Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1982/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sitadela 1.14.0 (landing page) Panagiotis Moulos
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: sitadela |
Version: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2024-11-20 02:47:48 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 02:56:22 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 513.6 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sitadela.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sitadela/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sitadela’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ... 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 1.441 0.093 10.895 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/sitadela.Rcheck/00check.log’ for details.
sitadela.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sitadela ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 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://jan2024.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/Rtmpz0RUZZ/file1477910c68bca Importing GTF /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/sitadela/dummy.gtf.gz as GTF to make id map Making id map Importing GTF /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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/Rtmpz0RUZZ/file1477910c68bca Scheduling 2 tests ================================================== Running test 1 of 2 scheduled ******************************************************** This is sitadela 1.14.0 genomic region annotation builder ******************************************************** sitadela database found at /tmp/Rtmpz0RUZZ directory ======================================================== 2024-11-20 02:55:42 - Try 1 ======================================================== Opening sitadela SQLite database /tmp/Rtmpz0RUZZ/file147795b038360 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/Rtmpz0RUZZ/file147795b038360 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 -- Wed Nov 20 02:56:14 2024 *********************************************** 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 35.765 1.826 59.410
sitadela.Rcheck/sitadela-Ex.timings
name | user | system | elapsed | |
addAnnotation | 0 | 0 | 0 | |
addCustomAnnotation | 3.540 | 0.163 | 3.730 | |
getAnnotation | 1.441 | 0.093 | 10.895 | |
getInstalledAnnotations | 0.001 | 0.000 | 0.002 | |
getSeqInfo | 0.133 | 0.017 | 0.548 | |
getUserAnnotations | 0.001 | 0.001 | 0.002 | |
getsetDbPath | 0.001 | 0.001 | 0.054 | |
importCustomAnnotation | 0.001 | 0.000 | 0.001 | |
loadAnnotation | 0.001 | 0.000 | 0.002 | |
removeAnnotation | 2.319 | 0.078 | 2.415 | |
testFuns | 2.292 | 0.066 | 3.461 | |