[Bug]: sqlitebrowser 3.12.2 failes to install

Prerequisites

[X] I have written a descriptive issue title.
[X] I have searched all issues/PRs to ensure it has not already been reported or fixed.
[X] I have verified that I am using the latest version of Scoop and corresponding bucket.

Package Name
sqlitebrowser
Expected/Current Behaviour
Scoop cannot seem to install sqlitebrowser. It downloads the archive from the repo, but 7-Zip does not find any files inside to extract.
Steps to Reproduce
PS> scoop install sqlitebrowser
Installing 'sqlitebrowser' (3.12.2) [64bit] from 'extras' bucket
Loading DB.Browser.for.SQLite-3.12.2-win64.zip from cache
Checking hash of DB.Browser.for.SQLite-3.12.2-win64.zip ... ok.
Extracting DB.Browser.for.SQLite-3.12.2-win64.zip ... Could not find 'DB Browser for SQLite'! (error 16)
At C:\Users\user\scoop\apps\scoop\current\lib\core.ps1:860 char:9
+         throw "Could not find '$(fname $from)'! (error $($proc.ExitCo ...
+         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : OperationStopped: (Could not find ...te'! (error 16):String) [], RuntimeException
    + FullyQualifiedErrorId : Could not find 'DB Browser for SQLite'! (error 16)

Possible Solution
7-Zip seems to not be able to find any files inside the archive. The 7-Zip log is as follows:
7-Zip 23.01 (x64) : Copyright (c) 1999-2023 Igor Pavlov : 2023-06-20
Scanning the drive for archives:
1 file, 20446868 bytes (20 MiB)
Extracting archive: C:\Users\user\scoop\apps\sqlitebrowser\3.12.2\DB.Browser.for.SQLite-3.12.2-win64.zip
--
Path = C:\Users\user\scoop\apps\sqlitebrowser\3.12.2\DB.Browser.for.SQLite-3.12.2-win64.zip
Type = zip
Physical Size = 20446868
No files to process
Everything is Ok
Files: 0
Size:       0
Compressed: 20446868
Scoop and Buckets Version
PS> scoop --version
Current Scoop version:
d285bb08 (HEAD -> master, tag: v0.4.1, origin/master, origin/HEAD) chore(release): Bump to version 0.4.1 (#5924)

'main' bucket:
99baa6cea (HEAD -> master, origin/master, origin/HEAD<EMAIL_ADDRESS>Fix hash (Closes #5809)

'extras' bucket:
99b90d231 (HEAD -> master, origin/master, origin/HEAD<EMAIL_ADDRESS>Fix hash (Closes #13254)

'aoisummer' bucket:
cf0c18d (HEAD -> master, origin/master, origin/HEAD) update bucket

'foosel' bucket:
393d557 (HEAD -> main, origin/main, origin/HEAD) freecad-weekly: Update to version 36391

'scoop-bucket' bucket:
04d891e (HEAD -> master, origin/master, origin/HEAD) Release v0.23.0

'wsl' bucket:
9689ba6 (HEAD -> master, origin/master, origin/HEAD) resolves issue #4

Scoop Config
PS> scoop config

last_update                       scoop_branch scoop_repo
-----------                       ------------ ----------
2024-05-08T10:27:18.9962082-05:00 master       https://github.com/ScoopInstaller/Scoop

PowerShell Version
PS> $PSVersionTable

Name                           Value
----                           -----
PSVersion                      5.1.19041.2364
PSEdition                      Desktop
PSCompatibleVersions           {1.0, 2.0, 3.0, 4.0...}
BuildVersion                   10.0.19041.2364
CLRVersion                     4.0.30319.42000
WSManStackVersion              3.0
PSRemotingProtocolVersion      2.3
SerializationVersion           <IP_ADDRESS>

Additional Softwares
No response

I believe this is a bug in Scoop itself rather than a bug with the manifest.
Possibly because $ExtractDir contains spaces? (file lib\decompress.ps1 line 35)
https://github.com/ScoopInstaller/Scoop/blob/d285bb08d4852e0a7d524387fee53aa47c7b2a99/lib/decompress.ps1#L35

This issue may be related: #13221

This is already being addressed here: https://github.com/ScoopInstaller/Scoop/pull/5945


Explore option for allowing to run all cells in a folded markdown region

Separating this out from #132690
When a markdown cell has code cells folded underneath, the suggestions is to surface the total number of cells folded and to show a run action next to it:

Running the cell would show progress for the cells (with a stop action that will interrupt the kernel). And when the cell is finished, the cell returns the previous state. You can also click on the cell ... to expand the collapsed state (which is equivalent to opening the folded markdown region)

This was completed several iterations ago, with the functionality described. When header md cells are collapsed, a run button is surfaced if there are code cells within the section.


Alarm Function

Heya,
Given that this is an ESP based project, would you know of any way of modifying this to have an alarm clock function at all?
I'm aware that this particular unit probably doesn't have a speaker etc, but I'm just looking at expansion ideas currently!
Cheers!

Hmmm - looking at this https://www.printables.com/model/1003981-alarm-clock-esphome-d1-mini/files there may be a way of utilising an external HA alarm function by utilising other speakers etc.

Sure there are ways of expanding these units physically.  I already did but haven't posted details of it yet because it's kind of messed-up to be soldering wires directly to the back of a board like this.  On one of mine (a large one, the smaller one has almost no room to work with), I added an XH2.54 female port wired directly to GPIOs 0, 1, 3, and 12 of the ESP12, and the power regulator at GND and 3V3.  But, the only real "free" GPIO is 12 (GPIO 0 is the button, 1 is TX, 3 is RX).
And yes, you could add alarms to the YAML too.  This clock YAML files were originally drawn from the https://github.com/trip5/EspHome-Led-Clock and I put a lot of the same routines in both.  It uses Nokia-styl;e ringtones.  It wouldn't be hard to look at the code for both and just put in the missing bits.  My code is pretty well-commented.
But, the speaker modules of ESPHome actually use a non-significant amount of memory.  The fonts do, too.  While playing with my expansion, I noticed adding anything that wasn't already there (in my case it was an RF receiver) meant I had to remove things too or the clock would crash (like reducing from 2 fonts to 1 and removing un-needed glyphs). My YAML already pushes the poor ESP12 to its limit - which is why I had to split the YAMLs in 2 flavors anyway.
You're welcome to continue this conversation but if all you're looking for is an alarm, the XY-Clocks already have one built onto them, and they're much cheaper (and my YAMLs support them)... or go full-out and get an Ulanzi TC-001 and try EHMTXv2.

Sorry for my late reply, I missed the notification.
Thank you so much for the indepth reply, I think you've covered every question I could have on that subject and why it'd be somewhat difficult to do so.
Sincerely appreciate it, I'll have a think about the best way forward!


Update Scenario0_Tests.xaml.cs

New features added:

Test case Static Accuracy can stop at any time during the test by clicking the cancel button when testing.
Improved the algorithm to calculate Magnet Interference, now the test case Magnet Interference can start any points instead of start at magnet north.
Added some instruction words before the static accuracy test to remind users to turn on the screen rotation lock.
Code Change:
Useless blank lines removed.

@jialzhu could you please review this pull request and merge if it's acceptable? Thank you.


adding lkm rule

What type of PR is this?
/kind rule-create
Any specific area of the project related to this PR?
/area rules
What this PR does / why we need it:
This PR adds a new falco rule that looks for when insmod is called as part of a execve event. Injecting LKM modules on (post build) running production instances should be rare and is a common way for rootkits that employ kernel hooking to obfuscate themselves.
Which issue(s) this PR fixes:
Fixes #
Special notes for your reviewer:
This is a rehashed of PR#1389 just cleaned up DCO as well as https://github.com/falcosecurity/falco/pull/1401
Does this PR introduce a user-facing change?:
Yes new rule in falco_rules.yml

rule(Linux Kernel Module injection detected): adds a new rule that detects when a LKM module is inject using insmod typically used by rookits looking to obfuscate their behavior via kernel hooking.

[APPROVALNOTIFIER] This PR is NOT APPROVED
This pull-request has been approved by:
To complete the pull request process, please assign kaizhe
You can assign the PR to them by writing /assign @kaizhe in a comment when ready.
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/assign @kaizhe

LGTM label has been added.  Git tree hash: 2ee506df05207f99812923945e2e4fdde04cda42

[APPROVALNOTIFIER] This PR is APPROVED
This pull-request has been approved by: leodido
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[APPROVALNOTIFIER] This PR is APPROVED
This pull-request has been approved by: leodido, leogr
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[APPROVALNOTIFIER] This PR is APPROVED
This pull-request has been approved by: fntlnz, leodido, leogr
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/milestone 0.27.0

I think @d1vious changed everything as requested (also by @Kaizhe).
Thus, let this PR go in! 🎈
/hold cancel

Great job @d1vious ! Works like a charm
10:52:27.343581308: Warning Linux Kernel Module injection using insmod detected (user=root user_loginuid=1000 parent_process=sudo module=evilmodule.ko)

@fntlnz @leodido thank you for being patient with me and the help in slack! As a huge fan the project, I now know its creators are awesome great humans 😊. Will contribute more rules as the opportunity arises!

You're welcome @d1vious - Thanks for your help!


Powershell 6.2 facing issue on opening my application

Hi i have downloaded powershell 6.2 package for my windows 7 sp 1 version.and i ensured that wmf 5.1,.net core and c runtime also installed when i open powershell 6.2 application the window opens and closes immediately and iam sure installed can someone please help me on this

@manoj2994 Please update the issue description. Perhaps Google translate helps you.

@isazonov may be my english is not good anyway thanks. i found the solution.its just missing of  dotnet core dependency packages for win 7 .its working now


bookstack randomly returns "SQLSTATE[HY000] [1045] Access denied for user<EMAIL_ADDRESS>

Hello all,
I have been running bookstack for more than a year now. I have used the following version in docker:
bookstack: solidnerd/bookstack:0.27.5
database: mysql:5.7.12
I'm running everything behind an nginx proxy using lets encrypt certificates.  Nearly 2 months ago I started getting the "an unknown error occurred" in bookstack homepage (the bookstack logo was visible) I tried to upgrade bookstack, it didn't help. I then enabled debug mode and I started seeing that the following message is randomly produced.
SQLSTATE[HY000] [1045] Access denied for user<EMAIL_ADDRESS>...
The odd behavior is sometimes when I get this error if I reload the page then it works, and I can go to the books section, then I choose a book and I get this error again, and if I reload 2 or 3 times it works again!!!! I tried granting all privileges to my user in the database but nothing seems to work. My docker-compose.yml file is as follow:
version: '2'
services:

  mysql:
    container_name: name-mysql
    restart: unless-stopped
    image: mysql:5.7.12
    environment:
    - PUID=1000
    - PGID=1000
    - MYSQL_ROOT_PASSWORD=rootpass
    - MYSQL_DATABASE=db
    - MYSQL_USER=user
    - MYSQL_PASSWORD=pass
    volumes:
    - /address/in/host:/var/lib/mysql
    ports:
    - 3307:3306

  bookstack:
    container_name: bookstack
    restart: unless-stopped
    image: solidnerd/bookstack:0.27.5
    depends_on:
    - mysql
    environment:
    - PUID=1000
    - PGID=1000
    - APP_ENV=production
    - APP_DEBUG=true
    - APP_URL=https://bookstack.domain.com
    - VIRTUAL_HOST=bookstack.domain.com
    - LETSENCRYPT_HOST=bookstack.domain.com
    -<EMAIL_ADDRESS>    #- WKHTMLTOPDF=
    - DB_HOST=mysql
    - DB_DATABASE=db
    - DB_USERNAME=user
    - DB_PASSWORD=pass
    volumes:
    - /address/in/host:/var/www/bookstack/.env
    - /address/in/host:/var/www/BookStack/public/uploads
    - /address/in/host:/var/www/BookStack/storage/uploads
    ports:
    - "6875:80"
    expose:
    - "6875"
networks:
    default:
       external:
         name: network

I would appreciate if somebody could help me here.

Did you ever find a fix for this? Having the same issue after moving all the files onto a different server and re-pulling the images and trying to spin it back up again

Since the last comment on this issue is relatively old I'm going to close this. If the issue remains and is something you still require to be fixed please open a new issue, referencing this one.


Training & validation datasets

Are the datasets for training open source as well?
could only find 2023-12-20_train.jsonl and 2023-12-20_val.jsonl referenced in the trainign README.md, BUt not the files themselves.
Woudl be great to at least have the validation dataset to use it as calibration dataset for best AWQ quantisation.

Hi, we have not open-sourced the datasets and we don't have plans to do at the moment.


Snackbar is shown behind the Soft Navigation bar (button)

Thanks. It has been fixed in the latest update (v2.0.2).
dependencies {
    compile 'com.github.javiersantos:AppUpdater:2.0.2'
}


cbit.vcell.solver.ode.CVodeSolverStandalone@2899a8db

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Python 3.6.9

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (10.1 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_c4af0696-1b3d-4fbf-8294-35530f5610b94045130433407303600

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp4354241131846928653.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2899a8db

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Python 3.6.9

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (9.9 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f051cb87-7748-4b0d-993f-47b90a05ca5c734468254808487403

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp7207694371306643784.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2899a8db

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Python 3.6.9

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log:

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (2.9 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:56:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_08a8178e-0c46-46fb-8607-ec294dbec4736211193860680079365

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (2.9 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:56:08 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_06680fac-afd8-42c3-9f1c-cad095b60ff64263000564633423254

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (10.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:57:02 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_61b53ce1-5123-4e65-8880-19bed10deb5d2164112066424597407

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp6456269974659456207.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@515f4131

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Python 3.6.9

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (11.1 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:57:22 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_9a23b4fa-2e75-4252-b0bb-91312cb46ada7978077594729947892

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp1732094086080366257.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5bb8f9e2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Python 3.6.9

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (12.6 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpbuqk4guf/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:57:33 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_45941a3c-1215-4b2e-bb28-f718f8b11a1f6248658860022756542

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp6772232138528264518.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@50b1f030

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@60222fd8

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

-----------------------------------------------------------------------------------------------------

Generating report `report__copy_2`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 165, in exec_sed_doc

    data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(dtype ='float64')

  File "/usr/local/lib/python3.6/dist-packages/pandas/core/base.py", line 846, in to_numpy

    result = np.asarray(self._values, dtype=dtype)

  File "/usr/local/lib/python3.6/dist-packages/numpy/core/_asarray.py", line 83, in asarray

    return array(a, dtype, copy=False, order=order)

ValueError: could not convert string to float: 'NaN.9'

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (12.7 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp2cky6byg/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:57:46 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_3a8fe49f-7399-4ca1-8d6a-c7f47a2ab0c54873316157137103914

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp4314448882277769965.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@74518890

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@589b028e

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 305, in gen_plot_pdfs

    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 281, in get_report_dataframes

    report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 145, in exec_sed_doc

    data_set_df = pd.read_csv(report_filename).transpose()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

HDF conversion failed

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (11.5 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:57:58 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_3beab292-c89c-4132-9789-7c81c93792f58826074252882331320

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp9131521968194204135.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6872f9c8

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `report`.

Python 3.6.9

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (5.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp8lb6gy7e/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:43 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_83434c00-c095-4b7b-ab70-e58754ff7d5e7588493023539507451

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_83434c00-c095-4b7b-ab70-e58754ff7d5e7588493023539507451/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:46 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_44d48f7b-be84-43bd-b126-e88f2a058c5a1929649032840893429

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_44d48f7b-be84-43bd-b126-e88f2a058c5a1929649032840893429/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (5.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmprhls4j7m/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:48 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_7fe15bc0-a772-40ed-bb5e-a6ba99f82ebb3386665554037587174

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_7fe15bc0-a772-40ed-bb5e-a6ba99f82ebb3386665554037587174/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_ca2ac5d1-108e-4aab-86ab-9ce0c8890e7a2161048482674638564

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_ca2ac5d1-108e-4aab-86ab-9ce0c8890e7a2161048482674638564/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.4 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpip1vm6zf/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:53 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f74be53a-1e73-460f-9daa-e13bc072a0955629912109967015253

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_f74be53a-1e73-460f-9daa-e13bc072a0955629912109967015253/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.9 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpe02ec8dp/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_0525fd1c-54ba-4fc5-a72b-f1b7314f21856442389469899564188

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_0525fd1c-54ba-4fc5-a72b-f1b7314f21856442389469899564188/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.5 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp_ine9n29/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:58:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_c006279c-55e0-414f-a136-cd09091130a24427452362630523437

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_c006279c-55e0-414f-a136-cd09091130a24427452362630523437/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.9 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpo6dxkgo_/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:59:01 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_4a65b614-180f-47e5-9a0b-97f93d224b636306668810354755456

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_4a65b614-180f-47e5-9a0b-97f93d224b636306668810354755456/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.4 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpi_udja1y/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex

Jun 23, 2021 7:59:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_2153c3bf-1480-4a3f-971c-92a70a0fe6618131503468551747520

Python 3.6.9

utilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils

...

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
-
- The complete log of your validation/submission job, including further information about the failure, is available [here](https://github.com/biosimulators/Biosimulators/actions/runs/965595015). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/965595015).


Flutter showing odd borders that don't actually exist.

Steps to Reproduce
I'm not sure how to reproduce since my app is pretty large. But, this is a pretty simple page. I've attached the bit of code that has anything to do with the affected part.
Expected results:
The menu to display normally
Actual results:
The menu items are surrounded by borders when at the top of the screen. But, if I scroll down they disappear. I originally though it was just an emulator problem. But I built an APK and see this on my actual phone as well.
I am getting these odd borders around my containers. I have a Column made up of ProfileMenuItem's. There is nothing about any borders in this code. I have a divider I've made to split sections of the menu, but that's showing up correctly. Below is a bit of code and the screenshot. Then my user_profile screen calls this ProfileMenu class to render it.

code sample
        return Container(
          color: Colors.white,
          child: Center(
            child: Column(
              children: [
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/saved_tips_icon.svg',
                    title: 'Saved tips',
                    onTap: () {
                      // something
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/skin_concerns_icon.svg',
                    title: 'Skin concerns',
                    onTap: () {
                      // something
                    }),
                profileDivider(),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/about_icon.svg',
                    title: 'About skica',
                    onTap: () {
                      _launchWebsiteAbout();
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/feedback_icon.svg',
                    title: 'Feedback',
                    onTap: () {
                      _launchWebsiteContact();
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/rate_us_icon.svg',
                    title: 'Rate us',
                    onTap: () {
                      // something
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/facebook_follow_icon.svg',
                    title: 'Follow us on Facebook',
                    onTap: () {
                      _launchFacebook();
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/rate_us_icon.svg',
                    title: 'Invite a friend',
                    onTap: () {
                      // something
                    }),
                profileDivider(),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/svg/user_profile/logout_icon.svg',
                    title: 'Logout',
                    onTap: () {
                      _confirmLogout();
                    }),
              ],
            ),
          ),
        );
      }

      Widget profileDivider({double verticalPadding = 10}) {
        return Container(
          padding: EdgeInsets.only(top: verticalPadding, bottom: verticalPadding),
          child: SvgPicture.asset('assets/svg/user_profile/divider.svg'),
        );
      }

      Widget profileMenuItem(
          {@required BuildContext context,
          @required String svgAsset,
          @required String title,
          @required Function onTap}) {
        return Material(
          child: InkWell(
            // When the user taps the button, show a snackbar.
            onTap: onTap,
            splashColor: Colors.orange,
            child: Ink(
              width: MediaQuery.of(context).size.width * 1,
              color: Colors.white,
              child: Row(
                children: [
                  Container(
                    child: SvgPicture.asset(svgAsset, height: 60),

                  ),
                  Container(
                    color: Colors.transparent,
                    margin: EdgeInsets.only(left: 20),
                    child:
                        Text(title, style: Theme.of(context).textTheme.bodyText1),
                  ),
                  Expanded(
                    child: Container(
                      alignment: Alignment.centerRight,
                      child:
                          SvgPicture.asset('assets/svg/next_icon.svg', height: 34),
                    ),
                  ),
                ],
              ),
            ),
          ),
        );
      }

And here it is if I scroll to the bottom. They magically disappear.

Logs

   info • Unused import: '../../theme/skica_icons.dart' • lib/app/pages/advanced_routine.dart:5:8 •
          unused_import
   info • Unused import: '../../theme/skica_icons.dart' • lib/app/pages/basic_routine.dart:5:8 •
          unused_import
   info • Unused import: 'package:flutter_svg/flutter_svg.dart' •
          lib/app/widgets/routine_chip_widget.dart:2:8 • unused_import
   info • This class (or a class that this class inherits from) is marked as '@immutable', but one or
          more of its instance fields aren't final: RoutineChipWidget.selected •
          lib/app/widgets/routine_chip_widget.dart:7:7 • must_be_immutable
   info • The declaration '_addRemoveButton' isn't referenced •
          lib/app/widgets/routine_chip_widget.dart:34:10 • unused_element
   info • The value of the field '_themeType' isn't used • lib/models/theme_model.dart:10:13 •
          unused_field
   info • 'await' applied to 'void', which is not a 'Future' • lib/providers/auth_provider.dart:30:7 •
          await_only_futures
   info • 'await' applied to 'void', which is not a 'Future' • lib/providers/auth_provider.dart:51:7 •
          await_only_futures

[✓] Flutter (Channel stable, 2.0.4, on macOS 11.2.3 20D91 darwin-arm, locale en-US)
    • Flutter version 2.0.4 at /Users/nolan/.flutter/flutter
    • Framework revision b1395592de (11 days ago), 2021-04-01 14:25:01 -0700
    • Engine revision 2dce47073a
    • Dart version 2.12.2

[✓] Android toolchain - develop for Android devices (Android SDK version 30.0.3)
    • Android SDK at /Users/nolan/Library/Android/sdk
    • Platform android-30, build-tools 30.0.3
    • Java binary at: /Applications/Android Studio.app/Contents/jre/jdk/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b3-6915495)
    • All Android licenses accepted.

[✓] Xcode - develop for iOS and macOS
    • Xcode at /Applications/Xcode.app/Contents/Developer
    • Xcode 12.4, Build version 12D4e
    • CocoaPods version 1.10.1

[✓] Chrome - develop for the web
    • Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome

[✓] Android Studio (version 4.1)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b3-6915495)

[✓] VS Code (version 1.55.1)
    • VS Code at /Applications/Visual Studio Code.app/Contents
    • Flutter extension version 3.21.0

[✓] Connected device (2 available)
    • iPhone 12 Pro Max (mobile) • 89BF1B69-DABD-4CB2-964A-DB3A4EFEEE02 • ios            •
      com.apple.CoreSimulator.SimRuntime.iOS-14-4 (simulator)
    • Chrome (web)               • chrome                               • web-javascript • Google
      Chrome 89.0.4389.114

• No issues found!

Hi @nolyoi
Thanks for filing the issue, to reproduce I've created a minimal runnable code sample for your code with svg. However when running the code sample. the issue doesn't reproduce
Please try the code sample (feel free edit and provide the updated code sample that reproduces the issue)

code sample
import 'package:flutter/material.dart';
import 'package:flutter_svg/flutter_svg.dart';

void main() => runApp(MyApp());

class MyApp extends StatelessWidget {
  @override
  Widget build(BuildContext context) {
    return MaterialApp(
      title: 'Material App',
      home: Home(),
    );
  }
}

class Home extends StatelessWidget {
  @override
  Widget build(BuildContext context) {
    return Scaffold(
      appBar: AppBar(
        title: Text('Material App Bar'),
      ),
      body: Container(
        color: Colors.white,
        child: Center(
          child: SingleChildScrollView(
            child: Column(
              children: [
                FlutterLogo(
                  size: 400,
                ),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Saved tips',
                    onTap: () {
                      // something
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Skin concerns',
                    onTap: () {
                      // something
                    }),
                profileDivider(),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'About skica',
                    onTap: () {}),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Feedback',
                    onTap: () {}),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Rate us',
                    onTap: () {
                      // something
                    }),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Follow us on Facebook',
                    onTap: () {}),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Invite a friend',
                    onTap: () {
                      // something
                    }),
                profileDivider(),
                profileMenuItem(
                    context: context,
                    svgAsset: 'assets/flutter.svg',
                    title: 'Logout',
                    onTap: () {}),
              ],
            ),
          ),
        ),
      ),
    );
  }

  Widget profileDivider({double verticalPadding = 10}) {
    return Container(
      color: Colors.grey,
      height: 1,
      margin: EdgeInsets.only(top: verticalPadding, bottom: verticalPadding),
    );
  }

  Widget profileMenuItem(
      {@required BuildContext context,
      @required String svgAsset,
      @required String title,
      @required Function onTap}) {
    return Material(
      child: InkWell(
        // When the user taps the button, show a snackbar.
        onTap: onTap,
        splashColor: Colors.orange,
        child: Ink(
          width: MediaQuery.of(context).size.width * 1,
          color: Colors.white,
          child: Row(
            children: [
              Container(
                child: SvgPicture.asset(svgAsset, height: 60),
              ),
              Container(
                color: Colors.transparent,
                margin: EdgeInsets.only(left: 20),
                child:
                    Text(title, style: Theme.of(context).textTheme.bodyText1),
              ),
              Expanded(
                child: Container(
                  alignment: Alignment.centerRight,
                  child: SvgPicture.asset('assets/next.svg', height: 34),
                ),
              ),
            ],
          ),
        ),
      ),
    );
  }
}

Preview

Screenshot 1
Screnshot 2

Assets
assets.zip

pubspec.yaml
name: stable_flutter
description: A new Flutter project.

# The following line prevents the package from being accidentally published to
# pub.dev using `pub publish`. This is preferred for private packages.
publish_to: 'none' # Remove this line if you wish to publish to pub.dev

# The following defines the version and build number for your application.
# A version number is three numbers separated by dots, like 1.2.43
# followed by an optional build number separated by a +.
# Both the version and the builder number may be overridden in flutter
# build by specifying --build-name and --build-number, respectively.
# In Android, build-name is used as versionName while build-number used as versionCode.
# Read more about Android versioning at https://developer.android.com/studio/publish/versioning
# In iOS, build-name is used as CFBundleShortVersionString while build-number used as CFBundleVersion.
# Read more about iOS versioning at
# https://developer.apple.com/library/archive/documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html
version: 1.0.0+1

environment:
  sdk: ">=2.7.0 <3.0.0"

dependencies:
  flutter:
    sdk: flutter
  cupertino_icons: ^1.0.2
  flutter_svg: ^0.21.0+1

dev_dependencies:
  flutter_test:
    sdk: flutter

# For information on the generic Dart part of this file, see the
# following page: https://dart.dev/tools/pub/pubspec
# The following section is specific to Flutter.
flutter:

  # The following line ensures that the Material Icons font is
  # included with your application, so that you can use the icons in
  # the material Icons class.
  uses-material-design: true
  # To add assets to your application, add an assets section, like this:
  assets:
    - assets/
  #   - images/a_dot_ham.jpeg
  # An image asset can refer to one or more resolution-specific "variants", see
  # https://flutter.dev/assets-and-images/#resolution-aware.
  # For details regarding adding assets from package dependencies, see
  # https://flutter.dev/assets-and-images/#from-packages
  # To add custom fonts to your application, add a fonts section here,
  # in this "flutter" section. Each entry in this list should have a
  # "family" key with the font family name, and a "fonts" key with a
  # list giving the asset and other descriptors for the font. For
  # example:
  # fonts:
  #   - family: Schyler
  #     fonts:
  #       - asset: fonts/Schyler-Regular.ttf
  #       - asset: fonts/Schyler-Italic.ttf
  #         style: italic
  #   - family: Trajan Pro
  #     fonts:
  #       - asset: fonts/TrajanPro.ttf
  #       - asset: fonts/TrajanPro_Bold.ttf
  #         weight: 700
  #
  # For details regarding fonts from package dependencies,
  # see https://flutter.dev/custom-fonts/#from-packages

flutter doctor -v
[✓] Flutter (Channel stable, 2.0.4, on macOS 11.2.3 20D91 darwin-x64, locale
    en-GB)
    • Flutter version 2.0.4 at /Users/tahatesser/Code/flutter_stable
    • Framework revision b1395592de (11 days ago), 2021-04-01 14:25:01 -0700
    • Engine revision 2dce47073a
    • Dart version 2.12.2

[✓] Android toolchain - develop for Android devices (Android SDK version 30.0.3)
    • Android SDK at /Volumes/Extreme/SDK
    • Platform android-30, build-tools 30.0.3
    • ANDROID_HOME = /Volumes/Extreme/SDK
    • Java binary at: /Applications/Android
      Studio.app/Contents/jre/jdk/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build
      1.8.0_242-release-1644-b3-6915495)
    • All Android licenses accepted.

[✓] Xcode - develop for iOS and macOS
    • Xcode at /Volumes/Extreme/Xcode.app/Contents/Developer
    • Xcode 12.4, Build version 12D4e
    • CocoaPods version 1.10.1

[✓] Chrome - develop for the web
    • Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome

[✓] Android Studio (version 4.1)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build
      1.8.0_242-release-1644-b3-6915495)

[✓] VS Code (version 1.55.1)
    • VS Code at /Applications/Visual Studio Code.app/Contents
    • Flutter extension version 3.21.0

[✓] Connected device (3 available)
    • iPhone 12 (mobile) • 83060656-28E7-44CD-801E-B11EC3EC89BA • ios
      • com.apple.CoreSimulator.SimRuntime.iOS-14-4 (simulator)
    • macOS (desktop)    • macos                                • darwin-x64
      • macOS 11.2.3 20D91 darwin-x64
    • Chrome (web)       • chrome                               • web-javascript
      • Google Chrome 89.0.4389.114

• No issues found!

Hi @nolyoi
Thanks for filing the issue, to reproduce I've created a minimal runnable code sample for your code with svg. However when running the code sample. the issue doesn't reproduce
Please try the code sample (feel free edit and provide the updated code sample that reproduces the issue)
code sample
Preview
Screenshot 1	Screnshot 2

Assets
assets.zip
pubspec.yaml
flutter doctor -v

I have the repo here that can be cloned. https://github.com/nolyoi/skica_app
The files where this is occuring is lib/app/widgets/user_profile_menu.dart and lib/app/pages/user_profile.dart. It's really bizarre because this just happened recently and I didn't even make any changes to those files. It displayed normally before I upgraded Flutter.

So, I just rebuilt for my physical phone and it's not doing it anymore. But, it's still doing it on the emulator which is a pretty odd.

This looks a bit like a known problem with antialiasing and mapping from logical pixels to device pixels. There's an open issue for a documentation fix: #14288
More info about the problem can be found here:
https://github.com/flutter/flutter/issues/14288#issuecomment-361375791
https://github.com/flutter/flutter/issues/17084#issuecomment-385718108
https://github.com/flutter/flutter/issues/15035#issuecomment-370028740

This looks a bit like a known problem with antialiasing and mapping from logical pixels to device pixels. There's an open issue for a documentation fix: #14288
More info about the problem can be found here:
#14288 (comment)
#17084 (comment)
#15035 (comment)

Yeah that sounds about right. But, what I don't understand is how mine disappeared without altering the code.  It makes no sense. It was never there before, then it randomly appeared and just as randomly disappeared. No idea what could've caused it on my end.

This looks a bit like a known problem with antialiasing and mapping from logical pixels to device pixels. There's an open issue for a documentation fix: #14288
More info about the problem can be found here:
#14288 (comment)
#17084 (comment)
#15035 (comment)

Sounds about right. Found out with mine it was on the dark theme only where the Material widget was given a default gray/black background. Thats what was bleeding through.

@nolyoi
https://github.com/flutter/flutter/issues/80330#issuecomment-818952583, that definitely sounds antialiasing, not the widgets themselves.
Closing as duplicate of https://github.com/flutter/flutter/issues/14288


404 at /engine/installation/linux/docker-ce/linux-postinstall/

Hi,
On this page: https://docs.docker.com/engine/installation/linux/docker-ce/centos/#install-using-the-repository
In this text:
'Continue to Linux postinstall to allow non-privileged users to run Docker commands and for other optional configuration steps.'
The link to 'Linux postinstall' does not work:
URL: /engine/installation/linux/docker-ce/linux-postinstall/
Should it link here?
https://docs.docker.com/engine/installation/linux/linux-postinstall/

Broken link is resolved.


Update index.html

Added contributor names and cleaned up minor grammar.

Thanks for updating the index page. I was wondering how to do this. :-) (And now I see)


setup instructions don't include minio server

For local development, a minio server is required to upload data to. There is no instructions on how to set one up or configure it.

Could you provide some?

This was done in https://github.com/trompamusic/tpc/commit/bc8354531801fd1a217a77bf0f9ff6dd7958d63c


Refresh will cause app to froze

I am using nopaystation link for the config.txt, when refresh is clicked, the app is frozed, and then I will need to restart the app to see the lists being updated.

are you using the latest version, v1.0.0 ? what's your PSP model, CFW, firmware version, etc+++

I am using the latest version, I encountered this issue basically by creating the config.txt file with nopaystation links, and three empty .txt files with there corresponding name. The first refresh basically froze the app. But after a few for times of restarting the console and refreshing now it works fine. Maybe it's because I wanted to update the empty .Txt file, and it's just too big?


push snap metadata when publishing the snap

Currently, we only push the snap file itself up to the store, which doesn't always update the metadata about the snap if there's a conflict. We can do so with:
snapcraft push-metadata file.snap --force

I'm not sure at this point if we should always use --force, I think yes because we want as much of the details/metadata from the snap to come from the code in this repo as it's easier to update.

While I am at it, I will also enable run snapcraft with SNAPCRAFT_ENABLE_SILENT_REPORT=1 so that if an error is ever encountered in the build, it will automatically submit a report and not ask for input.


Update concept and architecture

Ⅰ. Describe what this PR does
Update concept and architecture
Ⅱ. Does this pull request fix one issue?

None
Ⅲ. List the added test cases (unit test/integration test) if any, please explain if no tests are needed.
Ⅳ. Describe how to verify it
Ⅴ. Special notes for reviews

LGTM.


feat: allow also str for 'sound_file_path' argument in add_sound()

arg: sound_file_path: Union[Path, str]
+
implement logic: isinstance(sound_file_path, str) -> sound_file_path = Path(sound_file_path)

done


Update robotcleaner.md

There is a typo in the example. I just added the missing character :-)

Thanks!


When the logs rotate will haproxy restart by itself or it will still write on the archived logs

Hi, I have it setup to use copytruncate.
daily
rotate 7
missingok
copytruncate
notifempty
compress
delaycompress

copytruncate

Truncate the original log file to zero size in place after creating a copy, instead of moving the old log file and optionally creating a new one. It can be used when some program cannot be told to close its logfile and thus might continue writing (appending) to the previous log file forever. Note that there is a very small time slice between copying the file and truncating it, so some logging data might be lost. When this option is used, the create option will have no effect, as the old log file stays in place.

thanks I have got it. initially i thought you had to restart haproxy


traceroute pack

Traceroute pack initially will accept 3 arguements. One is mandatory that is the host to traceroute, the rest of the two are optional.  Limiting the max number of  hops, Number of queries to each hop.
default command:
traceroute google.com
Passing arguements:
traceroute 10 3 google.com
if Default arguments are not passed it will pick up default

Great, thanks.
As far as the pack name goes - It looks like this action is Linux specific so it's probably better to move it to the existing linux pack (https://github.com/StackStorm/st2contrib/tree/master/packs/linux).

+1 to moving it to linux pack over it own pack.

I've moved action into linux pack and merged changes into master. Thanks.
On top of that, I also changed the action to use remote runner (just thought about that when moving the action). Previously it was using a local runner which means the action would only run on the same host as the action runner service. Now the action can run on any host to which action runner has access.

ok, thats great !! Thanks


DDO-386 add monitoring

This pr adds in standard monitoring policies for GAE applications via stackdriver. The policies will be created in a stackdriver workspace hosted in the same gcp project as import service.
More information about what these policies monitoring can be found here

yes, service_name is just for naming the alert that would appear in slack.


Integration with CKEditor / TinyMCE

I tried to integrate jquery-textcomplete with ckeditor, then I got this error.
TypeError: CKEDITOR.instances.issue_notes is undefined
Can you guise give me a little help to accomplish this. I will put the code sample bellow. You can quickly look at this. Thanks.
This is jsfiddle : https://jsfiddle.net/btjapqkp/

Oh my...
When I made the patch, I was integrating it into Redmine (EasyRedmine). Looks like Redmine specific code sneaked into the jquery-textcomplete - this is of course wrong. In this line, it should be the CKEDITOR instance.
I can not dig deeper into it at this moment, but maybe that helps you to make a fix?

Thanks @amenk, It is will be understandable for me if you can edit jsfiddle. Thanks.

I would have to look deeper in it - it is a bug in the textcomplete package - "proudly" introduced by me :'-(

@namaljayathunga Please check my patch

wow It's working 👍. Thanks @amenk for your quick contributing. However, there is an error when selected text replaced. check this jsfiddle. I'm using latest jquery-textcomplete.

Did you rebuild jquery-textcomplete? In my pull request I changed only the src/ folder - not dist/.
Additionally in the fiddle I think you should call textcomplete on the CKEditor textarea first before intialize the CKeditor.

Okay .. It is working, as long as there are not so much other edits on the page:
https://jsfiddle.net/btjapqkp/8/
Further PRs are appreciated :)

Thanks a lot @amenk for dedicate your value time. using ID as a selector, I could use more editor.


Inference from the box?

Hi! Thank you for posting the model. Could you please provide how to make inference from the box? If I understood correctly, model from dropbox has already been fitted, so we should be able to run it, but by the design model require original data and building of optimisers to run
class CorefModel:
    Attributes:
        config (coref.config.Config): the model's configuration,
            see config.toml for the details
        epochs_trained (int): number of epochs the model has been trained for
        trainable (Dict[str, torch.nn.Module]): trainable submodules with their
            names used as keys
        training (bool): used to toggle train/eval modes

    Submodules (in the order of their usage in the pipeline):
        tokenizer (transformers.AutoTokenizer)
        bert (transformers.AutoModel)
        we (WordEncoder)
        rough_scorer (RoughScorer)
        pw (PairwiseEncoder)
        a_scorer (AnaphoricityScorer)
        sp (SpanPredictor)
    """
    def __init__(self,
                 config_path: str,
                 section: str,
                 epochs_trained: int = 0):
        """
        A newly created model is set to evaluation mode.

        Args:
            config_path (str): the path to the toml file with the configuration
            section (str): the selected section of the config file
            epochs_trained (int): the number of epochs finished
                (useful for warm start)
        """
        self.config = CorefModel._load_config(config_path, section)
        self.epochs_trained = epochs_trained
        self._docs: Dict[str, List[Doc]] = {}
        self._build_model()
        self._build_optimizers()
        self._set_training(False)
        self._coref_criterion = CorefLoss(self.config.bce_loss_weight)
        self._span_criterion = torch.nn.CrossEntropyLoss(reduction="sum")

So maybe there is an option to run it without all this stuff?

Hmmm. Are you using the same versions of dependencies as listed in requirements.txt?
Boolean masks can be freely used as indices in pytorch, so I am a little confused. Please, make sure that you install the versions from requirements.txt, if it doesn't work, send me the output of your pip freeze and I'll try to reproduce your error.

@vdobrovolskii  I use the latest pytorch version(1.9), so the trouble was here:
out, _ = self.bert(
            subwords_batches_tensor,
            attention_mask=torch.tensor(
                attention_mask, device=self.config.device))

In latest  pytorch versions self.bert return <class 'transformers.modeling_outputs.BaseModelOutputWithPoolingAndCrossAttentions'>, so you need just to get only out and then to extract 'last_hidden_state' manually. After this code is running successfully.

I will fix this later myself in the master branch, thanks again.

Looking forward to it, @vdobrovolskii. Thanks for your awesome research!

@Dzz1th Can you please the sample file. I am having issues using sample input {
"document_id": "tc_mydoc_001",
"cased_words": ["Hi", "!", "Bye", "."],
"sent_id": [0, 0, 1, 1]
}
stores in a jsonl file.
Please share the input file and how to run successfully using pretrained weights from dropbox. I am having issues.

@vdobrovolskii I use the latest pytorch version(1.9), so the trouble was here:
out, _ = self.bert(
            subwords_batches_tensor,
            attention_mask=torch.tensor(
                attention_mask, device=self.config.device))

In latest pytorch versions self.bert return <class 'transformers.modeling_outputs.BaseModelOutputWithPoolingAndCrossAttentions'>, so you need just to get only out and then to extract 'last_hidden_state' manually. After this code is running successfully.

I am stuck at this can you please describe it? Thank you

@ShahzebPurelogics The output of AutoModel is now different, so try downgrading or using this line of code as a replacement:
out = self.bert(subwords_batches_tensor, attention_mask=torch.tensor(attention_mask, device=self.config.device)).last_hidden_state


Have consistent Year Numbering

Suggest having the season be listed as "2018/19 - Rover Ruckus" instead of "2019 - Rover Ruckus", etc., for consistency.
FIRST lists rookie year and last active year by the "Fall" year, so this would make the numbering consistent. Also, listing Rover Ruckus as a 2019 game is particularly inaccurate in regions like FIM for example where all Rover Ruckus events occur in 2018.

Like this?

Yes, perfect! Thanks.