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 "RGUI.h"
#import "RDocument.h"
#import "RDocumentController.h"
#import "RDocumentWinCtrl.h"
#import "RController.h"
#import "Preferences.h"
#import "RChooseEncodingPopupAccessory.h"
#import "REngine.h"
#import "HelpManager.h"
#import "NSString_RAdditions.h"

// R defines "error" which is deadly as we use open ... with ... error: where error then gets replaced by Rf_error
#ifdef error
#undef error
#endif

@implementation RDocument

- (id)init
{
    self = [super init];
    if (self) {
        SLog(@"RDocument(%@) init", self);
        documentEncoding = NSUTF8StringEncoding;
        initialContents=nil;
        initialContentsType=nil;
        isEditable=YES;
        isREdit=NO;
        myWinCtrl=nil;
        rdToolsAreWorking=NO;
        fileTypeWasChangedWhileSaving = NO;
    }
    return self;
}

- (void)close {
    SLog(@"RDocument.close <%@> (wctrl=%@)", self, myWinCtrl);
    if (initialContents) [initialContents release], initialContents=nil;
    if (initialContentsType) [initialContentsType release], initialContentsType=nil;
    if (myWinCtrl) {
        SLog(@" - window: %@", [myWinCtrl window]);
        [self removeWindowController:myWinCtrl];
        [myWinCtrl close];
        // --- something is broken - winctrl close doesn't work - I have no idea why - this is a horrible hack to cover up
        //NSWindow *w = [myWinCtrl window];
        //if (w) [NSApp removeWindowsItem: w];
        //[[(RDocumentController*)[NSDocumentController sharedDocumentController] walkKeyListBack] makeKeyAndOrderFront:self];
        // --- end of hack
        [myWinCtrl release];
        myWinCtrl=nil;
    }
    
    [super close];
}

- (void)dealloc {
    if (myWinCtrl) [self close];
    [super dealloc];
}

// FIXME: I don't like this - we should use common text storage instead; conceptually textView is NOT the storage part
- (NSTextView *)textView {
    return [myWinCtrl textView];
}

- (void) makeWindowControllers {
    SLog(@"RDocument.makeWindowControllers: creating RDocumentWinCtrl");
    if (myWinCtrl) {
        SLog(@"*** RDocument.makeWindowControllers: my assumption is that I have only one win controller, but I already have %@! I'll autorelease the first one but won't detach it - don't blame me if this crashes...", myWinCtrl);
        [myWinCtrl autorelease];
    }
    // create RDocumentWinCtrl which is a window controller - it loads the corresponding NIB and sets up the window
    myWinCtrl = [[RDocumentWinCtrl alloc] initWithWindowNibName:@"RDocument"];
    [self addWindowController:myWinCtrl];
    
}

- (NSString*)windowNibName
{
    return @"RDocument";
}

- (int) fileEncoding
{
    return (int) documentEncoding;
}

- (void) setFileEncoding: (int) encoding
{
    SLog(@" - setFileEncoding: %d", encoding);
    documentEncoding = (NSStringEncoding) encoding;
}

- (void)didSaveSelector
{

    // Reopen file if file type was changed while saving
    if(fileTypeWasChangedWhileSaving) {
        NSError *theError = nil;
        fileTypeWasChangedWhileSaving = NO;
        [myWinCtrl close];
        [[NSDocumentController sharedDocumentController] openDocumentWithContentsOfURL:[self fileURL] display:YES error:&theError];
        if (theError) {
            NSLog(@"*** openDocumentWithContentsOfURL: failed with %@", theError);
            NSBeep();
        }
        return;
    }

    // Remain focus on current document after closing SaveAs panel
    [[myWinCtrl window] makeKeyWindow];
    encodingPopUp = nil;

}

- (void)runModalSavePanelForSaveOperation:(NSSaveOperationType)saveOperation delegate:(id)delegate didSaveSelector:(SEL)didSaveSelector contextInfo:(void *)contextInfo
{
    // dispatch didSaveSelector: in order to remain input focus to current document
    [super runModalSavePanelForSaveOperation:saveOperation delegate:self didSaveSelector:@selector(didSaveSelector) contextInfo:contextInfo];
}

// customize Save panel by adding "encoding" view for R documents
- (BOOL)prepareSavePanel:(NSSavePanel *)savePanel
{

    if([[self fileType] isEqualToString:ftRSource]) {
        [savePanel setAllowedFileTypes:[NSArray arrayWithObject:@"R"]];
        if (myWinCtrl)
            [savePanel setAccessoryView:[[[NSDocumentController sharedDocumentController] class] encodingAccessory:(NSStringEncoding)documentEncoding 
                                                                                               includeDefaultEntry:NO 
                                                                                                     encodingPopUp:&encodingPopUp]];
        if(encodingPopUp) [encodingPopUp setEnabled:YES];
        [savePanel setAllowsOtherFileTypes:YES];
    }
    else if([[self fileType] isEqualToString:ftRdDoc]) {
        [savePanel setAllowedFileTypes:[NSArray arrayWithObject:@"Rd"]];
        if (myWinCtrl)
            [savePanel setAccessoryView:[[[NSDocumentController sharedDocumentController] class] encodingAccessory:(NSStringEncoding)documentEncoding 
                                                                                               includeDefaultEntry:NO 
                                                                                                     encodingPopUp:&encodingPopUp]];
        if(encodingPopUp) [encodingPopUp setEnabled:YES];
        [savePanel setAllowsOtherFileTypes:YES];
    }
    else if(initialContentsType && [initialContentsType hasSuffix:@".rtf"]) {
        [savePanel setAllowedFileTypes:[NSArray arrayWithObject:@"rtf"]];
        [savePanel setAllowsOtherFileTypes:NO];
        [savePanel setAccessoryView:nil];
    }

    [savePanel setCanSelectHiddenExtension:YES];

    return YES;

}

- (BOOL)writeToURL:(NSURL *)absoluteURL ofType:(NSString *)docType error:(NSError **)outError
{

    SLog(@"RDocument.writeToFile: %@ ofType: %@ ", absoluteURL, docType);

    NSString *oldFileType = (initialContentsType)?:ftRSource; 

    if([[[absoluteURL absoluteString] lowercaseString] hasSuffix:@".rtf"]) {
        SLog(@" - docType was changed to rtf due to file extension");
        if(initialContentsType) [initialContentsType release], initialContentsType = nil;
        initialContentsType = [[NSString stringWithString:@"public.rtf"] retain];
    }
    else if([[[absoluteURL absoluteString] lowercaseString] hasSuffix:@".rd"]) {
        SLog(@" - docType was changed to Rd due to file extension");
        if(initialContentsType) [initialContentsType release], initialContentsType = nil;
        initialContentsType = [[NSString stringWithString:ftRdDoc] retain];
        [self setFileType:ftRdDoc];
    }
    else {
        if(initialContentsType) [initialContentsType release], initialContentsType = nil;
        initialContentsType = [[NSString stringWithString:ftRSource] retain];
        [self setFileType:ftRSource];
    }

    SLog(@" - used docType %@", (initialContentsType)?:ftRSource);

    fileTypeWasChangedWhileSaving = ([initialContentsType isEqualToString:oldFileType]) ? NO : YES;

    return [super writeToURL:absoluteURL ofType:(initialContentsType)?:ftRSource error:outError];

}

- (void) loadInitialContents
{

    if (!initialContents) {
        SLog(@"RDocument.loadInitialContents: empty contents, skipping");
        return;
    }
    
    SLog(@"RDocument.loadInitialContents: loading");
    NSEnumerator *e = [[self windowControllers] objectEnumerator];
    RDocumentWinCtrl *wc = nil;
    while ((wc = (RDocumentWinCtrl*)[e nextObject])) { 
        if ([initialContentsType hasSuffix:@".rtf"]) {
            SLog(@" - new RTF contents (%d bytes) for window controller %@", [initialContents length], wc);
            [wc replaceContentsWithRtf: initialContents];
        } else {
            const unsigned char *ic = [initialContents bytes];
            NSString *cs;
            SLog(@" - try to auto-detect file encoding");
            documentEncoding = NSUTF8StringEncoding;
            if ([initialContents length] > 1 
                    && ((ic[0] == 0xff && ic[1] == 0xfe) || (ic[0] == 0xfe && ic[1] == 0xff))) // Unicode BOM
                documentEncoding = NSUnicodeStringEncoding;

            cs = [[NSString alloc] initWithData:initialContents encoding:documentEncoding];
            if(!cs && [self fileURL]) {
                SLog(@" - failed to load as %d encoding, try to autodetect via initWithContentsOfURL:documentEncoding:error:", documentEncoding);
                cs = [[NSString alloc] initWithContentsOfURL:[self fileURL] usedEncoding:&documentEncoding error:nil];
            }
            if (!cs) { // fall back to Latin1 since it's widely used
                SLog(@" - failed to load as %d encoding, falling back to Latin1", documentEncoding);
                documentEncoding = NSISOLatin1StringEncoding;
                cs = [[NSString alloc] initWithData:initialContents encoding:documentEncoding];
            }
            if (!cs) { // fall back to MacRoman - old default
                SLog(@" - failed to load as %d encoding, falling back to MacRoman", documentEncoding);
                documentEncoding = NSMacOSRomanStringEncoding;
                cs = [[NSString alloc] initWithData:initialContents encoding:documentEncoding];
            }
            if (cs) {
                SLog(@" - new string contents (%d chars) for window controller %@", [cs length], wc);
                // Important! otherwise the save box won't know
                [wc setFileEncoding:documentEncoding];
                if(![initialContentsType isEqualToString:ftRSource] && ![initialContentsType isEqualToString:ftRdDoc]) {
                    SLog(@" - set plain text mode");
                    [wc setPlain:YES];
                }
                [wc replaceContentsWithString:cs];
            }
            [cs release];
        }
    }

    // release initialContents to clean heap esp. for large files
    if(initialContents) [initialContents release], initialContents=nil;

}
- (BOOL)revertToContentsOfURL:(NSURL *)absoluteURL ofType:(NSString *)typeName error:(NSError **)outError
{

    SLog(@"RDocument:revertToContentsOfURL %@ of type %@", absoluteURL, typeName);

    if([typeName hasSuffix:@".rtf"]) {
        NSData *cs = [[NSData alloc] initWithContentsOfURL:absoluteURL];
        if(cs) {
            [myWinCtrl replaceContentsWithRtf:cs];
            [cs release];

            // Remain focus
            [[myWinCtrl window] makeKeyWindow];
            // Clear edited status
            [self updateChangeCount:NSChangeCleared];
            return YES;
        }
    } else {
        NSString *cs = [[NSString alloc] initWithContentsOfURL:absoluteURL encoding:documentEncoding error:nil];
        if(cs) {
            [myWinCtrl replaceContentsWithString:cs];
            [cs release];

            // Remain focus
            [[myWinCtrl window] makeKeyWindow];
            // Clear edited status
            [self updateChangeCount:NSChangeCleared];
            return YES;
        }
    }

    SLog(@" - couldn't revert document");

    NSBeginAlertSheet(NLS(@"Reverting Document"), NLS(@"OK"), nil, nil,
        [myWinCtrl window], self,
        @selector(sheetDidEnd:returnCode:contextInfo:), nil, nil,
        NLS(@"Couldn't revert to saved document"));

    outError = nil;

    return YES;

}


- (void) reinterpretInEncoding: (NSStringEncoding) encoding
{
    SLog(@"RDocument:reinterpretInEncoding - new encoding: %ld", encoding);

    NSString *sc = [myWinCtrl contentsAsString];

    NSData *data = [sc dataUsingEncoding:documentEncoding allowLossyConversion:YES];
    if(!data) {
        NSBeginAlertSheet(NLS(@"Convertion Error"), NLS(@"OK"), nil, nil,
            [myWinCtrl window], self,
            @selector(sheetDidEnd:returnCode:contextInfo:), nil, nil,
            [NSString stringWithFormat:@"%@ %@", NLS(@"Couldn't reinterpret the text by using the encoding"), 
                [NSString localizedNameOfStringEncoding:encoding]]);
        SLog(@"- can't get data");
        return;
    }

    NSString *ns = [[NSString alloc] initWithData:data encoding:encoding];
    if (!ns) {
        [ns release];
        NSBeginAlertSheet(NLS(@"Convertion Error"), NLS(@"OK"), nil, nil,
            [myWinCtrl window], self,
            @selector(sheetDidEnd:returnCode:contextInfo:), nil, nil,
            [NSString stringWithFormat:@"%@ %@", NLS(@"Couldn't reinterpret the text by using the encoding"), 
                [NSString localizedNameOfStringEncoding:encoding]]);
        SLog(@" - can't create string");
        return;
    }

    // Check for any non-valid (surrogate issues esp. if UTF16 is chosen)
    if ([ns UTF8String] == NULL) {
        [ns release];
        NSBeginAlertSheet(NLS(@"Convertion Error"), NLS(@"OK"), nil, nil,
            [myWinCtrl window], self,
            @selector(sheetDidEnd:returnCode:contextInfo:), nil, nil,
            [NSString stringWithFormat:@"%@ %@", NLS(@"Couldn't reinterpret the text by using the encoding"), 
                [NSString localizedNameOfStringEncoding:encoding]]);
        SLog(@" - string contains invalid bytes for chosen encoding");
        return;
    }

    documentEncoding = encoding;
    [myWinCtrl setFileEncoding:documentEncoding];

    // replace text in such a way that the user can perform undo:
    [[myWinCtrl textView] selectAll:nil];
    [[myWinCtrl textView] insertText:ns];

    [ns release];

}

- (NSData *)dataRepresentationOfType:(NSString *)aType
{
    if(encodingPopUp) {
        [[NSUserDefaults standardUserDefaults] setInteger:[[[encodingPopUp selectedItem] representedObject] unsignedIntegerValue] forKey:lastUsedFileEncoding];
        documentEncoding = (NSStringEncoding)[[[encodingPopUp selectedItem] representedObject] unsignedIntegerValue];
    }

    encodingPopUp = nil;

    // Insert code here to write your document from the given data.  You can also choose to override -fileWrapperRepresentationOfType: or -writeToFile:ofType: instead.
    NSEnumerator *e = [[self windowControllers] objectEnumerator];
    RDocumentWinCtrl *wc = nil;
    while ((wc = (RDocumentWinCtrl*)[e nextObject])) { 
        if([aType hasSuffix:@".rtf"])
            return [wc contentsAsRtf];
        else
            return [[wc contentsAsString] dataUsingEncoding: documentEncoding];
    }
    return nil;
}

/* This method is implemented to allow image data file to be loaded into R using open
or drag and drop. In case of a successfull loading of image file, we don't want to
create the UI for the document.
*/
- (BOOL)readFromFile:(NSString *)fileName ofType:(NSString *)docType{
    if( [docType isEqual:@"R Data File"] || [[RController sharedController] isImageData:fileName] == 0){
        [[RController sharedController] sendInput: [NSString stringWithFormat:@"load(\"%@\")",fileName]];
        // [[NSDocumentController sharedDocumentController]  setShouldCreateUI:NO];
        return(YES);
    } else {
        // [[NSDocumentController sharedDocumentController] setShouldCreateUI:YES];
        return( [super readFromFile: fileName ofType: docType] );
    }
}

- (BOOL) loadDataRepresentation: (NSData *)data ofType:(NSString *)aType{

    if (initialContents) [initialContents release], initialContents=nil;
    if (initialContentsType) [initialContentsType release], initialContentsType = nil;

    initialContentsType = [[NSString alloc] initWithString:aType];

    initialContents = [data retain];

    SLog(@"RDocument.loadDataRepresentation loading %d bytes of data and docType %@", [data length], initialContentsType);

    return YES;
}

+ (void) changeDocumentTitle: (NSDocument *)document Title:(NSString *)title{
    NSEnumerator *e = [[document windowControllers] objectEnumerator];
    NSWindowController *wc = nil;
    
    while ((wc = [e nextObject])) {
        NSWindow *dw = [wc window];
        [dw setTitle: title];
    }
}

- (void) setEditable: (BOOL) editable
{
    isEditable=editable;
    NSEnumerator *e = [[self windowControllers] objectEnumerator];
    RDocumentWinCtrl *wc = nil;
    while ((wc = (RDocumentWinCtrl*)[e nextObject]))
        [wc setEditable: editable];
}

- (BOOL) editable
{
    return isEditable;
}

- (void) setREditFlag: (BOOL) flag
{
    isREdit=flag;
}

- (BOOL) hasREditFlag
{
    return isREdit;
}

- (NSString *)displayName
{
    if(isREdit) return NLS(@"Object Editor");
    return [super displayName];
}

- (BOOL) isRTF
{
    return (([self fileName] && [[[self fileName] lowercaseString] hasSuffix:@".rtf"]) || ([self fileType] && [[self fileType] hasSuffix:@".rtf"]));
}

- (BOOL) checkRdDocumentWithFilePath:(NSString*)inputFile reportSuccess:(BOOL)reportSuccess
{

    [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@ (%@)", NLS(@"Check Rd document…"), NLS(@"press ⌘. to cancel")]];

    NSError *error = nil;
    [[[myWinCtrl textView] string] writeToFile:inputFile atomically:YES encoding:NSUTF8StringEncoding error:&error];

    if(error != nil){
        NSBeep();
        NSLog(@"RDocument.checkRdDocument couldn't save a temporary file");
        [myWinCtrl setStatusLineText:@""];
        return NO;
    }

    NSString *convCmd = [NSString stringWithFormat:@"R --vanilla -q --slave --encoding=UTF-8 -e 'tools:::checkRd(\"%@\")'", inputFile];
    NSError *bashError = nil;
    NSString *errMessage = [convCmd evaluateAsBashCommandAndError:&bashError];

    if(bashError != nil) {
        if([bashError code] == 1) {
            errMessage = [NSString stringWithFormat:@"%@%@%@", errMessage, ([errMessage length])?@"\n":@"", [[bashError userInfo] objectForKey:NSLocalizedDescriptionKey]];
        } else {
            NSBeep();
            NSLog(@"RDocument.checkRdDocument bailed due to BASH error:\n%@", bashError);
            [myWinCtrl setStatusLineText:@""];
            return NO;
        }
    }

    NSInteger errorMessageMaxLength = 900;

    if(![errMessage length])
        errMessage = (reportSuccess) ? NLS(@"Check was successful.") : @"";
    else {
        errMessage = [errMessage stringByReplacingOccurrencesOfString:inputFile withString:NLS(@"Rd file")];
        errMessage = [errMessage stringByReplacingOccurrencesOfString:[inputFile lastPathComponent] withString:NLS(@"Rd file")];
    }

    if(![errMessage length]) {
        [myWinCtrl setStatusLineText:@""];
        return YES;
    }

    if([errMessage length] > errorMessageMaxLength)
        errMessage = [[errMessage substringWithRange:NSMakeRange(0,errorMessageMaxLength)] stringByAppendingString:@"\n…"];

    NSArray *errorLines = [errMessage componentsMatchedByRegex:[NSString stringWithFormat:@"%@:\\s*\\(?(\\d+)(\\)|-)?\\s*:?", NLS(@"Rd file")] capture:1L];

    // Find first error line number since checkRd messages are appended and in
    // most cases more precise
    NSInteger errorLineNumber = -1;
    if([errorLines count]) {
        NSInteger i;
        NSInteger firstErrorLine = 10000000;
        NSInteger anErrorLine;
        for(i=0; i<[errorLines count]; i++) {
            anErrorLine = [(NSString*)[errorLines objectAtIndex:i] integerValue];
            if(anErrorLine > 0 && (anErrorLine < firstErrorLine))
                firstErrorLine = anErrorLine;
        }
        errorLineNumber = firstErrorLine;
    }

    [myWinCtrl setStatusLineText:@""];

    NSAlert *alert = [NSAlert alertWithMessageText:NLS(@"Rd Check") 
            defaultButton:NLS(@"OK") 
            alternateButton:nil 
            otherButton:nil 
            informativeTextWithFormat:errMessage];

    [alert setAlertStyle:NSWarningAlertStyle];
    [alert runModal];

    [[myWinCtrl window] makeKeyAndOrderFront:self];
    [[myWinCtrl window] makeFirstResponder:[myWinCtrl textView]];

    if(errorLineNumber >=0) {
        NSRange currentLineRange = NSMakeRange(0, 0);
        NSString *s = [[[myWinCtrl textView] textStorage] string];
        NSInteger lineCounter = 0;

        while(lineCounter++ < errorLineNumber)
            currentLineRange = [s lineRangeForRange:NSMakeRange(NSMaxRange(currentLineRange), 0)];

        SLog(@" - go to error line number %d", errorLineNumber);
        // select found line
        [[myWinCtrl textView] setSelectedRange:currentLineRange];
        // scroll to found line
        [[myWinCtrl textView] centerSelectionInVisibleArea:nil];
        // remove selection after 500ms
        [[myWinCtrl textView] performSelector:@selector(moveLeft:) withObject:nil afterDelay:0.5];
    }

    return NO;

}

- (BOOL) checkRdDocument
{

    if(rdToolsAreWorking) return NO;
    rdToolsAreWorking = YES;

    NSString *tempName = [NSTemporaryDirectory() stringByAppendingPathComponent: [NSString stringWithFormat: @"%.0f.", [NSDate timeIntervalSinceReferenceDate] * 1000.0]];
    NSString *inputFile = [NSString stringWithFormat: @"%@%@", tempName, @"rd"];

    BOOL success = [self checkRdDocumentWithFilePath:inputFile reportSuccess:YES];

    [[NSFileManager defaultManager] removeItemAtPath:inputFile error:NULL];

    rdToolsAreWorking = NO;
    return success;

}

- (void) insertRdDataTemplate
{

    if(rdToolsAreWorking) return;
    rdToolsAreWorking = YES;

    [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@", NLS(@"press ⌘. to cancel")]];

    NSError *bashError = nil;
    NSString *templateStr = [@"R --vanilla --slave -e 'cat(unlist(prompt(Formaldehyde,NA)), sep=\"§\")'" evaluateAsBashCommandAndError:&bashError];

    [myWinCtrl setStatusLineText:@""];

    if(bashError != nil) {
        NSBeep();
        NSLog(@"RDocumentWinCtrl.insertRdDataTemplate bailed due to BASH error:\n%@", bashError);
        rdToolsAreWorking = NO;
        return;
    }

    if(!templateStr) {
        NSBeep();
        NSLog(@"RDocumentWinCtrl.insertRdDataTemplate bailed; no response from called R session");
        rdToolsAreWorking = NO;
        return;
    }

    templateStr = [templateStr stringByReplacingOccurrencesOfString:@"§" withString:@"\n"];
    templateStr = [templateStr stringByReplacingOccurrencesOfString:@"Formaldehyde" withString:NLS(@"DATA_NAME")];
    templateStr = [templateStr stringByReplacingOccurrencesOfString:@"carb" withString:NLS(@"VAR_NAME_1")];
    templateStr = [templateStr stringByReplacingOccurrencesOfString:@"optden" withString:NLS(@"VAR_NAME_2")];
    [[myWinCtrl textView] insertText:templateStr];

    NSRange newFunRange = [templateStr rangeOfString:NLS(@"DATA_NAME")];
    [[myWinCtrl textView] setSelectedRange:newFunRange];
    [[myWinCtrl textView] scrollRangeToVisible:newFunRange];

    rdToolsAreWorking = NO;

}

- (void) insertRdFunctionTemplate
{

    if(rdToolsAreWorking) return;
    rdToolsAreWorking = YES;

    [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@", NLS(@"press ⌘. to cancel")]];

    NSError *bashError = nil;
    NSString *templateStr = [@"R --vanilla --slave -e 'cat(unlist(prompt(mean.POSIXct,NA)), sep=\"§\")'" evaluateAsBashCommandAndError:&bashError];

    [myWinCtrl setStatusLineText:@""];

    if(bashError != nil) {
        NSBeep();
        NSLog(@"RDocumentWinCtrl.insertRdFunctionTemplate bailed due to BASH error:\n%@", bashError);
        rdToolsAreWorking = NO;
        return;
    }

    if(!templateStr) {
        NSBeep();
        NSLog(@"RDocumentWinCtrl.insertRdFunctionTemplate bailed; no response from called R session");
        rdToolsAreWorking = NO;
        return;
    }

    templateStr = [templateStr stringByReplacingOccurrencesOfString:@"§" withString:@"\n"];
    templateStr = [templateStr stringByReplacingOccurrencesOfString:@"mean.POSIXct" withString:NLS(@"FUNCTION_NAME")];
    templateStr = [templateStr stringByReplacingOccurrencesOfRegex:@"\\n\\.POSIXct[^\\n]+" withString:@""];
        
    [[myWinCtrl textView] insertText:templateStr];

    NSRange newFunRange = [templateStr rangeOfString:NLS(@"FUNCTION_NAME")];
    [[myWinCtrl textView] setSelectedRange:newFunRange];
    [[myWinCtrl textView] scrollRangeToVisible:newFunRange];

    rdToolsAreWorking = NO;

}

- (BOOL) convertRd2PDF
{

    if(rdToolsAreWorking) return NO;
    rdToolsAreWorking = YES;

    BOOL success = YES;
    NSError *bashError = nil;

    // Try to find the path to the default tex distribution
    NSString *texPath = @"";
    [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@", NLS(@"press ⌘. to cancel")]];
    NSString *aPath = [@"which tex" evaluateAsBashCommand];
    [myWinCtrl setStatusLineText:@""];
    if(aPath && [aPath length]) {
        ;
    } else {
        [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@", NLS(@"press ⌘. to cancel")]];
        aPath = [@"eval `/usr/libexec/path_helper -s` && dirname `which tex`" evaluateAsBashCommand];
        [myWinCtrl setStatusLineText:@""];
        if(aPath && [aPath length]) {
            texPath = [NSString stringWithFormat:@"export PATH=$PATH:%@", aPath];
        }
    }

    NSString *tempName = [NSTemporaryDirectory() stringByAppendingPathComponent: [NSString stringWithFormat: @"%.0f.", [NSDate timeIntervalSinceReferenceDate] * 1000.0]];
    NSError *error;
    NSString *inputFile = [NSString stringWithFormat: @"%@%@", tempName, @"rd"];
    NSString *pdfOutputFile = [NSString stringWithFormat: @"%@%@", tempName, @"pdf"];
    NSString *errOutputFile = [NSString stringWithFormat: @"%@%@", tempName, @"txt"];

    NSURL *pdfOutputFileURL = [NSURL URLWithString:pdfOutputFile];

    [[[myWinCtrl textView] string] writeToFile:inputFile atomically:YES encoding:NSUTF8StringEncoding error:&error];

    if(![self checkRdDocumentWithFilePath:inputFile reportSuccess:NO]) {
        [[NSFileManager defaultManager] removeItemAtPath:inputFile error:NULL];
        [[NSFileManager defaultManager] removeItemAtPath:pdfOutputFile error:NULL];
        [myWinCtrl setStatusLineText:@""];
        rdToolsAreWorking = NO;
        return NO;
    }

    NSString *convCmd = [NSString stringWithFormat:@"#!/bin/sh\n%@\nR CMD Rd2pdf --no-preview --title='%@' --force --output='%@' '%@' 2>'%@'", texPath, [self displayName], pdfOutputFile, inputFile, errOutputFile];
    bashError = nil;

    [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@ (%@)", NLS(@"Rd → PDF…"), NLS(@"press ⌘. to cancel")]];
    [convCmd runAsBashCommandAndError:&bashError];
    [myWinCtrl setStatusLineText:@""];

    NSFileManager *man = [NSFileManager defaultManager];

    if(bashError == nil) {
        if([man fileExistsAtPath:pdfOutputFile])
            [[HelpManager sharedController] showHelpFileForURL:pdfOutputFileURL];
    } else {
        NSString *errMessage = [[bashError userInfo] objectForKey:NSLocalizedDescriptionKey];
        if([man fileExistsAtPath:errOutputFile]) {
            bashError = nil;
            NSString *errMessages = [[[NSString alloc]
                initWithContentsOfFile:errOutputFile
                    encoding:NSUTF8StringEncoding
                        error:&bashError] autorelease];
            if(bashError == nil && errMessages && [errMessages length])
                errMessage = [errMessage stringByAppendingString:errMessages];
        }
        
        NSAlert *alert = [NSAlert alertWithMessageText:NLS(@"Error") 
                defaultButton:NLS(@"OK") 
                alternateButton:nil 
                otherButton:nil 
                informativeTextWithFormat:[errMessage stringByReplacingOccurrencesOfString:inputFile withString:NLS(@"Rd file")]];

        [alert setAlertStyle:NSWarningAlertStyle];
        [alert runModal];

        [[myWinCtrl window] makeKeyAndOrderFront:self];
        [[myWinCtrl window] makeFirstResponder:[myWinCtrl textView]];
        [[NSFileManager defaultManager] removeItemAtPath:inputFile error:NULL];
        [[NSFileManager defaultManager] removeItemAtPath:pdfOutputFile error:NULL];
        [[NSFileManager defaultManager] removeItemAtPath:errOutputFile error:NULL];
        rdToolsAreWorking = NO;
        return NO;
    }

    rdToolsAreWorking = NO;

    // After 100 secs all temporary files will be deleted even if R was quitted meanwhile
    [self performSelector:@selector(removeFiles:) withObject:[NSArray arrayWithObjects:inputFile, pdfOutputFile, errOutputFile, nil] afterDelay:100];

    return success;
}

- (BOOL) convertRd2HTML
{

    if(rdToolsAreWorking) return NO;
    rdToolsAreWorking = YES;

    BOOL success = YES;

    NSString *tempName = [NSTemporaryDirectory() stringByAppendingPathComponent: [NSString stringWithFormat: @"%.0f.", [NSDate timeIntervalSinceReferenceDate] * 1000.0]];
    NSString *RhomeCSS = @"R.css";
    NSString *Rhome = [[RController sharedController] home];
    
    if(!Rhome || ![Rhome length]) {
        [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@", NLS(@"press ⌘. to cancel")]];
        Rhome = [@"R --slave --vanilla -e 'cat(R.home())'" evaluateAsBashCommand];
        [myWinCtrl setStatusLineText:@""];
    }

    if(Rhome && [Rhome length]) {
        RhomeCSS = [NSString stringWithFormat:@"file://%@/doc/html/R.css", Rhome];
    }

    NSError *error;
    NSString *inputFile = [NSString stringWithFormat: @"%@%@", tempName, @"rd"];
    NSString *htmlOutputFile = [NSString stringWithFormat: @"%@%@", tempName, @"html"];

    NSURL *htmlOutputFileURL = [NSURL URLWithString:htmlOutputFile];

    [[[myWinCtrl textView] string] writeToFile:inputFile atomically:YES encoding:NSUTF8StringEncoding error:&error];

    if(![self checkRdDocumentWithFilePath:inputFile reportSuccess:NO]) {
        [[NSFileManager defaultManager] removeItemAtPath:inputFile error:NULL];
        rdToolsAreWorking = NO;
        return NO;
    }

    error = nil;

    [myWinCtrl setStatusLineText:[NSString stringWithFormat:@"%@ (%@)", NLS(@"Rd → HTML…"), NLS(@"press ⌘. to cancel")]];
    NSString *convCmd = [NSString stringWithFormat:@"R CMD Rdconv -t html '%@' 2>/dev/null | perl -pe 's!R.css!%@!'> '%@'", inputFile, RhomeCSS, htmlOutputFile];
    [convCmd evaluateAsBashCommandAndError:&error];
    [myWinCtrl setStatusLineText:@""];
    
    // Try to check if htmlOutputFile has content; if not don't come up with an empty window
    BOOL fsizeChecked = NO;
#if MAC_OS_X_VERSION_MIN_REQUIRED >= MAC_OS_X_VERSION_10_5
    UInt32 fsize = 0;
    NSFileManager *man = [[NSFileManager alloc] init];
    NSDictionary *attrs = [man attributesOfItemAtPath:htmlOutputFile error:nil];
    if(attrs) {
        fsize = [attrs fileSize];
        fsizeChecked = YES;
    }
    [man release];
#endif

    if(!fsizeChecked || (fsizeChecked && fsize > 0)) {
        if(error == nil && [[NSFileManager defaultManager] fileExistsAtPath:htmlOutputFile])
            [[HelpManager sharedController] showHelpFileForURL:htmlOutputFileURL];
        else {
            NSBeep();
            success = NO;
        }
    }

    rdToolsAreWorking = NO;

    // After 100 secs all temporary files will be deleted even if R was quitted meanwhile
    [self performSelector:@selector(removeFiles:) withObject:[NSArray arrayWithObjects:inputFile, htmlOutputFile, nil] afterDelay:100];

    return success;

}

- (void)sheetDidEnd:(id)sheet returnCode:(int)returnCode contextInfo:(NSString*)contextInfo
{
    // Order out the sheet - could be a NSPanel or NSWindow
    if ([sheet respondsToSelector:@selector(orderOut:)]) {
        [sheet orderOut:nil];
    }
    else if ([sheet respondsToSelector:@selector(window)]) {
        [[sheet window] orderOut:nil];
    }

    // Set the input focus to the last doc after closing a sheet
    [[(RDocumentController*)[NSDocumentController sharedDocumentController] findLastWindowForDocType:ftRSource] makeKeyAndOrderFront:nil];

}
- (BOOL) validateToolbarItem: (NSToolbarItem *) toolbarItem
{

    NSString *iid = [toolbarItem itemIdentifier];
    if ([iid isEqualToString: RETI_Save ] || [iid isEqualToString: RDETI_Save ])
        return [self isDocumentEdited];

    return YES;
}

- (void) removeFiles:(NSArray*)files
{
    if(files && [files count]) {
        NSInteger i = 0;
        for(i=0; i<[files count]; i++)
            [[NSFileManager defaultManager] removeItemAtPath:[files objectAtIndex:i] error:NULL];
    }
}

@end