Daniel

hhblits seg fault on using custom database build via the instructions in the mmseqs docs

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## Expected Behavior running a hhblits search should complete when searching with a sequence on a custom database ## Current Behavior hhblits returns a segmentation fault ## Steps to Reproduce...

Build/autogen for Centos 8 and gnome 3.32 fails

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I have a fairly minimal install of Centos 8 so I had to use the following to get autogen to complete without error `dnf install autoconf-archive libappstream-glib-devel gobject-introspection-devel vala vala-devel`...

Can't start django 1.11.3 application after python3.6 upgrade

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python 3.6 Django 1.11.3 djangorestframework 3.6.3 djangorestframework-xml 1.3.0 Starting application returns: ImportError: Could not import 'rest_framework_xml.parsers.XMLParser' for API setting 'DEFAULT_PARSER_CLASSES'. AttributeError: module 'xml.etree.ElementTree' has no attribute '_IterParseIterator'. Have tried djangorestframework-xml...

Failure to parse data after get

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I'm using Django rest framework to auto generate a schema for a very simple API, one endpoint listGenes returns a json object which is an array of objects: ``` [...

Update network.py

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As of torch 2.x torch.symeigh() is no longer available. torch.linalg.eigh can be used to replace this instead

Chapter 3: error executing ggsave to create final plot of results

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The following command in email_classify.R fails ggsave(plot = class.plot, filename = file.path("images", "03_final_classification.pdf"), height = 10, width = 10) Throws this error: Error in seq.default(min, max, by = by) :...

Chapter 12 libraries

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The SVM examples require you to load library('e1071') but this library is not in the list of packages in chapter 1 table 1-2. I only noticed as I'd installed the...

ggplot 0.9.x warnings and errors

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For every ggplot() function call the "legend = FALSE" setting/parameter needs to be changed to guide="none" Also when plotting figure 9-4 in chapter 9 the latest ggplot now requires that...

Hi, I see that the path http://wwwuser.gwdg.de/~compbiol/uniclust/current_release/uniclust30_2018_08_hhsuite.tar.gz isn't stable for using any kind of simple automated update. It would be useful if there was a persistent URI such as http://wwwuser.gwdg.de/~compbiol/uniclust/current_release/uniclust30_hhsuite.tar.gz...

Feature request: PSSM output and input

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It would be very useful at the end of search run to have Diamond output a BLAST compatible PSSM file with of the search. And additionally be able to provide...