Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1364/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
multiMiR 1.29.0 (landing page) Spencer Mahaffey
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the multiMiR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiMiR.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: multiMiR |
Version: 1.29.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:multiMiR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings multiMiR_1.29.0.tar.gz |
StartedAt: 2024-12-23 10:04:38 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 10:07:16 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 158.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: multiMiR.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:multiMiR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings multiMiR_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/multiMiR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘multiMiR/DESCRIPTION’ ... OK * this is package ‘multiMiR’ version ‘1.29.0’ * 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 ‘multiMiR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... WARNING Error: package or namespace load failed for ‘multiMiR’: .onLoad failed in loadNamespace() for 'multiMiR', details: call: NULL error: Internal Server Error Execution halted * checking whether the namespace can be loaded with stated dependencies ... WARNING Error: .onLoad failed in loadNamespace() for 'multiMiR', details: call: NULL error: Internal Server Error Execution halted A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... WARNING Error: .onLoad failed in loadNamespace() for 'multiMiR', details: call: NULL error: Internal Server Error Execution halted * checking loading without being on the library search path ... WARNING Error: package or namespace load failed for ‘multiMiR’: .onLoad failed in loadNamespace() for 'multiMiR', details: call: NULL error: Internal Server Error Execution halted It looks like this package has a loading problem when not on .libPaths: see the messages for details. * checking dependencies in R code ... NOTE Error: .onLoad failed in loadNamespace() for 'multiMiR', details: call: NULL error: Internal Server Error Call sequence: 3: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 2: runHook(".onLoad", env, package.lib, package) 1: loadNamespace(package, lib.loc) Execution halted * checking S3 generic/method consistency ... WARNING Error: .onLoad failed in loadNamespace() for 'multiMiR', details: call: NULL error: Internal Server Error Call sequence: 3: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s", hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], conditionMessage(res)), call. = FALSE, domain = NA) 2: runHook(".onLoad", env, package.lib, package) 1: loadNamespace(package, lib.loc) Execution halted See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * 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 get_multimir 1.718 0.124 5.86 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 5 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/multiMiR.Rcheck/00check.log’ for details.
multiMiR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL multiMiR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘multiMiR’ ... ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (multiMiR)
multiMiR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > library(testthat) > library(multiMiR) Welcome to multiMiR. multiMiR database URL has been set to the default value: http://multimir.org/ Database Version: 2.4.0 Updated: 2024-08-28 > > test_check("multiMiR") -- -- Table structure for table `mirna` -- DROP TABLE IF EXISTS `mirna`; CREATE TABLE `mirna` ( mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID org VARCHAR(4) NOT NULL, -- organism abbreviation mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name PRIMARY KEY (mature_mirna_uid), KEY org (org), KEY mature_mirna_acc (mature_mirna_acc), KEY mature_mirna_id (mature_mirna_id) ); -- -- Table structure for table `target` -- DROP TABLE IF EXISTS `target`; CREATE TABLE `target` ( target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID org VARCHAR(4) NOT NULL, -- organism abbreviation target_symbol VARCHAR(80) default NULL, -- target gene symbol target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID PRIMARY KEY (target_uid), KEY org (org), KEY target_symbol (target_symbol), KEY target_entrez (target_entrez), KEY target_ensembl (target_ensembl) ); -- -- Table structure for table `mirecords` -- DROP TABLE IF EXISTS `mirecords`; CREATE TABLE `mirecords` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID target_site_number INT(10) default NULL, -- target site number target_site_position INT(10) default NULL, -- target site position experiment VARCHAR(160) default NULL, -- supporting experiment support_type VARCHAR(40) default NULL, -- type of supporting experiment pubmed_id VARCHAR(10) default NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT ); -- -- Table structure for table `mirtarbase` -- DROP TABLE IF EXISTS `mirtarbase`; CREATE TABLE `mirtarbase` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID experiment VARCHAR(160) NOT NULL, -- supporting experiment support_type VARCHAR(40) NOT NULL, -- type of supporting experiment pubmed_id VARCHAR(10) default NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT ); -- -- Table structure for table `tarbase` -- DROP TABLE IF EXISTS `tarbase`; CREATE TABLE `tarbase` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID experiment VARCHAR(160) NOT NULL, -- supporting experiment support_type VARCHAR(40) NOT NULL, -- type of supporting experiment pubmed_id VARCHAR(10) default NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT ); -- -- Table structure for table `miranda` -- DROP TABLE IF EXISTS `miranda`; CREATE TABLE `miranda` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID conservation REAL NOT NULL, -- conservation score mirsvr_score REAL NOT NULL, -- mirSVR downregulation score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY conservation (conservation), KEY mirsvr_score (mirsvr_score) ); -- -- Table structure for table `targetscan` -- DROP TABLE IF EXISTS `targetscan`; CREATE TABLE `targetscan` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html) context_plus_score REAL NOT NULL, -- context+ score conserved_site ENUM('N','Y'), -- whether the target site is conserved FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY context_plus_score (context_plus_score), KEY conserved_site (conserved_site) ); -- -- Table structure for table `diana_microt` -- DROP TABLE IF EXISTS `diana_microt`; CREATE TABLE `diana_microt` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID miTG_score REAL NOT NULL, -- miRNA target gene score UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY miTG_score (miTG_score) ); -- -- Table structure for table `elmmo` -- DROP TABLE IF EXISTS `elmmo`; CREATE TABLE `elmmo` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure" FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY p (p) ); -- -- Table structure for table `pita` -- DROP TABLE IF EXISTS `pita`; CREATE TABLE `pita` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible) conservation REAL NOT NULL, -- site conservation (range 0~1) FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY ddG (ddG), KEY conservation (conservation) ); -- -- Table structure for table `microcosm` -- DROP TABLE IF EXISTS `microcosm`; CREATE TABLE `microcosm` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID score REAL NOT NULL, -- miRanda score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY score (score) ); -- -- Table structure for table `pictar` -- DROP TABLE IF EXISTS `pictar`; CREATE TABLE `pictar` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID score REAL NOT NULL, -- score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY score (score) ); -- -- Table structure for table `mirdb` -- DROP TABLE IF EXISTS `mirdb`; CREATE TABLE `mirdb` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID score REAL NOT NULL, -- score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY score (score) ); -- -- Table structure for table `mir2disease` -- DROP TABLE IF EXISTS `mir2disease`; CREATE TABLE `mir2disease` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID disease VARCHAR(100) NOT NULL, -- disease mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal) experiment VARCHAR(40) NOT NULL, -- supporting experiment year INTEGER UNSIGNED NOT NULL, -- year of the paper title TEXT NOT NULL, -- title of the paper FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY disease (disease) ); -- -- Table structure for table `pharmaco_mir` -- DROP TABLE IF EXISTS `pharmaco_mir`; CREATE TABLE `pharmaco_mir` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID drug VARCHAR(40) NOT NULL, -- disease pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY drug (drug) ); -- -- Table structure for table `phenomir` -- DROP TABLE IF EXISTS `phenomir`; CREATE TABLE `phenomir` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID disease VARCHAR(60) NOT NULL, -- disease disease_class VARCHAR(20) NOT NULL, -- disease class mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc) experiment VARCHAR(40) NOT NULL, -- supporting experiment pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY disease (disease), KEY disease_class (disease_class) ); -- -- Table structure for table `metadata` -- DROP TABLE IF EXISTS `metadata`; CREATE TABLE metadata ( name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) ); -- -- Table structure for table `map_metadata` -- DROP TABLE IF EXISTS `map_metadata`; CREATE TABLE map_metadata ( map_name VARCHAR(80) PRIMARY KEY, source_name VARCHAR(80) NOT NULL, source_version VARCHAR(20), source_date VARCHAR(20), source_url VARCHAR(255) NOT NULL ); -- -- Table structure for table `map_counts` -- DROP TABLE IF EXISTS `map_counts`; CREATE TABLE map_counts ( map_name VARCHAR(80) PRIMARY KEY, human_count INTEGER UNSIGNED NOT NULL, mouse_count INTEGER UNSIGNED NOT NULL, total_count INTEGER UNSIGNED NOT NULL ); -- -- Table structure for table `mirna` -- DROP TABLE IF EXISTS `mirna`; CREATE TABLE `mirna` ( mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID org VARCHAR(4) NOT NULL, -- organism abbreviation mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name PRIMARY KEY (mature_mirna_uid), KEY org (org), KEY mature_mirna_acc (mature_mirna_acc), KEY mature_mirna_id (mature_mirna_id) ); -- -- Table structure for table `target` -- DROP TABLE IF EXISTS `target`; CREATE TABLE `target` ( target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID org VARCHAR(4) NOT NULL, -- organism abbreviation target_symbol VARCHAR(80) default NULL, -- target gene symbol target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID PRIMARY KEY (target_uid), KEY org (org), KEY target_symbol (target_symbol), KEY target_entrez (target_entrez), KEY target_ensembl (target_ensembl) ); -- -- Table structure for table `mirecords` -- DROP TABLE IF EXISTS `mirecords`; CREATE TABLE `mirecords` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID target_site_number INT(10) default NULL, -- target site number target_site_position INT(10) default NULL, -- target site position experiment VARCHAR(160) default NULL, -- supporting experiment support_type VARCHAR(40) default NULL, -- type of supporting experiment pubmed_id VARCHAR(10) default NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT ); -- -- Table structure for table `mirtarbase` -- DROP TABLE IF EXISTS `mirtarbase`; CREATE TABLE `mirtarbase` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID experiment VARCHAR(160) NOT NULL, -- supporting experiment support_type VARCHAR(40) NOT NULL, -- type of supporting experiment pubmed_id VARCHAR(10) default NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT ); -- -- Table structure for table `tarbase` -- DROP TABLE IF EXISTS `tarbase`; CREATE TABLE `tarbase` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID experiment VARCHAR(160) NOT NULL, -- supporting experiment support_type VARCHAR(40) NOT NULL, -- type of supporting experiment pubmed_id VARCHAR(10) default NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT ); -- -- Table structure for table `miranda` -- DROP TABLE IF EXISTS `miranda`; CREATE TABLE `miranda` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID conservation REAL NOT NULL, -- conservation score mirsvr_score REAL NOT NULL, -- mirSVR downregulation score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY conservation (conservation), KEY mirsvr_score (mirsvr_score) ); -- -- Table structure for table `targetscan` -- DROP TABLE IF EXISTS `targetscan`; CREATE TABLE `targetscan` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html) context_plus_score REAL NOT NULL, -- context+ score conserved_site ENUM('N','Y'), -- whether the target site is conserved FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY context_plus_score (context_plus_score), KEY conserved_site (conserved_site) ); -- -- Table structure for table `diana_microt` -- DROP TABLE IF EXISTS `diana_microt`; CREATE TABLE `diana_microt` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID miTG_score REAL NOT NULL, -- miRNA target gene score UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY miTG_score (miTG_score) ); -- -- Table structure for table `elmmo` -- DROP TABLE IF EXISTS `elmmo`; CREATE TABLE `elmmo` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure" FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY p (p) ); -- -- Table structure for table `pita` -- DROP TABLE IF EXISTS `pita`; CREATE TABLE `pita` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible) conservation REAL NOT NULL, -- site conservation (range 0~1) FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY ddG (ddG), KEY conservation (conservation) ); -- -- Table structure for table `microcosm` -- DROP TABLE IF EXISTS `microcosm`; CREATE TABLE `microcosm` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID score REAL NOT NULL, -- miRanda score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY score (score) ); -- -- Table structure for table `pictar` -- DROP TABLE IF EXISTS `pictar`; CREATE TABLE `pictar` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID score REAL NOT NULL, -- score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY score (score) ); -- -- Table structure for table `mirdb` -- DROP TABLE IF EXISTS `mirdb`; CREATE TABLE `mirdb` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID score REAL NOT NULL, -- score FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY score (score) ); -- -- Table structure for table `mir2disease` -- DROP TABLE IF EXISTS `mir2disease`; CREATE TABLE `mir2disease` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID disease VARCHAR(100) NOT NULL, -- disease mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal) experiment VARCHAR(40) NOT NULL, -- supporting experiment year INTEGER UNSIGNED NOT NULL, -- year of the paper title TEXT NOT NULL, -- title of the paper FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY disease (disease) ); -- -- Table structure for table `pharmaco_mir` -- DROP TABLE IF EXISTS `pharmaco_mir`; CREATE TABLE `pharmaco_mir` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID drug VARCHAR(40) NOT NULL, -- disease pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, FOREIGN KEY (target_uid) REFERENCES target(target_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY drug (drug) ); -- -- Table structure for table `phenomir` -- DROP TABLE IF EXISTS `phenomir`; CREATE TABLE `phenomir` ( mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID disease VARCHAR(60) NOT NULL, -- disease disease_class VARCHAR(20) NOT NULL, -- disease class mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc) experiment VARCHAR(40) NOT NULL, -- supporting experiment pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID FOREIGN KEY (mature_mirna_uid) REFERENCES mirna(mature_mirna_uid) ON UPDATE CASCADE ON DELETE RESTRICT, KEY disease (disease), KEY disease_class (disease_class) ); -- -- Table structure for table `metadata` -- DROP TABLE IF EXISTS `metadata`; CREATE TABLE metadata ( name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) ); -- -- Table structure for table `map_metadata` -- DROP TABLE IF EXISTS `map_metadata`; CREATE TABLE map_metadata ( map_name VARCHAR(80) PRIMARY KEY, source_name VARCHAR(80) NOT NULL, source_version VARCHAR(20), source_date VARCHAR(20), source_url VARCHAR(255) NOT NULL ); -- -- Table structure for table `map_counts` -- DROP TABLE IF EXISTS `map_counts`; CREATE TABLE map_counts ( map_name VARCHAR(80) PRIMARY KEY, human_count INTEGER UNSIGNED NOT NULL, mouse_count INTEGER UNSIGNED NOT NULL, total_count INTEGER UNSIGNED NOT NULL ); [ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ] > > proc.time() user system elapsed 6.392 0.285 10.144
multiMiR.Rcheck/multiMiR-Ex.timings
name | user | system | elapsed | |
all_tables | 0.001 | 0.000 | 0.000 | |
get_multimir | 1.718 | 0.124 | 5.860 | |
list_multimir | 0.100 | 0.000 | 2.369 | |
multimir_dbInfo | 0.061 | 0.008 | 2.338 | |
multimir_switchDBVersion | 0.039 | 0.000 | 0.974 | |
search_multimir | 0.055 | 0.000 | 1.504 | |