Spencer Mahaffey
| Snapshot Date: 2024-12-16 13:00 -0500 (Mon, 16 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/multiMiR |
| git_branch: RELEASE_3_20 |
| git_last_commit: c1e2289 |
| git_last_commit_date: 2024-10-29 10:22:24 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-19 12:07 -0500 (Thu, 19 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4743 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4486 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4466 |
| 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 1370/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| multiMiR 1.28.0 (landing page) Spencer Mahaffey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | ERROR | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: multiMiR |
| Version: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multiMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multiMiR_1.28.0.tar.gz |
| StartedAt: 2024-12-18 02:46:42 -0500 (Wed, 18 Dec 2024) |
| EndedAt: 2024-12-18 02:49:08 -0500 (Wed, 18 Dec 2024) |
| EllapsedTime: 146.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: multiMiR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multiMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multiMiR_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/multiMiR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiMiR/DESCRIPTION’ ... OK
* this is package ‘multiMiR’ version ‘1.28.0’
* 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 ... 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 ... 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
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/multiMiR.Rcheck/00check.log’
for details.
multiMiR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL multiMiR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
> 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
5.678 0.301 8.899
multiMiR.Rcheck/multiMiR-Ex.timings
| name | user | system | elapsed | |
| all_tables | 0.000 | 0.001 | 0.001 | |
| get_multimir | 1.244 | 0.042 | 4.528 | |
| list_multimir | 0.080 | 0.005 | 1.882 | |
| multimir_dbInfo | 0.056 | 0.010 | 2.095 | |
| multimir_switchDBVersion | 0.033 | 0.003 | 0.777 | |
| search_multimir | 0.049 | 0.004 | 1.201 | |