| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:45 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 sitadela package: - Please 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 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 1861/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sitadela 1.4.0 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: sitadela |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2022-10-19 08:10:09 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 08:19:57 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 587.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sitadela.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/sitadela.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sitadela/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sitadela’ version ‘1.4.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getAnnotation 10.705 0.424 13.951
addCustomAnnotation 7.612 0.172 7.798
removeAnnotation 6.898 0.073 6.983
testFuns 6.256 0.078 8.816
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
sitadela.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sitadela ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 /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)
sitadela.Rcheck/tests/runTests.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> 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://dec2021.archive.ensembl.org
Test 1 successful!
Created 55320 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://dec2021.archive.ensembl.org
Test 1 successful!
Created 142339 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://dec2021.archive.ensembl.org
Test 1 successful!
Created 32020 features
Sample data:
chromosome start end gene_id gc_content strand
ENSDARG00000099104 chr1 6408 12027 ENSDARG00000099104 43.42 -
ENSDARG00000102407 chr1 11822 16373 ENSDARG00000102407 54.39 +
ENSDARG00000102097 chr1 18716 23389 ENSDARG00000102097 52.70 +
ENSDARG00000099319 chr1 25585 27255 ENSDARG00000099319 37.64 +
ENSDARG00000099640 chr1 27690 34330 ENSDARG00000099640 53.02 +
ENSDARG00000104071 chr1 36552 39191 ENSDARG00000104071 50.64 +
gene_name biotype
ENSDARG00000099104 rpl24 protein_coding
ENSDARG00000102407 cep97 protein_coding
ENSDARG00000102097 nfkbiz protein_coding
ENSDARG00000099319 CU651657.1 protein_coding
ENSDARG00000099640 eed protein_coding
ENSDARG00000104071 hikeshi protein_coding
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 danrer11 from latest version
Using Ensembl host https://dec2021.archive.ensembl.org
Test 1 successful!
Created 59253 features
Sample data:
chromosome start end transcript_id gene_id
ENSDART00000164359 chr1 6408 12027 ENSDART00000164359 ENSDARG00000099104
ENSDART00000157701 chr1 6642 9919 ENSDART00000157701 ENSDARG00000099104
ENSDART00000158290 chr1 6642 7335 ENSDART00000158290 ENSDARG00000099104
ENSDART00000167898 chr1 6644 11725 ENSDART00000167898 ENSDARG00000099104
ENSDART00000166393 chr1 11822 16373 ENSDART00000166393 ENSDARG00000102407
ENSDART00000161842 chr1 11992 14058 ENSDART00000161842 ENSDARG00000102407
strand gene_name biotype
ENSDART00000164359 - rpl24 protein_coding
ENSDART00000157701 - rpl24 protein_coding
ENSDART00000158290 - rpl24 protein_coding
ENSDART00000167898 - rpl24 protein_coding
ENSDART00000166393 + cep97 protein_coding
ENSDART00000161842 + cep97 protein_coding
Testing finished!
Summary
==================================================
Succesful tests: 1 out of 1
Failed tests : 0 out of 1
Scheduling 2 tests
==================================================
Running test 1 of 2 scheduled
Opening sitadela SQLite database /tmp/RtmpVMbx98/file729f5e17fafb
Importing GTF /Library/Frameworks/R.framework/Versions/4.2/Resources/library/sitadela/dummy.gtf.gz as GTF to make id map
Making id map
Importing GTF /Library/Frameworks/R.framework/Versions/4.2/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/4.2/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 /tmp/RtmpVMbx98/file729f5e17fafb
Scheduling 2 tests
==================================================
Running test 1 of 2 scheduled
********************************************************
This is sitadela 1.4.0 genomic region annotation builder
********************************************************
sitadela database found at /tmp/RtmpVMbx98 directory
========================================================
2022-10-19 08:18:26 - Try 1
========================================================
Opening sitadela SQLite database /tmp/RtmpVMbx98/file729f785ea4ff
Retrieving genome information for dm6 from ensembl
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, 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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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/RtmpVMbx98/file729f785ea4ff
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 -- Wed Oct 19 08:19:47 2022
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
sitadela RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
There were 17 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
89.999 2.619 159.408
sitadela.Rcheck/sitadela-Ex.timings
| name | user | system | elapsed | |
| addAnnotation | 0 | 0 | 0 | |
| addCustomAnnotation | 7.612 | 0.172 | 7.798 | |
| getAnnotation | 10.705 | 0.424 | 13.951 | |
| getInstalledAnnotations | 0.000 | 0.000 | 0.001 | |
| getSeqInfo | 0.266 | 0.014 | 0.494 | |
| getUserAnnotations | 0.001 | 0.000 | 0.001 | |
| getsetDbPath | 0.001 | 0.000 | 0.063 | |
| importCustomAnnotation | 0.001 | 0.000 | 0.002 | |
| loadAnnotation | 0.002 | 0.001 | 0.002 | |
| removeAnnotation | 6.898 | 0.073 | 6.983 | |
| testFuns | 6.256 | 0.078 | 8.816 | |