfo ON refFlat.name=hgFixed.gbCdnaInfo.acc GROUP BY refFlat.name ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 23491 features
Sample data:
  chromosome   start     end        gene_id gc_content strand gene_name biotype
1       chr1 3214481 3671498 NM_001011874.1          0      -      Xkr4      NA
2       chr1 4119865 4360303 NM_001370921.1          0      -       Rp1      NA
3       chr1 4490927 4497354    NM_011441.5          0      -     Sox17      NA
4       chr1 4773199 4785726 NM_001177658.1          0      -    Mrpl15      NA
5       chr1 4807822 4846735    NM_008866.3          0      +    Lypla1      NA
6       chr1 4857693 4897909    NM_011541.4          0      +     Tcea1      NA
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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

==========> Now testing danRer11
Connecting to UCSC database danRer11...

---------------------------------------------------
Running test 1 of 1 scheduled
Source: refseq
Type  : transcript
Query is: SELECT refFlat.chrom AS `chromosome`, refFlat.txStart AS `start`, refFlat.txEnd AS `end`, CONCAT(refFlat.name,'.',hgFixed.gbCdnaInfo.version) AS `transcript_id`, refFlat.strand AS `strand`, refFlat.geneName AS `gene_name`, ensemblSource.source AS `biotype` FROM `refFlat` INNER JOIN `ensemblToGeneName` ON refFlat.geneName=ensemblToGeneName.value INNER JOIN `ensemblSource` ON ensemblToGeneName.name=ensemblSource.name INNER JOIN hgFixed.gbCdnaInfo ON refFlat.name=hgFixed.gbCdnaInfo.acc GROUP BY `transcript_id` ORDER BY `chromosome`,`start`
Test 1 successful!
Fetched 15068 features
Sample data:
  chromosome start   end  transcript_id strand gene_name        biotype
1       chr1  6641 11878    NM_173235.3      -     rpl24 protein_coding
2       chr1 11966 16373    NM_198371.2      +     cep97 protein_coding
3       chr1 27687 34330 NM_001017766.2      +       eed protein_coding
4       chr1 36733 39191 NM_001017577.1      +   hikeshi protein_coding
5       chr1 39324 44525    NM_199632.1      -   tmem39a protein_coding
6       chr1 44838 49831    NM_200393.1      -    ildr1a protein_coding
---------------------------------------------------

Disconnecting from UCSC database...
Testing finished!

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

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


RUNIT TEST PROTOCOL -- Thu May  7 04:42:36 2026 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
sitadela RUnit Tests - 6 test functions, 0 errors, 1 failure
FAILURE in test_sitadela_ensembl_often: Error in checkTrue(is.null(f1)) : Test not TRUE


Test files with failing tests

   test_sitadela.R 
     test_sitadela_ensembl_often 


Error in BiocGenerics:::testPackage("sitadela") : 
  unit tests failed for package sitadela
In addition: There were 16 warnings (use warnings() to see them)
Execution halted