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"
};

@interface PackageEntry (PrivateMethods)
- (NSString*) name;
- (NSString*) iver;
- (NSString*) rver;
- (BOOL) status;

// this one allows us to run sortUsingSelector: on the enclosing array - the actual reason why I replaced the C structure
- (NSComparisonResult)caseInsensitiveCompare:(PackageEntry *)anEntry;
@end

@implementation PackageEntry

- (id) initWithName: (const char*) cName iVer: (const char*) iV rVer: (const char*) rV status: (BOOL) st
{
    self = [super init];
    if (self) {
        name=[[NSString alloc] initWithUTF8String: cName];
        iver=[[NSString alloc] initWithUTF8String: iV];
        rver=[[NSString alloc] initWithUTF8String: rV];
        status=st;
    }
    return self;
}

- (void) dealloc {
    [name release];
    [iver release];
    [rver release];
    [super dealloc];
}

- (NSString*) name { return name; };
- (NSString*) iver { return iver; };
- (NSString*) rver { return rver; };
- (BOOL) status { return status; };

- (NSComparisonResult)caseInsensitiveCompare:(PackageEntry *)anEntry
{
    return [name caseInsensitiveCompare:[anEntry name]];
}
@end

@implementation PackageInstaller

- (void) busy: (BOOL) really
{
    if (really) {
        SLog(@"PackageInstaller: I'm getting busy");
        [busyIndicator startAnimation:self];
        [updateAllButton setEnabled:NO];
        [installButton setEnabled:NO];
        [getListButton setEnabled:NO];
    } else {
        SLog(@"PackageInstaller: Stopped being busy");
        [busyIndicator stopAnimation:self];
        [updateAllButton setEnabled:!(pkgUrl==kLocalBin || pkgUrl==kLocalSrc || pkgUrl==kLocalDir)];
        [installButton setEnabled:YES];
        [getListButton setEnabled:!(pkgUrl==kLocalBin || pkgUrl==kLocalSrc || pkgUrl==kLocalDir)];
    }
}

- (IBAction)installSelected:(id)sender
{
    NSString *targetLocation = nil;
    BOOL success = YES;
    
    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 sharedController] 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 ...");
            }
        }
    }
    
    switch(pkgUrl) {
        case kLocalBin:
            [[RController sharedController] installFromBinary:self];
            break;
            
        case kLocalSrc:
            [[RController sharedController] installFromSource:self];
            break;
            
        case kLocalDir:
            [[RController sharedController] installFromDir:self];
            break;
            
        default:
        {
            NSMutableString *packagesToInstall = nil;
            NSIndexSet *rows =  [pkgDataSource selectedRowIndexes];
            NSString *repos = @"getOption(\"repos\")";
            NSString *type  = @"mac.binary";
            unsigned current_index = [rows firstIndex];
            
            if(current_index == NSNotFound) {
                [self busy: NO];
                NSBeginAlertSheet(NLS(@"Package installer"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"No packages selected, nothing to do."));
                break;
            }
            
            packagesToInstall = [[NSMutableString alloc] initWithString: @"c("];
            
            while (current_index != NSNotFound) {
                int cix = current_index;
                if (filter) cix=filter[cix];
                [packagesToInstall appendFormat:@"\"%@\"",[[packages objectAtIndex:cix] name]];
                current_index = [rows indexGreaterThanIndex: current_index];
                if(current_index != NSNotFound)
                    [packagesToInstall appendString:@","];
            }
            
            [packagesToInstall appendString:@")"];
            
            switch(pkgUrl) {
                
                case kCRANBin:
                    if([[RController sharedController] 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;
                    }
                    
                    break;
                    
                case kCRANSrc:
                    type = @"source";
                    break;
                    
                case kBIOCBin:
                    repos=@"getOption(\"BioC.Repos\")";
                    break;
                    
                case kBIOCSrc:
                    repos=@"getOption(\"BioC.Repos\")";
                    type=@"source";
                    break;
                    
                case kOTHER:
                case kOtherFlat:
                    if (pkgFormat == kSource) type=@"source";
                    repos = [NSString stringWithFormat:@"\"%@\"", [urlTextField stringValue]];
                    break;
            }
            
            if (repos && type) {
                if (pkgUrl == kOtherFlat)
                    success = [[REngine mainEngine] executeString: 
                        [NSString stringWithFormat:@"install.packages(%@,lib=\"%@\",contriburl=%@),type='%@')",
                            packagesToInstall, targetLocation, repos, type]
                        ];
                else
                    success = [[REngine mainEngine] executeString: 
                        [NSString stringWithFormat:@"install.packages(%@,lib=\"%@\",contriburl=contrib.url(%@,'%@'),type='%@')",
                            packagesToInstall, targetLocation, repos, type, type]
                        ];
            }
            
            [packagesToInstall release];
        }
    }
            
    if (!success) NSBeginAlertSheet(NLS(@"Package installation failed"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Package installation was not successful. Please see the R Console for details."));
    
    [self busy:NO];
    
    if (!(pkgUrl==kLocalBin || pkgUrl==kLocalSrc || pkgUrl==kLocalDir)) [self reloadURL:self];
}

- (void) checkOptions
{
#if (R_VERSION >= R_Version(2,1,0))
    // in 2.1.0 release 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;
        BOOL hadToChoose=NO;
#if (R_VERSION < R_Version(2,2,0))
        x = [[REngine mainEngine] evaluateString:@"getOption('CRAN')"];
        if (!x || ![x string]) { // CRAN is not set - let's try the repos
            SLog(@"PackageInstaller.reloadURL: checking options - CRAN is not set!");
            if (x) [x release];
#endif
            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
#if (R_VERSION < R_Version(2,2,0))
                [x release];
                [[REngine mainEngine] evaluateString:@"options(CRAN=getOption('repos')['CRAN'])"];
                x = [[REngine mainEngine] evaluateString:@"getOption('CRAN')"];
#endif
                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 (R_VERSION < R_Version(2,2,0))
        }
#endif
        if (!x || ![x string]) { // CRAN is still not set - bail out with an error
            [self busy:NO];
            NSRunAlertPanel(NLS(@"No CRAN Mirror Found"),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
}

- (IBAction)reloadURL:(id)sender
{
    BOOL success = NO;
    //  NSLog(@"pkgUrl=%d, pkgInst=%d, pkgFormat:%d",pkgUrl, pkgInst, pkgFormat);
    
    [self busy: YES];
    
    [self checkOptions];
    
    switch(pkgUrl){
        
        case kCRANBin:
            success = [[REngine mainEngine] executeString: 
                @"browse.pkgs(type=\"mac.binary\")"];
            break;
            
        case kCRANSrc:
            success = [[REngine mainEngine] executeString: 
                @"browse.pkgs(type=\"source\")"];
            break;
            
        case kBIOCBin:
            success = [[REngine mainEngine] executeString: 
                @"browse.pkgs(contriburl=contrib.url(getOption(\"BioC.Repos\"),\"mac.binary\"), type=\"mac.binary\")"];
            break;
            
        case kBIOCSrc:
            success = [[REngine mainEngine] executeString: 
                @"browse.pkgs(contriburl=contrib.url(getOption(\"BioC.Repos\"),\"source\"), type=\"source\")"];
            break;
            
        case kOTHER:
        case kOtherFlat:
            if( [[urlTextField stringValue] isEqual:@""]){
                [self busy:NO];
                NSBeginAlertSheet(NLS(@"Invalid Repository URL"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Please specify a valid URL first."));
                return;
            }
            
            [Preferences setKey:@"pkgInstaller.customURL" withObject:[urlTextField stringValue]];
            success = [[REngine mainEngine] executeString: 
                [NSString stringWithFormat:@"browse.pkgs(%@=\"%@\",type=\"%@\")",
                                               (pkgUrl == kOtherFlat)?@"contriburl":@"repos",
                                               [urlTextField stringValue], (pkgFormat == kSource)?@"source":@"mac.binary"]];
            break;
            
    }
    loadedPkgUrl=pkgUrl; // whether successful or not doesn't mattter - but the load was attempted
    if ([pkgDataSource numberOfRows]>0) [installButton setEnabled:YES];
    [self reRunFilter];
    
    if (!success) NSBeginAlertSheet(NLS(@"Fetching Package List Failed"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Please consult  R Console output for details."));
    
    [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('repos')['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:(loadedPkgUrl!=pkgUrl)]; // hide if it's not the loaded one 
    [installButton setEnabled:(loadedPkgUrl==pkgUrl || pkgUrl==kLocalBin || pkgUrl==kLocalSrc || pkgUrl==kLocalDir)];
    
    if (pkgUrl==kLocalBin || pkgUrl==kLocalSrc || pkgUrl==kLocalDir)
        [installButton setTitle:NLS(@"InstallÉ")];
    else
        [installButton setTitle:NLS(@"Install Selected")];
            
    
    switch(pkgUrl){
        
        
        case kCRANBin:
        case kBIOCBin:
            pkgFormat = kBinary;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setHidden:YES];
            [getListButton setEnabled:YES];
            [updateAllButton setEnabled:YES];
            break;
            
        case kCRANSrc:
        case kBIOCSrc:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setHidden:YES];
            [getListButton setEnabled:YES];
            [updateAllButton setEnabled:YES];
            break;
            
        case kOTHER:
        case kOtherFlat:
            pkgFormat = kBinary;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:YES];
            [urlTextField setHidden:NO];
            [getListButton setEnabled:YES];
            [updateAllButton setEnabled:YES];
            break;
            
        case kLocalBin:
            pkgFormat = kBinary;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setHidden:YES];
            [getListButton setEnabled:NO];
            [updateAllButton setEnabled:NO];
            break;
            
        case kLocalSrc:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setHidden:YES];
            [getListButton setEnabled:NO];
            [updateAllButton setEnabled:NO];
            break;
            
        case kLocalDir:
            pkgFormat = kSource;
            [formatCheckBox setState:pkgFormat];
            [formatCheckBox setEnabled:NO];
            [urlTextField setHidden:YES];
            [getListButton setEnabled:NO];
            [updateAllButton setEnabled:NO];
            break;
            
        default:
            break;
    }
}

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

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

- (void)awakeFromNib
{
    NSString *cURL = [Preferences stringForKey:@"pkgInstaller.customURL"];
    [formatCheckBox setEnabled:NO];
    if (cURL) [urlTextField setStringValue:cURL];
    [urlTextField setHidden:YES];
    [installButton 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];
    
    {
        NSArray *a = [[NSFileManager defaultManager] directoryContentsAtPath:@"/Library/Frameworks/R.framework/Versions"];
        int i;

        oldRPath = nil;
        [[pkgSearchMenu itemWithTag:2] setEnabled:NO];
        if (a && [a count]>1) {
            a = [a sortedArrayUsingSelector:@selector(caseInsensitiveCompare:)];
            i = [a count]-1;
            while (i>=0) {
                /* FIXME! hard-coded version. At this point we don't know the R version since R is not running */
                if ([(NSString*)[a objectAtIndex:i] compare:@"2.2"]<0) break;
                i--;
            }
            if (i>=0) {
                oldRPath=[[NSString stringWithFormat:@"/Library/Frameworks/R.framework/Versions/%@/Resources", [a objectAtIndex:i]] retain];
                SLog(@"PackageInstaller.awakeFromNib: found previous R at %@", oldRPath);
                [[pkgSearchMenu itemWithTag:2] setTitle:[NSString stringWithFormat:NLS(@"Select packages from R %@"), [a objectAtIndex:i]]];
            }
        }
    }
    if (!oldRPath) {
        SLog(@"PackageInstaller.awakeFromNib: no previous R version found.");
        [pkgSearchMenu removeItem:[pkgSearchMenu itemWithTag:2]];
    }
}

- (id)init
{
    self = [super init];
    if (self) {
        sharedController = self;
        [pkgDataSource setTarget: self];
        optionsChecked = NO;
        loadedPkgUrl = -1;
        packages = [[NSMutableArray alloc] init];
        filter = 0;
        filterlen = 0;
        filterString = nil;
        installedOnly = NO;
        oldRPath = nil;
    }
    
    return self;
}

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

- (void) resetPackages
{
    [packages removeAllObjects];
    if (filter) {
        free(filter);
        filter=0;
    }
    filterlen=0;
}

- (int)numberOfRowsInTableView: (NSTableView *)tableView
{
    return (filter)?filterlen:[packages count];
}

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

- (id) window
{
    return pkgWindow;
}

+ (id) sharedController {
    return sharedController;
}

- (IBAction) reloadPIData:(id)sender
{
    //  [[RController sharedController] 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 count]>0) [self resetPackages];
    if (count<1) {
        [self show];
        return;
    }
    
    if (label) repositoryLabel = [NSString stringWithUTF8String: label];

    while (i<count) {
        PackageEntry *pe = [[PackageEntry alloc] initWithName:name[i] iVer:iver[i] rVer:rver[i] status:stat[i]];
        [packages addObject:pe];
        [pe release]; // the array retained it
        i++;
    }
    [packages sortUsingSelector:@selector(caseInsensitiveCompare:)];
    
    [self show];
}

- (IBAction)updateAll:(id)sender
{
    NSString *targetLocation = nil;
    NSString *repos = nil;
    NSString *type = @"mac.binary";
    BOOL success = NO;

    if(pkgUrl == kOTHER && [[urlTextField stringValue] isEqual:@""]) {
        NSBeginAlertSheet(NLS(@"Invalid Repository URL"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Please specify a valid URL first."));
        return;
    }

    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];
    
    [self checkOptions];
    
    switch(pkgUrl){
        case kCRANBin:
            if([[RController sharedController] 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;
            }
            repos=@"getOption(\"repos\")";
            break;
            
        case kCRANSrc:
            repos=@"getOption(\"repos\")";
            type =@"source";
            break;
            
        case kBIOCBin:
            repos=@"getOption(\"BioC.Repos\")";
            break;
            
        case kBIOCSrc:
            repos=@"getOption(\"BioC.Repos\")";
            type =@"source";
            break;
            
        case kOTHER:
            repos=[NSString stringWithFormat:@"\"%@\"", [urlTextField stringValue]];
            if(pkgFormat == kSource) type =@"source";
    }
    if (pkgUrl != kOtherFlat)
        success = [[REngine mainEngine] executeString: 
            [NSString stringWithFormat:@"update.packages(lib=\"%@\",ask='graphics',contriburl=contrib.url(%@,'%@'),type='%@')",
                targetLocation, repos, type, type]
            ];
    else
        success = [[REngine mainEngine] executeString: 
            [NSString stringWithFormat:@"update.packages(lib=\"%@\",ask='graphics',contriburl='%@',type='%@')",
                targetLocation, [urlTextField stringValue], type]
            ];
    
    if (!success) NSBeginAlertSheet(NLS(@"Package update failed"), NLS(@"OK"), nil, nil, [self window], self, NULL, NULL, NULL, NLS(@"Package update was not successful. Please see the R Console for details."));
    
    [self reloadURL:self];
    [self busy:NO];
}

- (void) reRunFilter
{
    SLog(@"PackageInstaller.reRunFilter (search string is %@)",filterString?filterString:@"<none>");
    
    NSIndexSet *preIx = [pkgDataSource selectedRowIndexes];
    NSMutableIndexSet *postIx = [[NSMutableIndexSet alloc] init];
    NSMutableIndexSet *absSelIx = [[NSMutableIndexSet alloc] init];
    int i=0;
    
    if ([preIx count]>0) { // save selection in absolute index positions
        i = [preIx firstIndex];
        do {
            if (!filter || i<filterlen)
                [absSelIx addIndex:filter?filter[i]:i];
            i = [preIx indexGreaterThanIndex:i];
        } while (i!=NSNotFound);
        i=0;
    }
    
    if (filter) {
        filterlen=0;
        if (filter) free(filter);
        filter=0;
    }
    
    if (installedOnly || (filterString && [filterString length]>0)) {
        filterlen=0;
        while (i<[packages count]) {
            BOOL isCand = !installedOnly || [[[packages objectAtIndex:i] iver] length]>0;
            if (isCand && (!filterString || [[[packages objectAtIndex:i] name] rangeOfString:filterString options:NSCaseInsensitiveSearch].location!=NSNotFound)) filterlen++;
            i++;
        }
        SLog(@" - found %d matches", filterlen);
        filter=(int*)malloc(sizeof(int)*(filterlen+1));
        i=0; filterlen=0;
        while (i<[packages count]) {
            BOOL isCand = !installedOnly || [[[packages objectAtIndex:i] iver] length]>0;
            if (isCand && (!filterString || [[[packages objectAtIndex:i] name] rangeOfString:filterString options:NSCaseInsensitiveSearch].location!=NSNotFound)) {
                if ([absSelIx containsIndex:i])
                    [postIx addIndex:filterlen];
                filter[filterlen++]=i;
            }
            i++;
        }
    } else [postIx addIndexes:absSelIx];
    
    [pkgDataSource reloadData];
    [pkgDataSource selectRowIndexes:postIx byExtendingSelection:NO];
    [absSelIx release];
    [postIx release];
}

- (IBAction)runPkgSearch:(id)sender
{
    NSString *ss = [sender stringValue];
    if (filterString) [filterString release];
    if (!ss || [ss length]==0)
        filterString=nil;
    else {
        filterString = ss;
        [filterString retain];
    }
    [self reRunFilter];
}

- (IBAction)toggleShowInstalled:(id)sender
{
    installedOnly = !installedOnly;
    [(NSMenuItem*) sender setTitle:installedOnly?NLS(@"Show All"):NLS(@"Show Installed Only")];
    [self reRunFilter];
}

- (IBAction)selectOldPackages:(id)sender
{
    if (!oldRPath) return;
    NSArray *a = [[NSFileManager defaultManager] directoryContentsAtPath:[NSString stringWithFormat:@"%@/library", oldRPath]];
    if (!a || [a count]<1) return;
    NSMutableIndexSet *postIx = [[NSMutableIndexSet alloc] init];
    if (filter) {
        int i = 0;
        while (i<filterlen) {
            if ([a containsObject:[[packages objectAtIndex:filter[i]] name]])
                [postIx addIndex:i];
            i++;
        }
    } else {
        int i = 0, n = [packages count];
        while (i<n) {
            if ([a containsObject:[[packages objectAtIndex:i] name]])
                [postIx addIndex:i];
            i++;
        }
    }
    [pkgDataSource selectRowIndexes:postIx byExtendingSelection:NO];
    [postIx release];   
}

@end