monolix2simulx() does not work with COMMENT section

fabern commented 5 years ago

Hi Marc,

Using projects generated with Monolix2019 for simulation, I have noticed that the comment section causes an error message with monolix2simulx() (mlxR 4.0.0).

I have attached a minimum working example, containing: theophylline_data.txt theophylline_mlxt.txt theophylline_project2019.mlxtran.txt theophylline_project2019_modified.mlxtran.txt (remove .txt from the .mlxtran files)

Output of monolix2simulx(project="theophylline_project2019.mlxtran"):

> monolix2simulx(project="theophylline_project2019.mlxtran")
[ERROR]: Lixoft Exception [Delayed exceptions]
[Delayed exception] id:lixoft:Exception
source:translator::MlxProjectToMlxtran
message:The parse failed '***********************************************************************
filename: theophylline_project2019.mlxtran
description: 'list of identifiers type' was expected.
***********************************************************************
filename: theophylline_project2019.mlxtran
description: 'list of identifiers type' was expected.
***********************************************************************
filename: theophylline_project2019.mlxtran
description: Undefined block.
***********************************************************************
filename: theophylline_project2019.mlxtran
description: Bad monolix section name
'
file:C:\Users\lixoft\workspace\mlxsuite500\projects\lixoftLanguageTranslators\src\MlxProjectToXMLX.cpp
line:198

Document is empty
Error: 1: Document is empty

Commenting out the COMMENT section in the mlxtran works: monolix2simulx(project="theophylline_project2019_modified.mlxtran").

Thank you for looking into this.

Best regards, Fabian

MarcLavielle commented 5 years ago

Hi Fabian,

that's strange... but I was not able to reproduce this bug Are you sure that mlxR call Monolix2019 ?

best Marc

PS: it's better to write to Lixoft support for reporting a bug, thanks !

Le mer. 22 mai 2019 à 12:21, Fabian Bernhard notifications@github.com a écrit :

Hi Marc,

Using projects generated with Monolix2019 for simulation, I have noticed that the comment section causes an error message with monolix2simulx() (mlxR 4.0.0).

I have attached a minimum working example, containing (remove .txt from the .mlxtran files): theophylline_data.txt https://github.com/MarcLavielle/mlxR/files/3206908/theophylline_data.txt theophylline_mlxt.txt https://github.com/MarcLavielle/mlxR/files/3206909/theophylline_mlxt.txt theophylline_project2019.mlxtran.txt https://github.com/MarcLavielle/mlxR/files/3206915/theophylline_project2019.mlxtran.txt theophylline_project2019_modified.mlxtran.txt https://github.com/MarcLavielle/mlxR/files/3206916/theophylline_project2019_modified.mlxtran.txt

Output of monolix2simulx(project="theophylline_project2019.mlxtran"):

monolix2simulx(project="theophylline_project2019.mlxtran") [ERROR]: Lixoft Exception [Delayed exceptions] [Delayed exception] id:lixoft:Exception source:translator::MlxProjectToMlxtran message:The parse failed '*** filename: theophylline_project2019.mlxtran description: 'list of identifiers type' was expected.

filename: theophylline_project2019.mlxtran description: 'list of identifiers type' was expected.

filename: theophylline_project2019.mlxtran description: Undefined block.

filename: theophylline_project2019.mlxtran description: Bad monolix section name ' file:C:\Users\lixoft\workspace\mlxsuite500\projects\lixoftLanguageTranslators\src\MlxProjectToXMLX.cpp line:198

Document is empty Error: 1: Document is empty

Commenting out the COMMENT section in the mlxtran works: monolix2simulx(project="theophylline_project2019_modified.mlxtran").

Thank you for looking into this.

Best regards, Fabian

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fabern commented 5 years ago

Hi Marc, Thanks for the fast reply. No, I'm actually not entirely sure it uses Monolix2019. I have not understood this entirely:

Where can I find out which program mlxR calls?
Is this still the .ini file?
If so how to update it? (I'm a bit confused between mlxR::initMlxR() and lixoftConnectors::initializeLixoftConnectors().)

MarcLavielle commented 5 years ago

Fabian, ask to the Lixoft support, please Marc

Le mer. 22 mai 2019 à 13:27, Fabian Bernhard notifications@github.com a écrit :

Hi Marc, Thanks for the fast reply. No, I'm actually not entirely sure it uses Monolix2019. I have not understood this entirely:

Where can I find out which program mlxR calls?

Is this still the .ini file?

If so how to update it? (I'm a bit confused between mlxR::initMlxR() and lixoftConnectors::initializeLixoftConnectors().)

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fabern commented 5 years ago

Indeed, my current setup was not using Monolix2019 for monolix2simulx(). Now it works with the comments.

Thanks Marc and Lixoft support.

To complete this thread: since v.4.0.0 (Monolix2019) mlxR relies on lixoftConnectors to communicate with the Monolix calculation engine.

1) lixoftConnectors::getLixoftConnectorsState() gives the current state 2) By default mlxR uses the path defined in the lixoft.ini file (on Windows by default in C:\Users\xxx\lixoft\lixoft.ini). 3) Overriding the lixoft.ini can be achieved by mlxR::initMlxR(path = "C:/ProgramData/Lixoft/MonolixSuite2019R1/"). Overwriting the lixoft.ini seems to be possible by simply modifying the ini file according to the lixoft support.

abbakardvm commented 6 months ago

Hi Marc, I would like to ask for your guidance on how I can download and installed the Lixoftconnectors package for R. I already downloaded and installed monolix suite (monolix, PKanalix and simulix) but no Lixofconnector package seen as mention that it is with these apps. Please kindly help! Thank you.

MarcLavielle commented 6 months ago

Please ask to Lixoft support Best regards ML

Le dim. 7 janv. 2024 à 17:08, abbakardvm @.***> a écrit :

Hi Marc, I would like to ask for your guidance on how I can download and installed the Lixoftconnectors package for R. I already downloaded and installed monolix suite (monolix, PKanalix and simulix) but no Lixofconnector package seen as mention that it is with these apps. Please kindly help! Thank you.

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abbakardvm commented 5 months ago

Hi MarcLavielle/mlxR,

Thank you for your reply. Appreciate it.

Kind regards

Abubakar

On Mon, Jan 8, 2024, 12:45 AM Marc Lavielle @.***> wrote:

Please ask to Lixoft support Best regards ML

Le dim. 7 janv. 2024 à 17:08, abbakardvm @.***> a écrit :

Hi Marc, I would like to ask for your guidance on how I can download and installed the Lixoftconnectors package for R. I already downloaded and installed monolix suite (monolix, PKanalix and simulix) but no Lixofconnector package seen as mention that it is with these apps. Please kindly help! Thank you.

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monolix2simulx() does not work with COMMENT section #27