The R Project SVN R-packages

/*
 *  R.app : a Cocoa front end to: "R A Computer Language for Statistical Data Analysis"
 *  
 *  R.app Copyright notes:
 *                     Copyright (C) 2004-5  The R Foundation
 *                     written by Stefano M. Iacus and Simon Urbanek
 *
 *                  
 *  R Copyright notes:
 *                     Copyright (C) 1995-1996   Robert Gentleman and Ross Ihaka
 *                     Copyright (C) 1998-2001   The R Development Core Team
 *                     Copyright (C) 2002-2004   The R Foundation
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  A copy of the GNU General Public License is available via WWW at
 *  http://www.gnu.org/copyleft/gpl.html.  You can also obtain it by
 *  writing to the Free Software Foundation, Inc., 59 Temple Place,
 *  Suite 330, Boston, MA  02111-1307  USA.
 */

#import "PackageInstaller.h"
#import "RController.h"
#import "REngine/RCallbacks.h"
#import "REngine/REngine.h"
#import "Tools/Authorization.h"
#import "Preferences.h"
#import <Rversion.h>
#include <unistd.h>

static id sharedController;

NSString *location[2] = {
    @"/Library/Frameworks/R.framework/Resources/library/",
    @"~/Library/R/library"
};

@implementation PackageInstaller

- (void) busy: (BOOL) really
{
    if (really) {
        SLog(@"PackageInstaller: I'm getting busy");
        [busyIndicator startAnimation:self];
    } else {
        SLog(@"PackageInstaller: Stopped being busy");
        [busyIndicator stopAnimation:self];
    }
}

- (IBAction)installSelected:(id)sender
{
    NSString *targetLocation = nil;

    if(pkgInst == kOtherLocation){
        NSOpenPanel *op;
        int answer;
        
        op = [NSOpenPanel openPanel];
        [op setCanChooseDirectories:YES];
        [op setCanChooseFiles:NO];
        [op setTitle:NLS(@"Select Installation Directory")];
        
        answer = [op runModalForDirectory:nil file:nil types:[NSArray arrayWithObject:@""]];
        [op setCanChooseDirectories:NO];
        [op setCanChooseFiles:YES];
        if(answer == NSOKButton)
            targetLocation = [op directory];
        else
            return;
    } else
        targetLocation = location[pkgInst];
    
    [self busy:YES];

    {
        NSString *testFile;
        targetLocation = [targetLocation stringByExpandingTildeInPath];
        testFile = [targetLocation stringByAppendingString:@"/.aqua.test"];
        if ([[NSFileManager defaultManager] createFileAtPath:testFile contents:[NSData dataWithBytes:"foo" length:4] attributes:nil])
            [[NSFileManager defaultManager] removeFileAtPath:testFile handler:nil];
        else {
            if (requestRootAuthorization(0)) {
                [self busy: NO];
                NSRunAlertPanel(NLS(@"Package Installer"),NLS(@"The package has not been installed."),NLS(@"OK"),nil,nil);  
                return;
            } else {
                [[RController getRController] setRootFlag:YES];
                // we need to make sure that the tempdir is root-writable
                SLog(@" - installing as root, we need to make sure tempdir() is writable");
                RSEXP *x = [[REngine mainEngine] evaluateString:@"tempdir()"];
                if (x) {
                    NSString *td = [x string];
                    if (td) {
                        NSDictionary *fa = [NSDictionary dictionaryWithObjectsAndKeys: @"wheel", NSFileGroupOwnerAccountName, [NSNumber numberWithInt: 0770], NSFilePosixPermissions, nil];
                        if (fa) {
                            BOOL succ = [[NSFileManager defaultManager] changeFileAttributes:fa atPath:td];
                            SLog(@" - changed group to wheel and permissions to 0770 (%s)", succ?"success":"FAILED!");
                        } else SLog(@" * cannot create file attributes dictionary!");
                    } else SLog(@" * cannot retrieve tempdir! (got NULL string) Installation is likely to fail ...");
                    [x release];                    
                } else SLog(@" * cannot retrieve tempdir! (RSEXP is nil) Installation is likely to fail ...");
            }
        }
    }
    
    if( (pkgUrl == kLocalBin) || (pkgUrl == kLocalSrc) || (pkgUrl == kLocalDir) ){
        
        switch(pkgUrl){
            case kLocalBin:
                [[RController getRController] installFromBinary:self];
                break;
                
            case kLocalSrc:
                [[RController getRController] installFromSource:self];
                break;
                
            case kLocalDir:
                [[RController getRController] installFromDir:self];
                break;
                
            default:
                break;
        }
        
    } else {
        NSIndexSet *rows =  [pkgDataSource selectedRowIndexes];         
        unsigned current_index = [rows firstIndex];
        if(current_index == NSNotFound) {
            [self busy: NO];
            return;
        }
        
        NSMutableString *packagesToInstall = nil;
        
        packagesToInstall = [[NSMutableString alloc] initWithString: @"c("];
        
        while (current_index != NSNotFound) {
            [packagesToInstall appendFormat:@"\"%@\"",package[current_index].name];
            current_index = [rows indexGreaterThanIndex: current_index];
            if(current_index != NSNotFound)
                [packagesToInstall appendString:@","];
        }
        
        [packagesToInstall appendString:@")"];
        
        switch(pkgUrl){
            
            case kCRANBin:
                if([[RController getRController] getRootFlag]) {
                    NSBeginAlertSheet(NLS(@"Package installer"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Currently it is not possible to install binary packages from a remote repository as root.\nPlease use the CRAN binary of R to allow admin users to install system-wide packages without becoming root. Alternatively you can either use command-line version of R as root or install the packages from local files."));
                    break;
                }
                [[REngine mainEngine] executeString: 
                    [NSString stringWithFormat:@"install.binaries(%@,lib=\"%@\",CRAN=getOption(\"CRAN\"))",
                        packagesToInstall, targetLocation]                  
                    ];
                
                break;
                
            case kCRANSrc:
                [[REngine mainEngine] executeString: 
                    [NSString stringWithFormat:@"install.packages(%@,lib=\"%@\",CRAN=getOption(\"CRAN\"))",
                        packagesToInstall, targetLocation]];
                
                break;
                
            case kBIOCBin:
                [[REngine mainEngine] executeString: 
                    [NSString stringWithFormat:@"install.binaries(%@,lib=\"%@\",CRAN=getOption(\"BIOC\"))",
                        packagesToInstall, targetLocation]];
                break;
                
            case kBIOCSrc:
                [[REngine mainEngine] executeString: 
                    [NSString stringWithFormat:@"install.packages(%@,lib=\"%@\",CRAN=getOption(\"BIOC\"))",
                        packagesToInstall, targetLocation]];
                break;
                
            case kOTHER:
                if(pkgFormat == kSource)
                    [[REngine mainEngine] executeString: 
                        [NSString stringWithFormat:@"install.packages(%@,lib=\"%@\",contriburl=\"%@\")",
                            packagesToInstall, targetLocation, [urlTextField stringValue]]];
            else
                [[REngine mainEngine] executeString: 
                    [NSString stringWithFormat:@"install.binaries(%@,lib=\"%@\",contriburl=\"%@\")",
                        packagesToInstall, targetLocation, [urlTextField stringValue]]];
            break;

            default:
                break;
        }

        [packagesToInstall release];
    }
    
    [self busy:NO];
}


- (IBAction)reloadURL:(id)sender
{
    //  NSLog(@"pkgUrl=%d, pkgInst=%d, pkgFormat:%d",pkgUrl, pkgInst, pkgFormat);
    [self busy: YES];
    
    [pkgDataSource deselectAll:self];
    [pkgDataSource setHidden:YES];
    
#if (R_VERSION >= R_Version(2,1,0))
    // in 2.1 the proxy functions were not updated to accomodate for changes in
    // package installation - so we need to set options for backward compati-
    // bility
    if (!optionsChecked) {
        RSEXP *x = [[REngine mainEngine] evaluateString:@"getOption('CRAN')"];
        if (!x || ![x string]) { // CRAN is not set - let's try the repos
            BOOL hadToChoose=NO;
            SLog(@"PackageInstaller.reloadURL: checking options - CRAN is not set!");
            if (x) [x release];
            x = [[REngine mainEngine] evaluateString:@"getOption('repos')['CRAN']"];
            if (!x || ![x string] || [[x string] isEqualToString:@"@CRAN@"]) { // repos is not set
                if (x) [x release];
                SLog(@" - ['repos']['CRAN'] is not set, either. Launching mirror selector.");
                [[REngine mainEngine] executeString:@"chooseCRANmirror()"];
                hadToChoose=YES;
                x = [[REngine mainEngine] evaluateString:@"getOption('repos')['CRAN']"];
            }
            if (x && [x string] && ![[x string] isEqualToString:@"@CRAN@"]) { // repos is set now - push it to CRAN
                [x release];
                [[REngine mainEngine] evaluateString:@"options(CRAN=getOption('repos')['CRAN'])"];
                x = [[REngine mainEngine] evaluateString:@"getOption('CRAN')"];
                if (hadToChoose && ![Preferences flagForKey:stopAskingAboutDefaultMirrorSavingKey withDefault:NO])
                    NSBeginAlertSheet(NLS(@"Set as default?"), NLS(@"Yes"), NLS(@"Never"), NLS(@"No"), [self window], self, @selector(mirrorSaveAskSheetDidEnd:returnCode:contextInfo:), NULL, NULL, NLS(@"Do you want me to remember the mirror you selected for future sessions?"));
            } else {
                if (x) [x release]; // set x to nil - we need that in case x is @CRAN@
                x=nil;
            }
        }
        if (!x || ![x string]) { // CRAN is still not set - bail out with an error
            [self busy:NO];
            NSRunAlertPanel(NLS(@"Package Installer"),NLS(@"No valid CRAN mirror was selected.\nYou won't be able to install any CRAN packages unless you set the CRAN option to a valid mirror URL."),NLS(@"OK"),nil,nil);
            return;
        }
        if (x) [x release];
        optionsChecked = YES;
    }
#endif
    
    switch(pkgUrl){
        
        case kCRANBin:
            [[REngine mainEngine] executeString: 
                @"browse.pkgs(\"CRAN\",\"binary\")"];
            break;
            
        case kCRANSrc:
            [[REngine mainEngine] executeString: 
                @"browse.pkgs(\"CRAN\",\"source\")"];
            break;
            
        case kBIOCBin:
            [[REngine mainEngine] executeString: 
                @"browse.pkgs(\"BIOC\",\"binary\")"];
            break;
            
        case kBIOCSrc:
            [[REngine mainEngine] executeString: 
                @"browse.pkgs(\"BIOC\",\"source\")"];
            break;
            
        case kOTHER:
            if( [[urlTextField stringValue] isEqual:@""]){
                [self busy:NO];
                NSBeginAlertSheet(NLS(@"Package installer"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Please, specify a valid URL first."));
                return;
            }
            
            [[REngine mainEngine] executeString: 
                [NSString stringWithFormat:@"browse.pkgs(contriburl=\"%@\")",[urlTextField stringValue]]];
            break;
            
        default:
            break;
            
    }
    
    [self busy:NO];
}

- (void) mirrorSaveAskSheetDidEnd:(NSWindow *)sheet returnCode:(int)returnCode contextInfo:(void *)contextInfo
{
    switch(returnCode) {
        case NSAlertDefaultReturn: // Yes
            SLog(@"mirrorSaveAskSheetDidEnd: YES, Save");
        {
            RSEXP *x = [[REngine mainEngine] evaluateString:@"getOption('CRAN')"];
            if (x) {
                NSString *url = [x string];
                [x release];
                if (url && ![url isEqualToString:@"@CRAN@"])
                    [Preferences setKey:defaultCRANmirrorURLKey withObject:url];
            }
            break;
        }
        case NSAlertAlternateReturn: // Never
            SLog(@"mirrorSaveAskSheetDidEnd: NEVER!");
            [Preferences setKey:stopAskingAboutDefaultMirrorSavingKey withFlag:YES];
            break;
        default:
            SLog(@"mirrorSaveAskSheetDidEnd: NO, Don't Save");
    }
}

- (IBAction)setURL:(id)sender
{
    pkgUrl = [[ sender selectedCell] tag];
    [pkgDataSource setHidden:YES];
    
    switch(pkgUrl){
        
        
        case kCRANBin:
        case kBIOCBin:
            pkgFormat = kBinary;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setEnabled:NO];
            [getListButton setEnabled:YES];
            break;
            
        case kCRANSrc:
        case kBIOCSrc:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setEnabled:NO];
            [getListButton setEnabled:YES];
            break;
            
        case kOTHER:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:YES];
            [urlTextField setEnabled:YES];
            [getListButton setEnabled:YES];
            break;
            
        case kLocalBin:
            pkgFormat = kBinary;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [getListButton setEnabled:NO];
            break;
            
        case kLocalSrc:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [getListButton setEnabled:NO];
            break;
            
        case kLocalDir:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [getListButton setEnabled:NO];
            break;
            
        default:
            break;
    }
}

- (IBAction)setLocation:(id)sender
{
    pkgInst = [[ sender selectedCell] tag];
}

- (IBAction)setFormat:(id)sender
{
    pkgFormat = [[ sender selectedCell] state];
}

- (void)awakeFromNib
{
    [formatCheckBox setEnabled:NO];
    [urlTextField setEnabled:NO];
    pkgInst = isAdmin()?kSystemLevel:kUserLevel;
    pkgUrl = kCRANBin;
    pkgFormat = kBinary;
    [formatCheckBox setState:pkgFormat];
    [repositoryButton setTag:pkgUrl];
    [locationMatrix setTag:pkgInst];
    [locationMatrix selectCellWithTag:pkgInst];
    [busyIndicator setUsesThreadedAnimation:YES];
}

- (id)init
{
    self = [super init];
    if (self) {
        sharedController = self;
        [pkgDataSource setTarget: self];
        optionsChecked = NO;
        packages = 0;
    }
    
    return self;
}

- (void)dealloc {
    [self resetPackages];
    [super dealloc];
}

- (void) resetPackages
{
    if (!packages) return;
    int i=0;
    while (i<packages) {
        [package[i].name release];
        [package[i].iver release];
        [package[i].rver release];
        i++;
    }
    free(package);
    packages=0;
}

- (int)numberOfRowsInTableView: (NSTableView *)tableView
{
    return packages;
}

- (id)tableView: (NSTableView *)tableView objectValueForTableColumn: (NSTableColumn *)tableColumn row: (int)row
{
    if (row>=packages) return nil;
    if([[tableColumn identifier] isEqualToString:@"package"])
        return package[row].name;
    else if([[tableColumn identifier] isEqualToString:@"instVer"])
        return package[row].iver;
    else if([[tableColumn identifier] isEqualToString:@"repVer"])
        return package[row].rver;
    return nil;             
}

- (id) window
{
    return pkgWindow;
}

+ (id) sharedController {
    return sharedController;
}

- (IBAction) reloadPIData:(id)sender
{
    //  [[RController getRController] sendInput:@"package.manager()"];
    [pkgDataSource reloadData];
}

- (void) reloadData
{
    [pkgDataSource setHidden:NO];
    [pkgDataSource reloadData];
}

- (void) show
{
    [self reloadData];
    [[self window] makeKeyAndOrderFront:self];
}

- (void) updateInstalledPackages: (int) count withNames: (char**) name installedVersions: (char**) iver repositoryVersions: (char**) rver update: (BOOL*) stat label: (char*) label
{
    int i=0;
    
    if (packages) [self resetPackages];
    if (count<1) {
        [self show];
        return;
    }

    if (label) repositoryLabel = [NSString stringWithCString: label];
    
    package = malloc(sizeof(*package)*count);
    while (i<count) {
        package[i].name=[[NSString alloc] initWithCString: name[i]];
        package[i].iver=[[NSString alloc] initWithCString: iver[i]];
        package[i].rver=[[NSString alloc] initWithCString: rver[i]];
        package[i].status=stat[i];
        i++;
    }
    packages=count;
    
    [self show];
}

@end