Multiple platform build/check report for BioC 3.20 - CHECK results for multiMiR on nebbiolo2

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"	4739
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4482
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4510
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4462
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*

CHECK results for multiMiR on nebbiolo2

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.

raw results

Summary

Package: multiMiR

Version: 1.28.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiMiR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiMiR_1.28.0.tar.gz

StartedAt: 2024-11-29 03:26:24 -0500 (Fri, 29 Nov 2024)

EndedAt: 2024-11-29 03:32:34 -0500 (Fri, 29 Nov 2024)

EllapsedTime: 370.2 seconds

RetCode: 0

Status: OK

CheckDir: multiMiR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiMiR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiMiR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/multiMiR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...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 ‘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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/multiMiR.Rcheck/00check.log’
for details.

Installation output

multiMiR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL multiMiR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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)

Tests output

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: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 
  4.222   0.265   5.652

Example timings

multiMiR.Rcheck/multiMiR-Ex.timings

name	user	system	elapsed
all_tables	0.001	0.000	0.001
get_multimir	1.227	0.115	4.066
list_multimir	0.117	0.011	1.164
multimir_dbInfo	0.106	0.004	1.175
multimir_switchDBVersion	0.062	0.000	0.421
search_multimir	0.090	0.000	0.735