primordic/IssueDupesLite huggingface dataset:
Repository: satijalab/seurat

Issue #1570: Error when running FindMarkers with DESeq2
Created: 2019-05-20T20:55:12Z
I am trying to test out differential expression of our data using DESeq2 as the test in FindMarkers(). However, when I run it I end up getting this error:
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
  every gene contains at least one zero, cannot compute log geometric means

Do you have any recommendations for how to approach this or what the problem could be? Our counts were obtained using 10X.

Duplicate issue #2460: DEseq2 does not work in the function "FindMarkers" 
Created: 2019-12-27T22:50:42Z
Dear all,
I met the problem while I'm looking for the cluster markers using DESeq2 in the function "FindMarkers" after running the standard Seurat process and the previous steps are fine.
Here is my command:
cluster1.markers <- FindMarkers(B_seurat_object,only.pos = TRUE, min.pct = 0.25, ident.1 = 0, test.use = "DESeq2"
And Here is the error:
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  :  every gene contains at least one zero, cannot compute log geometric means
I tried not to tandardize the data to the log form in the previous steps but it didn't work. Other methods, like wilcox, MAST, work fine.

Closing comment (2020-01-09T14:46:03Z): Duplicate of #1570
Repository: satijalab/seurat

Issue #3331: error install Seurat v3 in R3.6
Created: 2020-07-29T04:23:52Z
Hi Seurat team,
I tried to install Seurat 3.2 in R 3.6 and I got the following error:
installing to /usr/lib64/R/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
terminate called after throwing an instance of 'std::length_error'
what():  basic_string::_M_create
/usr/lib64/R/bin/INSTALL: line 34: 34234 Done                    echo 'tools:::.install_packages()'
34235 Aborted                 (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
The downloaded source packages are in
‘/tmp/RtmpSM1cBH/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("Seurat") :
installation of package ‘Seurat’ had non-zero exit status
Could you give me some suggestions? Or somebody has experience a similar error ?
Many thanks,
STAR

Duplicate issue #3330: error install Seurat v3 in R3.6
Created: 2020-07-29T04:23:45Z
Hi Seurat team,
I tried to install Seurat 3.2 in R 3.6 and I got the following error:
installing to /usr/lib64/R/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
terminate called after throwing an instance of 'std::length_error'
what():  basic_string::_M_create
/usr/lib64/R/bin/INSTALL: line 34: 34234 Done                    echo 'tools:::.install_packages()'
34235 Aborted                 (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
The downloaded source packages are in
‘/tmp/RtmpSM1cBH/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("Seurat") :
installation of package ‘Seurat’ had non-zero exit status
Could you give me some suggestions? Or somebody has experience a similar error ?
Many thanks,
STAR

Closing comment (2020-07-30T19:03:22Z): duplicate of #3331
Repository: satijalab/seurat

Issue #1053: subset function in v3
Created: 2019-01-14T06:55:05Z
Hi,
Background: We developed an RShiny web interface SeuratWizard for seurat v2 (guided clustering workflow) and I am currently trying to migrate it to v3.
For the subset function, is there a way to use a variable containing the subset name. For example:
var1 = "name"
subset(x = object, subset = var1 > low & var1 < high)
Could be a simple oversight on my part. Appreciate the help

Duplicate issue #4058: subset abnormal in a function
Created: 2021-02-10T14:12:28Z
downSample=function(SeuratObj, n=100){
    #SeuratObj=pbmc3;   n=100
    set.seed(314649593)
    sampled.cells=c()
    for(item2 in levels(SeuratObj)){
        print( paste("item2 =", item2 ) )
        small_=subset(SeuratObj, cellType == item2) #########  error here #############
        cids=colnames(small_@assays$RNA@counts)
        #
        cells.to.sample=ifelse(length(cids)>n, n, length(cids)) 
        cat( tp, "\t", length(cids),'\t', cells.to.sample, "\n")
        
        cid.tmp <- sample(x = cids, size = cells.to.sample, replace = F)
        sampled.cells=c(sampled.cells, cid.tmp)
    }
    
    # Create a vector of cells on which variable genes will be computed
    subset(SeuratObj, cells = sampled.cells)
}

# test
pbmc.small=downSample(pbmc3, n=100)
pbmc.small

[1] "item2 = CD14+ Mono"
Error in eval(expr = expr): object 'item2' not found
Traceback:

1. downSample(pbmc3, n = 100)
2. subset(SeuratObj, cellType == item2)   # at line 8 of file <text>
3. subset.Seurat(SeuratObj, cellType == item2)
4. WhichCells(object = x, cells = cells, idents = idents, expression = subset, 
 .     ...)
5. WhichCells.Seurat(object = x, cells = cells, idents = idents, 
 .     expression = subset, ...)
6. subset.data.frame(x = data.subset, subset = eval(expr = expr))
7. eval(e, x, parent.frame())
8. eval(e, x, parent.frame())
9. eval(expr = expr)
10. eval(expr = expr)

when not in function(){}, it works.

Closing comment (2021-02-12T19:39:20Z): Duplicate of #1053
Repository: satijalab/seurat

Issue #207: Merging >2 Objects
Created: 2017-11-07T01:09:16Z
Hi all,
Love seurat's merge feature. However, is there a way to merge >2 objects in seurat while maintaining each object's identity?

Duplicate issue #239: merge objects
Created: 2017-12-07T01:03:15Z
Hi Seurat group:
Can I merge more than 2 Seurat Objects and create a new seurat object?
Bests,
Na

Closing comment (2017-12-07T07:31:52Z): duplicate of #207
Repository: satijalab/seurat

Issue #3435: Error during NormalizeData(): Attempting to add a different number of cells and/or features
Created: 2020-08-27T10:32:25Z
I created a seurat object using the count matrix from my seurat object. However, I encountered an error during normalization. Could you please help me?
> sm <- read.csv(file = 'Spring-counts.csv', sep = '.', header = F)
> sm<-sm[,-1]
> nrow(sm)
[1] 1000
> ncol(sm)
[1] 9790
> Patient.object <- CreateSeuratObject(counts = sm, min.cells = 0)
Warning message:
In storage.mode(from) <- "double" : NAs introduced by coercion
> Patient.object
An object of class Seurat 
1000 features across 9790 samples within 1 assay 
Active assay: RNA (1000 features, 0 variable features)
> Patient.object <- NormalizeData(Patient.object)
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error: Attempting to add a different number of cells and/or features

Duplicate issue #4444: Create seurat object from data frame
Created: 2021-05-05T15:36:19Z
Hi Seurat team,
thanks for the very informative tool!
I've downloaded a published dataset that have been formatted as matrix where genes are listed in a dedicated column, as well as the cell IDs, as here:
Feature AAACCTGAGACGCACA_lung AAACCTGAGATGCCTT_lung AAACCTGCAACTGGCC_lung AAACCTGCACATTAGC_lung
1:   Sox17             0.0000000              0.000000              0.000000              1.656833
2:  Mrpl15             0.9467373              0.000000              1.402331              0.000000
3:  Lypla1             0.0000000              2.029095              0.000000              1.656833
4:   Tcea1             0.9467373              0.000000              0.000000              0.000000
5: Atp6v1h             0.0000000              0.000000              0.000000              0.000000
I am not a bioinformatician, so probably it will be an easy solution, but when I try to build the seurat object it works, but I am not able to move forward.

seuratObject <- CreateSeuratObject(counts = dataMatrix[, -"Feature"])
seuratObject
An object of class Seurat
3972 features across 11174 samples within 1 assay
Active assay: RNA (3972 features, 0 variable features)
seuratObject <- NormalizeData(seuratObject)
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error: Attempting to add a different number of cells and/or features

Many thanks,
Mattia

Closing comment (2021-05-07T18:19:25Z): Hi @ML1990-Lab ,
This might be related to #3435, please try adding rownames to your dataMatrix and check if helps.
Repository: schemaspy/schemaspy

Issue #160: Oracle DB Error - Catalog name can't be null
Created: 2017-10-18T18:35:19Z
Using  6.0.0-rc2 with same command used for years. (custom orathin.properties only for the slash/colon difference with Oracle 12c
java -jar /apps/schemaspy/schemaspy-6.0.0-rc2.jar -noads -nologo -maxdet 100000 -t orathin -host HOSTNAME -port 1521 -db SERVICENAME -s DBSCHEMA -u DBUSER -p DBPASS -o /apps/www/schemaspy/OUTPUTDIR  -dp /apps/schemaspy/ojdbc7.jar
INFO  - Connected to Oracle - Oracle Database 12c Enterprise Edition Release 12.1.0.2.0 - 64bit Production
With the Partitioning, Real Application Clusters, Automatic Storage Management, OLAP,
Advanced Analytics and Real Application Testing options
ERROR - Catalog name can't be null
java.lang.IllegalArgumentException: Catalog name can't be null
at org.schemaspy.model.Catalog.(Catalog.java:33)
at org.schemaspy.model.Database.(Database.java:77)
at org.schemaspy.SchemaAnalyzer.analyze(SchemaAnalyzer.java:207)
at org.schemaspy.SchemaAnalyzer.analyze(SchemaAnalyzer.java:88)
at org.schemaspy.Main.runAnalyzer(Main.java:79)
at org.schemaspy.Main.run(Main.java:72)
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:732)
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:716)
at org.springframework.boot.SpringApplication.afterRefresh(SpringApplication.java:703)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:304)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1118)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1107)
at org.schemaspy.Main.main(Main.java:55)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51)
INFO  - Started Main in 6.128 seconds (JVM running for 7.896)

Duplicate issue #616: using schemaspy connect oracle, shows catalog problem
Created: 2019-10-24T02:47:23Z
schemaspy: schemaspy-6.0.0.jar
oralce jdbc:ojdbc6-12.1.0.1-atlassian-hosted.jar
command :java, -jar, lib/schemaspy-6.0.0.jar, -t, orathin, -dp, lib/ojdbc6-12.1.0.1-atlassian-hosted.jar, -host, 10.91.250.41, -port, 1521, -u, oracle, -p, passw0rd, -db, helowin, -o, C:\Users\pygou\output, -nohtml, -noimplied
ERROR LOG:
Catalog (-cat) was not provided and unable to deduce catalog, wildcard catalog can be used -cat %

Closing comment (2019-11-17T21:59:58Z): Duplicate #160
Repository: schemaspy/schemaspy

Issue #771: Configuration parameter for entries per page
Created: 2021-05-12T14:14:50Z
It would be nice to have a parameter somewhere in the configuration to be able to configure how many entries per page by default should paging use when displaying columns, indexes, tables, and any other list.
Expected Behavior
The parameter could be configurable. Perhaps 0 could be used to display them all (no paging).
Current Behavior
Defaults to 10.

Duplicate issue #790: Paging: select length of the table
Created: 2021-09-13T08:50:44Z
Please, add option to selection of lenght of table.
Expected Behavior
On the top/bottom of table will be form selection of lenght.
Current Behavior
Fixed number of results per page. It isn't possible variably select count or ALL. Or fixed show all records by parameter -nopages.
Possible Solution
Add parameter for showing selector of  lenght of table.
In datatables JS library it is parameter lengthChange → change to true.

Closing comment (2021-11-04T08:28:49Z): Maybe related to #771
Repository: schemaspy/schemaspy

Issue #793: Can't execute java command using docker on M1 Mac
Created: 2021-09-29T05:22:44Z
Expected Behavior

SchemaSpy jar file is executed correctly.

Current Behavior

Hang after main class name and drivers info are printed.

Possible Solution
Upgrade base image to one which supports arm.


Context




Full command including arguments how you run SchemaSpy:
docker run --rm --platform=linux/amd64 schemaspy/schemaspy:6.1.0 java --version

Your Environment


Version used: 6.1.0
Environment name and version (e.g. Chrome 39):
Operating System and version (e.g. Windows 10): macOS 11.3.1 (Apple M1 Chip)

Duplicate issue #1370: Docker: arm image
Created: 2024-01-02T10:45:11Z
Expected Behavior
The docker image available in the Docker Hub is for x86_64 archs only.
You should publish an image also for ARM64, to make it usable also on the mac with M1 chips, raspberry pi...
Current Behavior
The docker image is available only for x86_64 cpus
Possible Solution
Use docker buildx to make it available

Closing comment (2024-01-02T20:52:10Z): Duplicates #793 we have an example there and also a PR for it or two.
One old and one that I've been working on. So it's in progress.
Repository: schemaspy/schemaspy

Issue #109: Port definition in dbTypes is inconsistent
Created: 2017-06-13T20:50:01Z
Some have  and some expects PORT to be included in 
description=MariaDB

connectionSpec=jdbc:mariadb://<host>:<port>/<db>
host=hostname host where database resides with optional port
db=database name

description=MySQL

connectionSpec=jdbc:mysql://<host>/<db>
host=hostname[:port] host where database resides with optional port
db=database name

Duplicate issue #125: Run in Docker
Created: 2017-07-28T15:11:06Z
How to use Docker and passing only the data from the database?

Closing comment (2017-07-29T19:54:29Z): The port thing is related to #109.
I've added the write-thing for the output mount to documentation on hub.docker.
Anything else you feel missing in the documentation? I want to improve it, but to me (wrote it) it seems crystal clear =)
Repository: schemaspy/schemaspy

Issue #164: href in Parents column of table page gives 404
Created: 2017-11-01T10:22:58Z
Hi,
Running Schemaspy 6.0.0-rc2 against PostgreSQL db with standard public schema.
When going to the page of a table with a foreign key on a column, the parent table shown in the "Parents" column has href set to "../../public/tables/mytable.html", which makes it 404.
Guessing it should be either "../tables/mytable.html" or just "mytable.html" instead, and ../public might have something todo with if your are using multiples schemas.
Affects all tabs "Releated columns"/"Constraint"/"Comments".

Duplicate issue #117: Schema not required with release6.0.0-rc, but required with snapshot 6.0.0-rc1 for mysql
Created: 2017-06-29T07:01:28Z
Snapshot 2017-06-28
Needs investigation, documentation stats that it's optional in some cases and mysql should have it required. But it worked in release 6.0.0-rc1.
Issue reported from #112 comment
When schema -s is missing on command line, you'll get a nullpointer exception.

Closing comment (2017-11-10T09:47:36Z): @rafalkasa how do we want to proceed? Somewhat related to schema and in that case somewhat related to #164
Repository: scipy/scipy

Issue #20806: Failures for new `pytest-fail-slow` check in Windows CI jobs
Created: 2024-05-27T09:12:59Z
Issue to keep track of spurious failures after gh-20672 was merged yesterday.
This one showed up on gh-17924:
 ______________ TestDifferentialEvolutionSolver.test_strategy_fn _______________
[gw0] win32 -- Python 3.12.3 C:\hostedtoolcache\windows\Python\3.12.3\x64\python.exe
Test passed but took too long to run: Duration 1.9977539000001343s > 1.0s

Duplicate issue #21816: TST: `TestThreading.test_median_filter` slow failure
Created: 2024-11-06T16:31:52Z
Describe your issue.
Insofar as I can tell, #19549, should not be modifying anything that impacts TestThreading.test_median_filter.  Yet fail slow, fast, py3.12/npAny, dev.py fails with
___________________ TestThreading.test_median_filter[numpy] ___________________
[gw0] win32 -- Python 3.12.7 C:\hostedtoolcache\windows\Python\3.12.7\x64\python.exe
Test passed but took too long to run: Duration 1.5405415000000175s > 1.0s

Reproducing Code Example
#19549
Error message
___________________ TestThreading.test_median_filter[numpy] ___________________
[gw0] win32 -- Python 3.12.7 C:\hostedtoolcache\windows\Python\3.12.7\x64\python.exe
Test passed but took too long to run: Duration 1.5405415000000175s > 1.0s

SciPy/NumPy/Python version and system information
See the logs

Closing comment (2024-11-06T16:36:30Z): duplicate of #20806 (comment), but thanks!
Repository: scipy/scipy

Issue #17437: BUG: windows dll install directory changed from scipy/.libs to scipy.libs
Created: 2022-11-17T12:10:21Z
Describe your issue.
From scipy 1.9.1 to scipy 1.9.3 the directory used to install dlls on windows changed.
scipy-1.9.1: dlls are installed in .../site-packages/scipy/.libs
scipy-1.9.3: dlls are installed in .../site-packages/scipy.libs
This causes pyinstaller builds using scipy-1.9.3 to fail as the expected dll location changed.
If this change was intented I will file a bug report with pyinstaller to update the scipy installer hook.
Reproducing Code Example
None
Error message
None
SciPy/NumPy/Python version information
1.9.3 1.23.1 sys.version_info(major=3, minor=10, micro=6, releaselevel='final', serial=0)

Duplicate issue #17609: BUILD: openblas lib not found by pyinstaller in 1.9.3 on windows pypi installation
Created: 2022-12-15T17:03:05Z
Hi,
It's not clear to me what 2D/3D corner case I've found myself in between Scipy, pyinstaller, and GH actions, but since it seemed related to other issues (#14002), I wanted to report, feel free to close if best reported in one of those other tools instead.
As part of the CellProfiler build process on GH actions we pip install SciPy (just from PyPI, nothing fancy) as part of the process of installing CellProfiler then use pyinstaller to package in our dependencies via the linked spec . When we tested a release we put together yesterday, we found that on Windows but not Mac pyinstaller was unable to find the OpenBLAS dll, leading to a bunch of messages ala the below
2022-12-15T13:28:48.4432784Z 112298 WARNING: lib not found: libopenblas-57db09cfe174768fb409a6bb5a530d4c.dll dependency of c:\hostedtoolcache\windows\python\3.8.10\x64\lib\site-packages\scipy\sparse\linalg\_isolve\_iterative.cp38-win_amd64.pyd
2022-12-15T13:28:48.4550912Z 112314 WARNING: lib not found: libopenblas-57db09cfe174768fb409a6bb5a530d4c.dll dependency of c:\hostedtoolcache\windows\python\3.8.10\x64\lib\site-packages\scipy\special\_ufuncs.cp38-win_amd64.pyd

The application was built, but then failed on launch due to scipy.libs not being able to be found.
We had last built in August with 1.9.0, so after trying other stuff we tried pinning to that, and the build succeeded - I didn't test 1.9.1 or .2 . Is it expected that the location or packaging of that dll would be different in 1.9.0 vs 1.9.3 ? I did try a bunch of things (to be fair, my PyInstaller skills are poor hahaha) to try to get it to find the dll, but none succeded. Thanks in advance for any help you can give - happy to upload build logs or anything else you think may help.

Closing comment (2022-12-15T20:08:13Z): I think this is a duplicate of #17437. The pyinstaller hooks have been updated, but may not have been propagated to a release.
Thank you for reporting this.
Repository: scipy/scipy

Issue #11576: [set up dev environment] unable to run runtests.py
Created: 2020-02-23T15:25:25Z
Hello!
I'm a first-time contributor and attempting to set up a dev environment by following the instructions here: https://docs.scipy.org/doc/scipy/reference/dev/contributor/quickstart_ubuntu.html#quickstart-ubuntu
on step 19, I'm trying to run the runtests.py file but I am getting the following:
scipy/linalg/tests/test_decomp.py::TestEigh::test_eigh_integer realloc(): invalid next size Fatal Python error: Aborted  at 21% completed.
I'm sure this is not an actual bug, so apologies if this isn't the right place to post this, but I really want to contribute to SciPy and I haven't managed to find any sort of fix to this from googling. I also recently installed Ubuntu to go through this set up so there may be some sort of issue there.

Duplicate issue #11580: Invalid next size error while building scipy
Created: 2020-02-24T08:17:32Z
I am in the process of following the exact steps as mentioned in the scipy contributer guide in order to obtain a development version of scipy . When I run the code ' python3 runtests.py -v ' on terminal , on after passing 22% of the test , it gives an error :
scipy/linalg/tests/test_decomp.py::TestEigh::test_eigh_integer realloc(): invalid next size
Fatal Python error: Aborted
Sorry its not really possible to reproduce the error.
Specs :
Ubuntu  :  16.04

Closing comment (2020-02-24T08:24:30Z): duplicate of #11576
Repository: scipy/scipy

Issue #17470: BUG: Invalid package metadata: licensing
Created: 2022-11-24T04:47:56Z
Describe your issue.
The metadata of the package contains the license texts instead of an SPDX license ID expression. This is standardized.
See PEP 639
This makes it impossible for license scanning tools to properly detect licenses included in the package.
Reproducing Code Example
Simply look at your and other projects on pypi/Github and compare it to yours.
You can easily see that it is broken.
Error message
Not applicable
SciPy/NumPy/Python version information
Not applicable

Duplicate issue #19163: BUG?: complete License Text is put in field where only Licensename is expected?
Created: 2023-08-30T13:03:50Z
Hi
https://github.com/scipy/scipy/blob/c3ec353c503d23c1357e78ebff750755b3def8c6/pyproject.toml#L38C33-L38C33
lists the complets content of the file License
All the other packages I know display one the License name here: In this case here probably "BSD-3-Clause"

Closing comment (2023-08-31T05:58:28Z): Closing as this is a duplicate of #17470
Repository: scipy/scipy

Issue #8486: [Bug] '_<...> LinearOperator' object has no attribute '_transpose'
Created: 2018-02-26T13:25:43Z
As far as I understand, sparse.LinearOperator creates some instance of CustomLinearOperator when it is called by aslinearoperator() or when passed matvec=.
But neither CustomLinearOperator, nor, e.g., SumLinearOperator have transpose().
And the docs do not say much about how transpose() should be used or implemented.
Reproducing code example:
import numpy as np
import scipy as sp
import scipy.sparse.linalg as sla


dim = 8
shp = (dim, dim)

I = np.eye(*shp)

x0 = -sp.pi
xf = sp.pi
x = np.linspace(x0, xf, dim, endpoint=False)
# this is a vector representation of an operator with diagonal matrix
ref = (1-np.exp(-x))**2


def mv(y):
    # multiply this diag matrix by vector
    vv = ref
    return vv*y


LO = sla.LinearOperator(shp, matvec=mv)
(LO+LO).T

# not ever if a matrix was passed
M = sla.aslinearoperator(I)
M.transpose()

Error message:
'_CustomLinearOperator' object has no attribute '_transpose'

Scipy/Numpy/Python version information:
1.0.0 1.14.0 sys.version_info(major=3, minor=6, micro=4, releaselevel='final', serial=0)

Duplicate issue #7396: MatrixLinearOperator implements _adjoint(), but not _transpose()
Created: 2017-05-11T10:32:08Z
See title. Given a matrix A, this works:
aslinearoperator(A).H

but this not:
aslinearoperator(A).T

This seems like a basic oversight; is there a reason?

Closing comment (2023-02-14T06:40:30Z): For reference: This is a predating duplicate of #8486 and was fixed in #9064.
Repository: scrtlabs/catalyst

Issue #424: Algo state recover Problem - date_rules.every_day() fires on every start of the process
Created: 2018-08-01T09:46:52Z
Algo state recover described in https://enigma.co/catalyst/live-trading.html#algorithm-state does not include the save/recover of the state of the scheduled functions
For example:
schedule_function(func, date_rule=date_rules.every_day())
-> func will be executed on every start of the process and NOT once per day.
In my opinion the algo state recover should include the handling of the scheduled functions

Catalyst version 0.5.18

Duplicate issue #483: preserving live algo state info when algo is restarted
Created: 2018-10-01T09:30:23Z
I've recently found that once a live algo is stopped (for any reason) and then restarted, not all information that is for the algorithm is being preserved, specifically found that orders and transactions (link) are not.
as catalyst is still in alpha, and as there are a lot of issues raised from time to time when running an algo, and therefore, a lot of cases in which algo is being restarted, I think it should be considered on design level, that an algorithm restarted (under the same namespace) should pick upand preseve all relevant information, as if algo never stopped.
Thanks.

Closing comment (2018-10-01T10:39:40Z): I agree
I discovered similar problems in livemode
Also related to -> #424
Repository: scrtlabs/catalyst

Issue #231: _tkinter.TclError: no display name and no $DISPLAY environment variable
Created: 2018-02-13T08:14:45Z
Dear Catalyst Maintainers,
Before I tell you about my issue, let me describe my environment:
Environment

Operating System: (Windows Version or $ uname --all)
Python Version: $ python --version
Python Bitness: $ python -c 'import math, sys;print(int(math.log(sys.maxsize + 1, 2) + 1))'
How did you install Catalyst: (pip, conda, or other (please explain))
Python packages: $ pip freeze or $ conda list

Now that you know a little about me, let me tell you about the issue I am
having:
Description of Issue
i'm running mininet/examples/miniedit.py in MIninet
i received this issue.
MiniEdit running against Mininet 2.2.2
Traceback (most recent call last):
File "mininet/examples/miniedit.py", line 3579, in 
app = MiniEdit()
File "mininet/examples/miniedit.py", line 1110, in init
Frame.init( self, parent )
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 2537, in init
Widget.init(self, master, 'frame', cnf, {}, extra)
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 2049, in init
BaseWidget._setup(self, master, cnf)
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 2024, in _setup
_default_root = Tk()
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1767, in init
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
Sincerely,
`sekar

Duplicate issue #232: _tkinter.TclError: no display name and no $DISPLAY environment variable
Created: 2018-02-13T08:36:02Z
Dear Catalyst Maintainers,
Before I tell you about my issue, let me describe my environment:
Environment

Operating System: (Windows Version 8.1.pro`)
Python Version: 2.7
Python Bitness: $ python -c 'import math, sys;print(int(math.log(sys.maxsize + 1, 2) + 1))'
How did you install Catalyst: (pip)
Python packages: $ pip freeze

Now that you know a little about me, let me tell you about the issue I am
having:
Description of Issue
*i'm running mininet/examples/miniedit.py in MIninet
i received this issue.
MiniEdit running against Mininet 2.2.2
Traceback (most recent call last):
File "mininet/examples/miniedit.py", line 3579, in
app = MiniEdit()
File "mininet/examples/miniedit.py", line 1110, in init
Frame.init( self, parent )
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 2537, in init
Widget.init(self, master, 'frame', cnf, {}, extra)
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 2049, in init
BaseWidget._setup(self, master, cnf)
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 2024, in _setup
_default_root = Tk()
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1767, in init
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
Sincerely,
`sekar
Sincerely,
sekar

Closing comment (2018-02-13T17:11:18Z): Duplicate of #231, and #39, where this is resolved. It is also covered in our documentation here:
https://enigmampc.github.io/catalyst/install.html#macos-virtualenv-conda-matplotlib
Repository: scrtlabs/catalyst

Issue #197: [question] data availability for backtests
Created: 2018-01-30T02:44:34Z
I am working on a nightly 'refresh' process to update data, re-train models, re-run backtests, etc.  But in doing this I realized that data for the last 15 days or so is not available. I checked the status page and it appears data is only available until the 15th of Jan.
Is there any information anywhere on how this will work?  Has data on the catalyst servers ceased being updated?  Is it a periodic refresh?  If so how often can we expect data to be updated?  Is this the move towards the enigma platform, if so how do we access that data source?
Any info appreciated (sorry for the million questions, was just a bit of a surprise).

Duplicate issue #190: Live Trading Pricing Data is not loaded: Missing data Error
Created: 2018-01-26T16:15:42Z
Dear Catalyst Maintainers,
I wanted to run the live mode from jupyter. That caused the error... I changend run to live...
My environment:
Environment

Operating System: (Mac)
Python Version: $ python --3.5
How did you install Catalyst: (docker)

Now that you know a little about me, let me tell you about the issue I am
having:
Description of Issue

What did you expect to happen?
Testing papertrading
What happened instead?
Got an Exception

Live Trading PricingDataNotLoadedError: Missing data for bitfinex btc_usd in date range [2015-03-02 00:00:00+00:00 - 2018-01-25 00:00:00+00:00] Please run: catalyst ingest-exchange -x bitfinex -f daily -i btc_usd. See catalyst documentation for details.  During handling of the above exception, another exception occurred:
Here is how you can reproduce this issue on your machine:
Reproduction Steps

Script: https://github.com/enigmampc/catalyst/blob/master/catalyst/examples/buy_low_sell_high.py
Ingest all available data
Run script in live mode
...

What steps have you taken to resolve this already?
Trying to ingest more data
Anything else?
Would use my data instead but this seems complicated to me...
i have a database from the bitfinex wss....
Thanks in advance :)

Closing comment (2018-02-10T16:44:18Z): @gatapia the error you are encountering now is tracked in #197: data availability for backtests. Since the original error you reported in this issue is now different, I suggest we close this one and we track it on 197.
Repository: scrtlabs/catalyst

Issue #473: ExchangeAuthEmpty: Please enter your API token key and secret for exchange {exchange} in the following file: {filename}
Created: 2018-09-20T03:41:19Z
Dear Catalyst Maintainers,
Before I tell you about my issue, let me describe my environment:
Environment

Operating System: (Windows Version or $ uname --all)
Python Version: $ python --version
Python Bitness: $ python -c 'import math, sys;print(int(math.log(sys.maxsize + 1, 2) + 1))'
How did you install Catalyst: (pip, conda, or other (please explain))
Python packages: $ pip freeze or $ conda list

Now that you know a little about me, let me tell you about the issue I am
having:
Description of Issue

What did you expect to happen?
What happened instead?

Here is how you can reproduce this issue on your machine:
Reproduction Steps





...
What steps have you taken to resolve this already?
...
Anything else?
...
Sincerely,
$ whoami

Duplicate issue #474: Error:catalyst.exchange.exchange_errors.ExchangeAuthEmpty: Please enter your API token key and secret for exchange Binance in the following file: C:\Users\ASUS\.catalyst\data\exchanges\binance\auth.json
Created: 2018-09-20T04:29:28Z
Dear Catalyst Maintainers,
Before I tell you about my issue, let me describe my environment:
Environment

Operating System: (Windows Version or $ uname --all)
Python Version: $ python --version
Python Bitness: $ python -c 'import math, sys;print(int(math.log(sys.maxsize + 1, 2) + 1))'
How did you install Catalyst: (pip, conda, or other (please explain))
Python packages: $ pip freeze or $ conda list

Now that you know a little about me, let me tell you about the issue I am
having:
Description of Issue

What did you expect to happen?
What happened instead?

Here is how you can reproduce this issue on your machine:
Reproduction Steps





...
What steps have you taken to resolve this already?
...
Anything else?
...
Sincerely,
$ whoami

Closing comment (2018-09-20T09:58:10Z): This is a duplicate of #473
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #36: Tuner
Created: 2023-01-21T23:43:49Z
In order to make this more of an all-in-one solution, a tuner would be great.

Duplicate issue #339: [FEATURE] include a pop up tuner
Created: 2023-07-16T01:42:01Z

Closing comment (2023-07-18T14:35:45Z): Duplicate of #36
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #7: Currently there is only a stereo AU plugin - a mono instance would be more useful
Created: 2022-12-13T16:44:54Z
Stereo plugin would be handy for running stereo DI's through (assuming its possible to adjust L and R channels independently. For the time being Mono (and multi mono) would be more useful

Duplicate issue #25: Audio Unit Version only Stereo
Created: 2022-12-23T09:01:10Z
it would be nice to have a mono version auf der Audio Unit for Logic Pro X users.

Closing comment (2022-12-23T15:44:56Z): Closing as duplicate of #7
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #62: [BUG] Model and IR browsers don't open to their respective last folder
Created: 2023-02-05T23:29:19Z
Describe the bug
When opening the model picker or the IR picker, the browser goes to the last folder that was used for either.  E.g. if I just loaded a model, then when I got to pick an IR it starts at the model folder.
Expected behavior
It'd be nice if both kept track of their last folders visited separately
Additional context
Requested by a user.

Duplicate issue #77: [FEATURE] IR and model path variables acting weird
Created: 2023-02-27T07:34:04Z
Using NAM 0.5.0:

I successfully select an IR in the plugin & play with it
I want another IR, when I click on the IR section the plugin remembers the directory I last used - all good
I then want another .nam model and select one using the model directory section
If I want yet another IR and click on the IR directory section, the plugin takes me to the folder from where my .nam model was instead of recalling the IR folder I last visited
same thing happens the other way around; if I selected an IR and want to load a new .nam model, the plugin takes me to the IR directory

Closing comment (2023-02-28T05:21:31Z): Looks like a duplicate of #62, so closing.  Feel free to re-open w/ more info if you think it's different.
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #390: [BUG] Studio One 6.5.1 crashing when trying to load up NAM 0.7.5 on a track
Created: 2023-11-23T06:13:08Z
Thanks for taking the time to write a bug report! Use the following prompts to help you describe what's going on.  The more info you provide, the easier it'll be to understand how to fix it for you without having to come back and ask you questions.
Describe the bug
Studio One 6.5.1 immediately crashes when trying to load up NAM 0.7.5 on a track
To Reproduce
Steps to reproduce the behavior:

Open Studio One DAW
Create new "Song"
Add new track and add the NAM AU Plugin
Observe S1 immediately crashing with Studio One Crash Report shown

Expected behavior
Expecting NAM to be usable in my DAW (Presonus Studio One 6..x)
Desktop (please complete the following information):

OS == 14.1.1 (Sonoma)
Plugin version == 0.7.5
AU
DAW == Studio One 6.5.1

Additional context
NAM opens fine via standalone app
ATTACHED FILE:
NAM_S1_CRASH_REPORT.txt

Duplicate issue #463: "Studio One error"
Created: 2024-03-23T18:00:01Z
Hello. "Neural Amp Modeler" works perfectly standalone and in other DAWs, but for some unknown reason it doesn't work in Studio One. I would appreciate if you could help me.
Thank you for your help.

Closing comment (2024-04-12T01:28:34Z): Possible duplicate of #390
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #108: [FEATURE] Dual DSP processing aka "stereo plugin"
Created: 2023-03-08T20:21:13Z
For workflow reasons it would be great if NAM would allow for dual mono input (e.g. two hard panned guitar tracks).
Just a small suggestion...

Duplicate issue #142: [FEATURE] Stereo operation
Created: 2023-03-26T15:12:58Z
Currently NAM can't be used to process stereo track.s
Feature request: operate in stereo (dual mono), applying the same capture to both channels.
Optionally, allow separate captures for left and right channels. This would be necessary when a stereo device has been captured, such as "Studer A807 Tape Machine" by Joseph Chan.

Closing comment (2023-03-26T17:30:58Z): Dual mono is tracked in #108.
Mind updating this for specifically stereo models? That will require different work.
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #157: Standalone can only use interface's input 1 for mono input
Created: 2023-03-31T03:28:49Z
I have Focusrite Scarlett Solo 3rd Gen as my  audio interface. It uses Input channel 2 as Instrument input. It is not possible to select input channel 2 in NAM Standalone GUI. Please add this feature.

Duplicate issue #386: [BUG] MacOS standalone app's Input Device is selected system default by default and none other works upon selection
Created: 2023-11-06T15:09:29Z
Description
The standalone app by default always uses Default-Input from the system setting, however, if I change it to my audio interface from the NAM app it stops. In an earlier version, it used to work upon exiting and re-opening but now the app does not remember the previously selected setting as a result it only takes input from system mic which is default.
To Reproduce
Steps to reproduce the behavior:

Open NAM Standalone on Mac
Go to "NeuralAmpModeler > Settings"
Change "Input Device"
See error, it stops working

Expected behavior

Either it will start taking input from selected source right away or
At least it will remember the last selected input source

Device

OS - MacOS Ventura 13.6.1(intel)
Plugin version - 0.7.5
Standalone App

Closing comment (2023-12-19T07:12:10Z): Duplicate of #157
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #157: Standalone can only use interface's input 1 for mono input
Created: 2023-03-31T03:28:49Z
I have Focusrite Scarlett Solo 3rd Gen as my  audio interface. It uses Input channel 2 as Instrument input. It is not possible to select input channel 2 in NAM Standalone GUI. Please add this feature.

Duplicate issue #392: Audio settings not letting me choose which input I want on my audio interface.
Created: 2023-12-02T00:08:14Z
Bug
I have a Focusrite Scarlett Solo Audio Interface.
On the Audio Device Settings in preferences, the inputs and outputs don't show my desired input/output. This happens on DirectSound and ASIO. And both of the Left inputs and outputs it only gives me the option of 1, which is where my mic is inputed but I obviously want my guitar which is in input two. and on both of the Right ones It gives me the option of 1 and two but it's buggy (it sometimes doesn't want to change and sometimes it just goes blank).
I am on Windows 11 and am using the standalone v0.7.5
I also use FL Studio which it will hopefully work with but I would rather use the standalone when I don't want to sort it out every time I want to use it
Screenshots below -


Output 1 has the same selection on the drop menu as Input 1. Ditto for Output 2.

Closing comment (2023-12-03T06:19:58Z): duplicate #157
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #157: Standalone can only use interface's input 1 for mono input
Created: 2023-03-31T03:28:49Z
I have Focusrite Scarlett Solo 3rd Gen as my  audio interface. It uses Input channel 2 as Instrument input. It is not possible to select input channel 2 in NAM Standalone GUI. Please add this feature.

Duplicate issue #480: [BUG] ASIO Audio Input/Output Selection Doesn't Work With Fractal ASIO
Created: 2024-06-10T20:42:57Z
The Fractal Audio ASIO driver supports multiple Inputs and Outputs. I have successfully configured them with Guitar Rig 6/7, ToneX, Kemper, Amplitube, STL Tones, Studio One etc.
The ASIO options dialog is very rudimentary and doesn't work correctly. All the other plugins that I use list ALL the Inputs and Outputs using their fully qualified names (e.g. "IN 2 [OUTPUT 2 L + R]"), NAM only lists them as "1"/"2"/"3"/"4"/"5"/"6" etc. - and those choices don't enable the relevant Inputs/Outputs anyway.
Steps to reproduce the behaviour:

Start NAM
Select File > Preferences
Choose ASIO in the Audio dialog
Attempt to switch between the different Inputs and Outputs
No sound is received or sent by the NAM plugin.

Expected behaviour
The plugin should switch between the various ASIO inputs and outputs
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):

OS: Windows 11 23H2
Plugin version 0.7.9
Standalone & VST
Audio interface: Fractal Audio
Sample rate: 48khz
Buffer size: 256 samples

Closing comment (2025-01-02T00:01:26Z): Duplicates #157
Repository: sdatkinson/NeuralAmpModelerPlugin

Issue #365: [BUG] Code sign and notarize macOS binaries, installer, dmg
Created: 2023-09-02T06:48:35Z
Hey Steve,
the macOS NAM binaries are not getting code-signed and the installer is not getting notarized. They should be :-). This is probably the source of multiple user issues, including repeated permissions dialog for microphone access, not being able to browse for files in certain paths etc. Logic X on arm64 is especially sensitive.
here is a great article about how to do it: https://melatonin.dev/blog/how-to-code-sign-and-notarize-macos-audio-plugins-in-ci/
Here is a WIP Pr/Branch on the iPlug2OOS repo from which NamPlugin was started where I was working on adding it to the CI/CD scripts:
iPlug2/iPlug2OOS#9
oli@mac /Library/Audio/Plug-Ins/Components$ codesign -dv NeuralAmpModeler.component
Executable=/Library/Audio/Plug-Ins/Components/NeuralAmpModeler.component/Contents/MacOS/NeuralAmpModeler
Identifier=NeuralAmpModeler
Format=bundle with Mach-O universal (x86_64 arm64)
CodeDirectory v=20400 size=7081 flags=0x20002(adhoc,linker-signed) hashes=218+0 location=embedded
Signature=adhoc
Info.plist=not bound
TeamIdentifier=not set
Sealed Resources=none
Internal requirements=none
oli@mac /Library/Audio/Plug-Ins/Components$ codesign -dv VirtualCZ.component
Executable=/Library/Audio/Plug-Ins/Components/VirtualCZ.component/Contents/MacOS/VirtualCZ
Identifier=com.PluginBoutique.audiounit.VirtualCZ
Format=bundle with Mach-O universal (x86_64 arm64)
CodeDirectory v=20400 size=4874 flags=0x0(none) hashes=145+3 location=embedded
Signature size=9079
Timestamp=30 Oct 2022 at 12:27:47
Info.plist entries=24
TeamIdentifier=686EDA2T8T
Sealed Resources version=2 rules=13 files=51
Internal requirements count=1 size=200

Duplicate issue #185: [FEATURE] Sign and notarise the releases. 
Created: 2023-04-11T17:10:02Z
I would be happy to sponsor a year's Apple developer subscription for the author to sign releases and have Apple Notarise the DMG to lower the barrier for take-up amongst non-technical users on Apple.

Closing comment (2023-09-02T06:51:39Z): oops duplicate -> #365 but this is really important
Repository: sds/scss-lint

Issue #609: ColorVariable triggers for variable declarations w/ RGBA colors
Created: 2015-09-28T14:55:04Z
When upgrading to 0.42.0 w/ Improve ColorVariable to flag uses of rgb/rgba/hsl/hsla in the release, the ColorVariable lint gets triggered for the variable declarations that use rgba.
Examples of the variable declarations triggering the failure:
$some-variable: rgba(235, 141, 69, 0.8);
$some-other-variable: rgba(234, 130, 51, 1);
$transparent-white-background: rgba(255, 255, 255, 0.6);
$transparent-black: rgba(0, 0, 0, 0.2);
Is there something wrong w/ those variable declarations or is this an issue with the linter? Thank you!
Possibly related to #600.

Duplicate issue #611: ColorVariable rule and *CSS* color functions
Created: 2015-10-01T07:20:51Z
When rgb(), rgba(), hsl(), and hsla() colors assigned to a variable, scss-lint v0.42.1 warns these colors:
// test.scss
$a: rgb(1, 2, 3);
$b: rgba(1, 2, 3, 0);
$c: hsl(1, 2%, 3%);
$d: hsla(1, 2%, 3%, 0);
$e: #123456;
$ scss-lint test.scss
test.scss:1 [W] ColorVariable: Color literals like `rgb(1, 2, 3)` should only be used in variable declarations; they should be referred to via variable everywhere else.
test.scss:2 [W] ColorVariable: Color literals like `rgba(1, 2, 3, 0)` should only be used in variable declarations; they should be referred to via variable everywhere else.
test.scss:3 [W] ColorVariable: Color literals like `hsl(1, 2%, 3%)` should only be used in variable declarations; they should be referred to via variable everywhere else.
test.scss:4 [W] ColorVariable: Color literals like `hsla(1, 2%, 3%, 0)` should only be used in variable declarations; they should be referred to via variable everywhere else.
These colors should be allowed.

Closing comment (2015-10-02T16:11:28Z): Duplicate of #609. Fixed in #612.
Repository: sds/scss-lint

Issue #402: ColorVariable should support colors in maps and rgba function calls
Created: 2015-03-23T09:38:09Z
This is more a request for comments, as both these cases are arguably. Both of them are currently reported as errors, although I would argue, that they shouldn't be. If there is no concesus, these could be added as options to the linter.
Static color definition with alpha channel
$color-with-alpha: rgba(#000, .5);
Maps containing colors
$shades-of-gray: (#4c4c4c, #626262, #7d7d7d, #979797);

Duplicate issue #413: Bug: ColorVariable hex vs. rgb
Created: 2015-04-08T14:01:35Z
The following code results in an warning.
$color-bg: rgba(255, 255, 255, .8); // valid
$color-bg: rgba(#fff, .8);          // invalid

Error: ColorVariable: Color literals like #fff should only be used in variable declarations; they should be referred to via variable everywhere else.
I think this is a bug because I am using a variable to set the color. It shout not matter whether using hex or rgb as color format

Closing comment (2015-04-08T19:06:22Z): Hey @marcobiedermann, thanks for the report.
This was reported in #402 and fixed in 4b91c9e. In order to prevent further confusion, I've released a new version (0.36.0) of scss-lint with the fix.
Repository: sds/scss-lint

Issue #138: Keyframe false positive in DuplicateRoot
Created: 2014-04-22T00:34:26Z
Looks like I missed another edge case
@keyframes slideouttoleft {
    from {
        transform: translateX(0);
    }

    to {
        transform: translateX(-100%);
    }
}

@keyframes slideouttoright {
    from {
        transform: translateX(0);
    }

    to {
        transform: translateX(100%);
    }
}
This flags from and to as duplicates

Duplicate issue #145: DuplicateRoot: @keyframe values report as lint.
Created: 2014-04-22T16:04:23Z
A typical vendor-prefixed keyframe pattern:
@-moz-keyframes spin {
   0% { -moz-transform: rotate(0); }
   100% { -moz-transform: rotate(360deg); }
}
@-ms-keyframes spin {
   0% { -ms-transform: rotate(0); }
   100% { -ms-transform: rotate(360deg); }
}
@-o-keyframes spin {
   0% { -o-transform: rotate(0); }
   100% { -o-transform: rotate(360deg); }
}
@-webkit-keyframes spin {
   0% { -webkit-transform: rotate(0); }
   100% { -webkit-transform: rotate(360deg); }
}
@keyframes spin {
   0% { transform: rotate(0); }
   100% { transform: rotate(360deg); }
}
The 0% and 100% for each block are treated as "root rules", and throws this:
src/sass/module/_spinner.scss:75 [W] Merge root rule `0%` with identical rule on line 71
src/sass/module/_spinner.scss:76 [W] Merge root rule `100%` with identical rule on line 72
...
src/sass/module/_spinner.scss:87 [W] Merge root rule `0%` with identical rule on line 71
src/sass/module/_spinner.scss:88 [W] Merge root rule `100%` with identical rule on line 72

Closing comment (2014-04-22T16:13:58Z): Dupe of #138, which I have a PR submitted for it #140 😉
Might be a good extra test though since mine didn't test vendor prefixing