March 2012 - Pharo-users - lists.pharo.org

Pharo Conf has now a web site :)

by StÃ©phane Ducasse

Please distribute the call http://rmod.lille.inria.fr/web/pier/Events We will have fun. Stef

March 15, 2012

Re: [Pharo-users] [ANN] BioSmalltalk

by StÃ©phane Ducasse

thanks a lot hernan for your work Stef On Mar 15, 2012, at 1:32 PM, HernÃ¡n Morales Durand wrote: > Dear all, > > It's been two years since I've started to work in bioinformatics with > Smalltalk. It has been a difficult decision because the quality and > amount of bioinformatics libraries is absolutely amazing, but I've > received a lot of support from the main researchers at the Institute > of Genetics where I'm working in Argentina. > > Now the initial step for a BioSmalltalk release is done. I hope the > FOSS community receive this pre-release as the basis for future > enhacements for bioinformatics with any Smalltalk flavor. Although in > the short-term it is unlikely for a BioSmalltalk to reach the users, > maturity and competitive level of major Bio* toolkits (BioPerl, > BioPython, BioRuby or BioJava), it could take too many years more if I > continue this work alone. However, BioSmalltalk was not conceived to > replace or defeat any other similar packages, but to provide to the > bioinformatics community the features of a pure object system. So feel > free to spread the word for all bioinformaticians, newcomers, > developers, or life scientists, for helping in any way and discovering > why Smalltalk is such a special environment. > > This release was implemented in Pharo 1.3 custom Core, but cross > Smalltalk portability was a priority. I'm working now to release > versions for GemStone, Squeak and VisualWorks is there is enough > interest. Everybody is welcome to contribute. > > You may download a pre-compiled release from the project page: > http://code.google.com/p/biosmalltalk/ > > Best regards, > > HernÃ¡n > > > -- > HernÃ¡n Morales > Institute of Veterinary Genetics (IGEVET). > National Scientific and Technical Research Council (CONICET). > La Plata (1900), Buenos Aires, Argentina. > Telephone: +54 (0221) 421-1799. > Internal: 422 > Fax: 425-7980 or 421-1799. >

March 15, 2012

[ANN] BioSmalltalk

by HernÃ¡n Morales Durand

Dear all, It's been two years since I've started to work in bioinformatics with Smalltalk. It has been a difficult decision because the quality and amount of bioinformatics libraries is absolutely amazing, but I've received a lot of support from the main researchers at the Institute of Genetics where I'm working in Argentina. Now the initial step for a BioSmalltalk release is done. I hope the FOSS community receive this pre-release as the basis for future enhacements for bioinformatics with any Smalltalk flavor. Although in the short-term it is unlikely for a BioSmalltalk to reach the users, maturity and competitive level of major Bio* toolkits (BioPerl, BioPython, BioRuby or BioJava), it could take too many years more if I continue this work alone. However, BioSmalltalk was not conceived to replace or defeat any other similar packages, but to provide to the bioinformatics community the features of a pure object system. So feel free to spread the word for all bioinformaticians, newcomers, developers, or life scientists, for helping in any way and discovering why Smalltalk is such a special environment. This release was implemented in Pharo 1.3 custom Core, but cross Smalltalk portability was a priority. I'm working now to release versions for GemStone, Squeak and VisualWorks is there is enough interest. Everybody is welcome to contribute. You may download a pre-compiled release from the project page: http://code.google.com/p/biosmalltalk/ Best regards, HernÃ¡n -- HernÃ¡n Morales Institute of Veterinary Genetics (IGEVET). National Scientific and Technical Research Council (CONICET). La Plata (1900), Buenos Aires, Argentina. Telephone: +54 (0221) 421-1799. Internal: 422 Fax: 425-7980 or 421-1799.

March 15, 2012

WebSockets

by Bernat Romagosa

Hi list, I've installed the latest version of WebClient from the metacello configuration, and when I run WebSocket example I get the following output in the Transcript: New WebSocket(127.0.0.1:33022) WebSocket(127.0.0.1:33022) Which I guess is alright, but then if I access localhost:8080 I get the following: ConnectionClosed: Connection closed while waiting for data. [ConnectionClosed signal: 'Connection closed while waiting for data.'] in Socket>>waitForDataFor: Socket>>waitForDataFor:ifClosed:ifTimedOut: Socket>>waitForDataFor: Socket>>receiveDataSignallingTimeout:into:startingAt: SocketStream>>receiveData SocketStream>>next WebSocket>>readMessage [[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] in [[[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] on: Error do: [:ex | self handleError: ex]] in WebSocket>>run BlockClosure>>on:do: [[[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] on: Error do: [:ex | self handleError: ex]] in WebSocket>>run BlockClosure>>ensure: WebSocket>>run [:req | | ws | ws := req asWebSocket. ws timeout: 300. Transcript cr; show: 'New ' , ws. ws onMessage: [:data | mutex critical: [sockets do: [:s | s send: data]]]. ws onClose: [Transcript cr; show: 'Closing ' , ws. mutex critical: [sockets remove: ws ifAbsent: []]]. ws onError: [:ex | Transcript cr; show: ws. Transcript cr; show: ex description. Transcript cr; show: ex signalerContext longStack]. mutex critical: [sockets add: ws]. ws run] in WebSocket class>>example WebServer>>invokeAction:request: [self invokeAction: (action at: 2) request: request] in WebServer>>dispatchRequest:url: BlockClosure>>on:do: WebServer>>dispatchRequest:url: WebServer>>dispatchRequest: [| ssl | certName ifNil: [stream := SocketStream on: aSocket] ifNotNil: [ssl := Smalltalk at: #SqueakSSL ifAbsent: [self error: 'SqueakSSL not installed']. stream := ssl secureSocketStream on: aSocket. [stream sslAccept: certName] on: Error do: [^ stream destroy]]. [aSocket isConnected] whileTrue: [stream peek ifNil: [^ aSocket destroy]. request := self newRequest. [request readFrom: stream] on: Error do: [:ex | (ex isKindOf: NetworkError) ifFalse: [[request send400Response] on: Error do: [:ignore | nil]]. ^ aSocket destroy]. self dispatchRequest: request]. nil] in WebServer>>handleConnectionFrom: BlockClosure>>on:do: WebServer>>handleConnectionFrom: [self handleConnectionFrom: aSocket] in [[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] in [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: BlockClosure>>on:do: [[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] in [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: BlockClosure>>ensure: [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: [self value. Processor terminateActive] in BlockClosure>>newProcess Closing WebSocket(127.0.0.1:33022) New WebSocket(127.0.0.1:33024) WebSocket(127.0.0.1:33024) ConnectionClosed: Connection closed while waiting for data. [ConnectionClosed signal: 'Connection closed while waiting for data.'] in Socket>>waitForDataFor: Socket>>waitForDataFor:ifClosed:ifTimedOut: Socket>>waitForDataFor: Socket>>receiveDataSignallingTimeout:into:startingAt: SocketStream>>receiveData SocketStream>>next WebSocket>>readMessage [[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] in [[[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] on: Error do: [:ex | self handleError: ex]] in WebSocket>>run BlockClosure>>on:do: [[[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] on: Error do: [:ex | self handleError: ex]] in WebSocket>>run BlockClosure>>ensure: WebSocket>>run [:req | | ws | ws := req asWebSocket. ws timeout: 300. Transcript cr; show: 'New ' , ws. ws onMessage: [:data | mutex critical: [sockets do: [:s | s send: data]]]. ws onClose: [Transcript cr; show: 'Closing ' , ws. mutex critical: [sockets remove: ws ifAbsent: []]]. ws onError: [:ex | Transcript cr; show: ws. Transcript cr; show: ex description. Transcript cr; show: ex signalerContext longStack]. mutex critical: [sockets add: ws]. ws run] in WebSocket class>>example WebServer>>invokeAction:request: [self invokeAction: (action at: 2) request: request] in WebServer>>dispatchRequest:url: BlockClosure>>on:do: WebServer>>dispatchRequest:url: WebServer>>dispatchRequest: [| ssl | certName ifNil: [stream := SocketStream on: aSocket] ifNotNil: [ssl := Smalltalk at: #SqueakSSL ifAbsent: [self error: 'SqueakSSL not installed']. stream := ssl secureSocketStream on: aSocket. [stream sslAccept: certName] on: Error do: [^ stream destroy]]. [aSocket isConnected] whileTrue: [stream peek ifNil: [^ aSocket destroy]. request := self newRequest. [request readFrom: stream] on: Error do: [:ex | (ex isKindOf: NetworkError) ifFalse: [[request send400Response] on: Error do: [:ignore | nil]]. ^ aSocket destroy]. self dispatchRequest: request]. nil] in WebServer>>handleConnectionFrom: BlockClosure>>on:do: WebServer>>handleConnectionFrom: [self handleConnectionFrom: aSocket] in [[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] in [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: BlockClosure>>on:do: [[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] in [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: BlockClosure>>ensure: [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: [self value. Processor terminateActive] in BlockClosure>>newProcess Closing WebSocket(127.0.0.1:33024) listener terminating, socket: waitingForConnection listener starting (interface: * port: 8080)The method SmalltalkImage platformName has been deprecated. Use Smalltalk os platformName New WebSocket(127.0.0.1:33026) WebSocket(127.0.0.1:33026) ConnectionClosed: Connection closed while waiting for data. [ConnectionClosed signal: 'Connection closed while waiting for data.'] in Socket>>waitForDataFor: Socket>>waitForDataFor:ifClosed:ifTimedOut: Socket>>waitForDataFor: Socket>>receiveDataSignallingTimeout:into:startingAt: SocketStream>>receiveData SocketStream>>next WebSocket>>readMessage [[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] in [[[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] on: Error do: [:ex | self handleError: ex]] in WebSocket>>run BlockClosure>>on:do: [[[stream isConnected] whileTrue: [self readMessage. frameType = 255 ifTrue: [stream close. ^ self]. self handleMessage: frameData type: frameType]. nil] on: Error do: [:ex | self handleError: ex]] in WebSocket>>run BlockClosure>>ensure: WebSocket>>run [:req | | ws | ws := req asWebSocket. ws timeout: 300. Transcript cr; show: 'New ' , ws. ws onMessage: [:data | mutex critical: [sockets do: [:s | s send: data]]]. ws onClose: [Transcript cr; show: 'Closing ' , ws. mutex critical: [sockets remove: ws ifAbsent: []]]. ws onError: [:ex | Transcript cr; show: ws. Transcript cr; show: ex description. Transcript cr; show: ex signalerContext longStack]. mutex critical: [sockets add: ws]. ws run] in WebSocket class>>example WebServer>>invokeAction:request: [self invokeAction: (action at: 2) request: request] in WebServer>>dispatchRequest:url: BlockClosure>>on:do: WebServer>>dispatchRequest:url: WebServer>>dispatchRequest: [| ssl | certName ifNil: [stream := SocketStream on: aSocket] ifNotNil: [ssl := Smalltalk at: #SqueakSSL ifAbsent: [self error: 'SqueakSSL not installed']. stream := ssl secureSocketStream on: aSocket. [stream sslAccept: certName] on: Error do: [^ stream destroy]]. [aSocket isConnected] whileTrue: [stream peek ifNil: [^ aSocket destroy]. request := self newRequest. [request readFrom: stream] on: Error do: [:ex | (ex isKindOf: NetworkError) ifFalse: [[request send400Response] on: Error do: [:ignore | nil]]. ^ aSocket destroy]. self dispatchRequest: request]. nil] in WebServer>>handleConnectionFrom: BlockClosure>>on:do: WebServer>>handleConnectionFrom: [self handleConnectionFrom: aSocket] in [[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] in [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: BlockClosure>>on:do: [[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] in [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: BlockClosure>>ensure: [[[self handleConnectionFrom: aSocket] on: Error do: [:ex | aSocket destroy]. mutex critical: [connections remove: Processor activeProcess ifAbsent: []]] ensure: [aSocket destroy]] in WebServer>>asyncHandleConnectionFrom: [self value. Processor terminateActive] in BlockClosure>>newProcess Closing WebSocket(127.0.0.1:33026) Any idea what's going on? Thanks! -- Bernat Romagosa.

March 14, 2012

Re: [Pharo-users] Problems Starting Pharo 1.4 on Windows

by Runar Jordahl

Sorry for my ignorance, but what should I download to get the fix? >From the issue tracker i notice the bug is closed "in 14389". What component is this? Kind regards Runar 2012/3/12 Igor Stasenko <siguctua(a)gmail.com>: > http://code.google.com/p/pharo/issues/detail?id=5468 > > > -- > Best regards, > Igor Stasenko. >

March 13, 2012

Re: [Pharo-users] Problems Starting Pharo 1.4 on Windows

by Igor Stasenko

http://code.google.com/p/pharo/issues/detail?id=5468 -- Best regards, Igor Stasenko.

March 12, 2012

Re: [Pharo-users] Problems Starting Pharo 1.4 on Windows

by Igor Stasenko

check pharodebug.log On 12 March 2012 05:40, Tudor Girba <tudor(a)tudorgirba.com> wrote: > Indeed, I wanted to report a similar thing. > > However, with the old VM 13307, this message does not appear: > http://gforge.inria.fr/frs/download.php/29045/CogVM-Win-13307.zip > > Also, I tried to reproduce the problem consistently, but I could not manage. The message appears somehow randomly. I can offer to do more experiments, if you tell me what to look for. > > Cheers, > Doru > > > On 11 Mar 2012, at 21:26, StÃ©phane Ducasse wrote: > >> thanks igor. >> >> Stef >> >> On Mar 11, 2012, at 9:21 PM, Igor Stasenko wrote: >> >>> looks like some file handles not finalized/invalidated... when saving an image. >>> I will check this. >>> >>> On 11 March 2012 18:36, StÃ©phane Ducasse <stephane.ducasse(a)inria.fr> wrote: >>>> normally not :) >>>> >>>> Stef >>>> >>>> On Mar 11, 2012, at 2:34 PM, Runar Jordahl wrote: >>>> >>>>> I have downloaded cogwin.zip (for Windows) and Pharo-1.4.zip from >>>>> http://www.pharo-project.org/pharo-download/unstable-1-4 >>>>> >>>>> I have unzipped the files into a folder. Then I try to drop >>>>> Pharo-1.4.image over Croquet.exe. Pharo starts, but the message >>>>> "WARNING! Manufactured file handle detected!" is printed many times at >>>>> the bottom of the screen. Then the image exits. >>>>> >>>>> Are there some known problems with Pharo 1.4 on Windows? >>>>> >>>>> Runar >>>>> >>>> >>>> >>> >>> >>> >>> -- >>> Best regards, >>> Igor Stasenko. >>> >> >> > > -- > www.tudorgirba.com > > "Beauty is where we see it." > > > > -- Best regards, Igor Stasenko.

March 12, 2012

Re: [Pharo-users] Problems Starting Pharo 1.4 on Windows

by Tudor Girba

Indeed, I wanted to report a similar thing. However, with the old VM 13307, this message does not appear: http://gforge.inria.fr/frs/download.php/29045/CogVM-Win-13307.zip Also, I tried to reproduce the problem consistently, but I could not manage. The message appears somehow randomly. I can offer to do more experiments, if you tell me what to look for. Cheers, Doru On 11 Mar 2012, at 21:26, StÃ©phane Ducasse wrote: > thanks igor. > > Stef > > On Mar 11, 2012, at 9:21 PM, Igor Stasenko wrote: > >> looks like some file handles not finalized/invalidated... when saving an image. >> I will check this. >> >> On 11 March 2012 18:36, StÃ©phane Ducasse <stephane.ducasse(a)inria.fr> wrote: >>> normally not :) >>> >>> Stef >>> >>> On Mar 11, 2012, at 2:34 PM, Runar Jordahl wrote: >>> >>>> I have downloaded cogwin.zip (for Windows) and Pharo-1.4.zip from >>>> http://www.pharo-project.org/pharo-download/unstable-1-4 >>>> >>>> I have unzipped the files into a folder. Then I try to drop >>>> Pharo-1.4.image over Croquet.exe. Pharo starts, but the message >>>> "WARNING! Manufactured file handle detected!" is printed many times at >>>> the bottom of the screen. Then the image exits. >>>> >>>> Are there some known problems with Pharo 1.4 on Windows? >>>> >>>> Runar >>>> >>> >>> >> >> >> >> -- >> Best regards, >> Igor Stasenko. >> > > -- www.tudorgirba.com "Beauty is where we see it."

March 12, 2012

Re: [Pharo-users] Problems Starting Pharo 1.4 on Windows

by StÃ©phane Ducasse

thanks igor. Stef On Mar 11, 2012, at 9:21 PM, Igor Stasenko wrote: > looks like some file handles not finalized/invalidated... when saving an image. > I will check this. > > On 11 March 2012 18:36, StÃ©phane Ducasse <stephane.ducasse(a)inria.fr> wrote: >> normally not :) >> >> Stef >> >> On Mar 11, 2012, at 2:34 PM, Runar Jordahl wrote: >> >>> I have downloaded cogwin.zip (for Windows) and Pharo-1.4.zip from >>> http://www.pharo-project.org/pharo-download/unstable-1-4 >>> >>> I have unzipped the files into a folder. Then I try to drop >>> Pharo-1.4.image over Croquet.exe. Pharo starts, but the message >>> "WARNING! Manufactured file handle detected!" is printed many times at >>> the bottom of the screen. Then the image exits. >>> >>> Are there some known problems with Pharo 1.4 on Windows? >>> >>> Runar >>> >> >> > > > > -- > Best regards, > Igor Stasenko. >

March 11, 2012

Re: [Pharo-users] Problems Starting Pharo 1.4 on Windows

by Igor Stasenko

looks like some file handles not finalized/invalidated... when saving an image. I will check this. On 11 March 2012 18:36, StÃ©phane Ducasse <stephane.ducasse(a)inria.fr> wrote: > normally not :) > > Stef > > On Mar 11, 2012, at 2:34 PM, Runar Jordahl wrote: > >> I have downloaded cogwin.zip (for Windows) and Pharo-1.4.zip from >> http://www.pharo-project.org/pharo-download/unstable-1-4 >> >> I have unzipped the files into a folder. Then I try to drop >> Pharo-1.4.image over Croquet.exe. Pharo starts, but the message >> "WARNING! Manufactured file handle detected!" is printed many times at >> the bottom of the screen. Then the image exits. >> >> Are there some known problems with Pharo 1.4 on Windows? >> >> Runar >> > > -- Best regards, Igor Stasenko.

March 11, 2012