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This page was generated on 2024-05-17 11:36:31 -0400 (Fri, 17 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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

Package 1997/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sitadela 1.12.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2024-05-16 14:00:15 -0400 (Thu, 16 May 2024)
git_url: https://git.bioconductor.org/packages/sitadela
git_branch: RELEASE_3_19
git_last_commit: 19f078e
git_last_commit_date: 2024-04-30 11:32:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for sitadela on nebbiolo1


To the developers/maintainers of the sitadela package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sitadela.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: sitadela
Version: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sitadela.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sitadela_1.12.0.tar.gz
StartedAt: 2024-05-17 03:11:19 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 03:19:26 -0400 (Fri, 17 May 2024)
EllapsedTime: 487.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: sitadela.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sitadela.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sitadela_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sitadela.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 ... 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://nov2023.archive.ensembl.org
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://nov2023.archive.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
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: There were 17 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/sitadela.Rcheck/00check.log’
for details.


Installation output

sitadela.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL sitadela
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 /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)

Tests output

sitadela.Rcheck/tests/runTests.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 mm10 from latest version
Using Ensembl host https://nov2023.archive.ensembl.org
Test 1 failed with error:
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://nov2023.archive.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
Testing finished!

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

Succesful tests: 0 out of 1
Failed tests   : 1 out of 1
 
Check the output for failure details
Timing stopped at: 1.952 0.128 3.676
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://nov2023.archive.ensembl.org
Test 1 failed with error:
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://nov2023.archive.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
Testing finished!

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

Succesful tests: 0 out of 1
Failed tests   : 1 out of 1
 
Check the output for failure details
Timing stopped at: 0.688 0.097 1.075
Error in checkTrue(is.null(f1)) : Test not TRUE

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

Running test 1 of 2 scheduled
Opening sitadela SQLite database /tmp/Rtmpvoml39/file213b507ee67654
  Importing GTF /home/biocbuild/bbs-3.19-bioc/R/site-library/sitadela/dummy.gtf.gz as GTF to make id map
  Making id map
  Importing GTF /home/biocbuild/bbs-3.19-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-3.19-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/Rtmpvoml39/file213b507ee67654
Scheduling 2 tests
==================================================

Running test 1 of 2 scheduled

********************************************************
This is sitadela 1.12.0 genomic region annotation builder
********************************************************
sitadela database found at /tmp/Rtmpvoml39 directory

========================================================
2024-05-17 03:16:16 - Try 1
========================================================

Opening sitadela SQLite database /tmp/Rtmpvoml39/file213b509b72cdb
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 /tmp/Rtmpvoml39/file213b509b72cdb
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 31914 features
Sample data:
  chromosome start   end transcript_id strand gene_name
1       chr1 11873 14409     NR_046018      +   DDX11L1
2       chr1 14361 29370     NR_024540      -    WASH7P
3       chr1 14361 29370     NR_024540      -    WASH7P
4       chr1 34610 36081     NR_026820      -   FAM138F
5       chr1 34610 36081     NR_026820      -   FAM138F
6       chr1 34610 36081     NR_026822      -   FAM138C
                             biotype
1 transcribed_unprocessed_pseudogene
2             unprocessed_pseudogene
3             unprocessed_pseudogene
4                            lincRNA
5                            lincRNA
6                            lincRNA
---------------------------------------------------

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 71001 features
Sample data:
  chromosome start   end transcript_id strand gene_name
1       chr1 11873 14409    uc001aaa.3      +   DDX11L1
2       chr1 11873 14409    uc010nxr.1      +   DDX11L1
3       chr1 11873 14409    uc010nxq.1      +   DDX11L1
4       chr1 14361 16765    uc009vis.3      -    WASH7P
5       chr1 14361 19759    uc009vit.3      -    WASH7P
6       chr1 14361 19759    uc009viu.3      -    WASH7P
                             biotype
1               processed_transcript
2               processed_transcript
3 transcribed_unprocessed_pseudogene
4             unprocessed_pseudogene
5             unprocessed_pseudogene
6             unprocessed_pseudogene
---------------------------------------------------

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 22116 features
Sample data:
  chromosome  start    end        gene_id gc_content strand gene_name
1       chr1  11873  14409    NR_046018.2          0      +   DDX11L1
2       chr1  14361  29370    NR_024540.1          0      -    WASH7P
3       chr1  34610  36081    NR_026820.1          0      -   FAM138F
4       chr1  34610  36081    NR_026822.1          0      -   FAM138C
5       chr1  69090  70008 NM_001005484.1          0      +     OR4F5
6       chr1 134772 140566    NR_039983.2          0      - LOC729737
                             biotype
1 transcribed_unprocessed_pseudogene
2             unprocessed_pseudogene
3                            lincRNA
4                            lincRNA
5                     protein_coding
6                          antisense
---------------------------------------------------

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 -- Fri May 17 03:17:30 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: There were 17 warnings (use warnings() to see them)
Execution halted

Example timings

sitadela.Rcheck/sitadela-Ex.timings

nameusersystemelapsed
addAnnotation000
addCustomAnnotation4.1180.2524.370