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Cytoscape package corrupt on Windows #49731

Open
Mitmischer opened this issue Aug 1, 2024 · 7 comments
Open

Cytoscape package corrupt on Windows #49731

Mitmischer opened this issue Aug 1, 2024 · 7 comments

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@Mitmischer
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Mitmischer commented Aug 1, 2024

Hello,

I'm trying to install cytoscape on Windows 11 using conda.

Starting from a fresh environment, I get the following error:

Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: C:\Users\Public\miniconda3\envs\cytoscape_env

  added / updated specs:
    - cytoscape


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cytoscape-3.10.2           |       he65b2d3_0       223.1 MB  bioconda
    expat-2.6.2                |       h63175ca_0         224 KB  conda-forge
    font-ttf-dejavu-sans-mono-2.37|       hab24e00_0         388 KB  conda-forge
    fontconfig-2.14.2          |       hbde0cde_0         186 KB  conda-forge
    freetype-2.12.1            |       hdaf720e_2         498 KB  conda-forge
    libexpat-2.6.2             |       h63175ca_0         136 KB  conda-forge
    libiconv-1.17              |       hcfcfb64_2         621 KB  conda-forge
    libpng-1.6.43              |       h19919ed_0         339 KB  conda-forge
    libzlib-1.3.1              |       h2466b09_1          55 KB  conda-forge
    m2w64-gcc-libgfortran-5.3.0|                6         342 KB  conda-forge
    m2w64-gcc-libs-5.3.0       |                7         520 KB  conda-forge
    m2w64-gcc-libs-core-5.3.0  |                7         214 KB  conda-forge
    m2w64-gmp-6.1.0            |                2         726 KB  conda-forge
    m2w64-libwinpthread-git-5.0.0.4634.697f757|                2          31 KB  conda-forge
    msys2-conda-epoch-20160418 |                1           3 KB  conda-forge
    pthread-stubs-0.4          |    hcd874cb_1001           6 KB  conda-forge
    ucrt-10.0.22621.0          |       h57928b3_0         1.2 MB  conda-forge
    vc-14.3                    |      h8a93ad2_20          17 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       228.5 MB

The following NEW packages will be INSTALLED:

  cytoscape          bioconda/noarch::cytoscape-3.10.2-he65b2d3_0
  expat              conda-forge/win-64::expat-2.6.2-h63175ca_0
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  fontconfig         conda-forge/win-64::fontconfig-2.14.2-hbde0cde_0
  freetype           conda-forge/win-64::freetype-2.12.1-hdaf720e_2
  libexpat           conda-forge/win-64::libexpat-2.6.2-h63175ca_0
  libiconv           conda-forge/win-64::libiconv-1.17-hcfcfb64_2
  libpng             conda-forge/win-64::libpng-1.6.43-h19919ed_0
  libxcb             conda-forge/win-64::libxcb-1.16-hcd874cb_0
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_1
  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
  m2w64-gcc-libs     conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
  m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
  m2w64-gmp          conda-forge/win-64::m2w64-gmp-6.1.0-2
  m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
  msys2-conda-epoch  conda-forge/win-64::msys2-conda-epoch-20160418-1
  openjdk            conda-forge/win-64::openjdk-17.0.11-h57928b3_1
  pthread-stubs      conda-forge/win-64::pthread-stubs-0.4-hcd874cb_1001
  symlink-exe-runti~ conda-forge/win-64::symlink-exe-runtime-1.0-hcfcfb64_0
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.3-h8a93ad2_20
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20
  xorg-fixesproto    conda-forge/win-64::xorg-fixesproto-5.0-hcd874cb_1002
  xorg-inputproto    conda-forge/win-64::xorg-inputproto-2.3.2-hcd874cb_1002
  xorg-kbproto       conda-forge/win-64::xorg-kbproto-1.0.7-hcd874cb_1002
  xorg-libx11        conda-forge/win-64::xorg-libx11-1.8.9-h0076a8d_1
  xorg-libxau        conda-forge/win-64::xorg-libxau-1.0.11-hcd874cb_0
  xorg-libxdmcp      conda-forge/win-64::xorg-libxdmcp-1.1.3-hcd874cb_0
  xorg-libxext       conda-forge/win-64::xorg-libxext-1.3.4-hcd874cb_2
  xorg-libxfixes     conda-forge/win-64::xorg-libxfixes-5.0.3-hcd874cb_1004
  xorg-libxi         conda-forge/win-64::xorg-libxi-1.7.10-h013a479_1
  xorg-libxtst       conda-forge/win-64::xorg-libxtst-1.2.4-h013a479_0
  xorg-recordproto   conda-forge/win-64::xorg-recordproto-1.14.2-hcd874cb_1002
  xorg-xextproto     conda-forge/win-64::xorg-xextproto-7.3.0-hcd874cb_1003
  xorg-xproto        conda-forge/win-64::xorg-xproto-7.0.31-hcd874cb_1007


Proceed ([y]/n)?


Downloading and Extracting Packages:


InvalidArchiveError('Error with archive C:\\Users\\Public\\miniconda3\\pkgs\\cytoscape-3.10.2-he65b2d3_0.tar.bz2.  You probably need to delete and re-download or re-create this file.  Message was:\n\nfailed with error: seeking backwards is not allowed')

(cytoscape_env)

I'm not sure whether it is an issue with my setup.
I can install other packages fine, though. Also, I tried extracting the bz2 file, but Windows Explorer would yield errors on that one, where it would extract other archives in C:\\Users\\Public\\miniconda3\\pkgs just fine. So I think that actually the created package is faulty. The error also occurs for versions 3.10.1 and 3.9.1 of cytoscape.

I don't know if here is the right place to ask, so please forward me to the appropriate place to report the bug. Or - are there other alternative conda packages that I can try to get an installation of cytoscape?

@martin-g
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Contributor

martin-g commented Aug 1, 2024

❯ wget https://anaconda.org/bioconda/cytoscape/3.10.2/download/noarch/cytoscape-3.10.2-he65b2d3_0.tar.bz2
--2024-08-01 14:03:44--  https://anaconda.org/bioconda/cytoscape/3.10.2/download/noarch/cytoscape-3.10.2-he65b2d3_0.tar.bz2
Resolving anaconda.org (anaconda.org)... 104.19.145.37, 104.19.144.37, 2606:4700::6813:9125, ...
Connecting to anaconda.org (anaconda.org)|104.19.145.37|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://binstar-cio-packages-prod.s3.amazonaws.com/5cb0daca71b03f1cf9930533/66040f9f9132a919550d950b?response-content-disposition=attachment%3B%20filename%3D%22cytoscape-3.10.2-he65b2d3_0.tar.bz2%22%3B%20filename%2A%3DUTF-8%27%27cytoscape-3.10.2-he65b2d3_0.tar.bz2&response-content-type=application%2Fx-tar&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=ASIAWUI46DZFBBJ2W4HJ%2F20240801%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240801T110345Z&X-Amz-Expires=600&X-Amz-SignedHeaders=host&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEIv%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJIMEYCIQDQPO8%2ByWqPJthBhBkQPGM7vJPi1X7u6cYDAmoAFU7%2FpwIhAPb74PIHdECXm1egZS7dyD9yXDrms1%2FOsdNPyLd9PATwKv4ECHQQABoMNDU1ODY0MDk4Mzc4IgxKRQ4ncc9cF6bYZK4q2wQTHg2x3093%2FqXZoyxdVb6tapossR%2F6FtxINrBelzwP7xPfBZ%2FgCaC%2BIfDbZ2i1Ci9WNUh%2Bv%2FzJRQ1dfGuVUbAzmH049EzfqHxOheZQbi0BY7G1h1bYsTvzL3UvOWpQHcBGDKn3EA9yXt5qQ%2FUY21sYQAqoAjtZh45aclkTwdvHejO3a%2FxPss2dpdbXxK%2BQMq2OWCj93nNj9VCPRuud32r5XC%2FU8gWy0gxSEByW0QYkX2gBtrCyz7SCDnYCplXdHjgw%2FsvRdGOjjpWq6Q%2FPc1RKrJeoVRyrL0%2BSyRy2de2MGIVjB7ex%2BYvvA47B0Rf2xD1sH6w%2FkwORYnTWgfHOWvLbprUMsp7QWD2RR8qQyKpkxMPqVGpkLdKm5MTkC6fckAoDEDIGzjvWZH2%2F3XxUjjw7r4Ifp%2B3Rwdb%2B5Ga%2FdzbqwuFbq6AS9c%2FKXeagJGhMngFzAkwSmsDMchqFJFF1NJPqZvftInl7ILgBuLYj%2FcoKfxTm8HXdNpDjixYIpue8LHmoBvZ%2FrQWfKpAE9iGGTwVoI42U5FCpEvylouie4qm7zn8U7f2Ln%2BL7HdbbtLXTv2aFMp3EocRBSFOfkotPL93v7iUxgbtb8TzGytdZfdxot5I755BT57veMQECDBvL9zNa%2FkR9r4odIHl1CQ3PvO3grTURcacZcR4LRCGQxP9yNERlbjgdGeSHUwN21NuKcSXQFb2rSWFUSjtL2eswDBXvXyy3xIZG8J4lrqMAIAvuLt1VeEEMVuP1jHLalnHNcpzlCPOuUquF4YK061i70Q4jBapbpBrdyOKhuJUwwNattQY6mQGhud6r99CHskLqPNLpwMptnVQQvAdIPiyFhZQ%2FV9Q2BckG9LRqbP9TZxGRa%2B39MtANTEPa8eCTSqj1FGrdOXPmfsbx0H8W5DWhDkF%2FBc8zankRCKmwkKOffuK6ssx3FNt7Le2T5pdjwZiWQmbpP9xMKiYSXwnXV5KlqF5vkDE9SmTWeKRCyTG0VxTz0oMh4DwazR7UHbcryTA%3D&X-Amz-Signature=013b315a74e824e96ef1f7841d05153620cd698b39347aec89c477da71d9bbee [following]
--2024-08-01 14:03:45--  https://binstar-cio-packages-prod.s3.amazonaws.com/5cb0daca71b03f1cf9930533/66040f9f9132a919550d950b?response-content-disposition=attachment%3B%20filename%3D%22cytoscape-3.10.2-he65b2d3_0.tar.bz2%22%3B%20filename%2A%3DUTF-8%27%27cytoscape-3.10.2-he65b2d3_0.tar.bz2&response-content-type=application%2Fx-tar&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=ASIAWUI46DZFBBJ2W4HJ%2F20240801%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240801T110345Z&X-Amz-Expires=600&X-Amz-SignedHeaders=host&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEIv%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJIMEYCIQDQPO8%2ByWqPJthBhBkQPGM7vJPi1X7u6cYDAmoAFU7%2FpwIhAPb74PIHdECXm1egZS7dyD9yXDrms1%2FOsdNPyLd9PATwKv4ECHQQABoMNDU1ODY0MDk4Mzc4IgxKRQ4ncc9cF6bYZK4q2wQTHg2x3093%2FqXZoyxdVb6tapossR%2F6FtxINrBelzwP7xPfBZ%2FgCaC%2BIfDbZ2i1Ci9WNUh%2Bv%2FzJRQ1dfGuVUbAzmH049EzfqHxOheZQbi0BY7G1h1bYsTvzL3UvOWpQHcBGDKn3EA9yXt5qQ%2FUY21sYQAqoAjtZh45aclkTwdvHejO3a%2FxPss2dpdbXxK%2BQMq2OWCj93nNj9VCPRuud32r5XC%2FU8gWy0gxSEByW0QYkX2gBtrCyz7SCDnYCplXdHjgw%2FsvRdGOjjpWq6Q%2FPc1RKrJeoVRyrL0%2BSyRy2de2MGIVjB7ex%2BYvvA47B0Rf2xD1sH6w%2FkwORYnTWgfHOWvLbprUMsp7QWD2RR8qQyKpkxMPqVGpkLdKm5MTkC6fckAoDEDIGzjvWZH2%2F3XxUjjw7r4Ifp%2B3Rwdb%2B5Ga%2FdzbqwuFbq6AS9c%2FKXeagJGhMngFzAkwSmsDMchqFJFF1NJPqZvftInl7ILgBuLYj%2FcoKfxTm8HXdNpDjixYIpue8LHmoBvZ%2FrQWfKpAE9iGGTwVoI42U5FCpEvylouie4qm7zn8U7f2Ln%2BL7HdbbtLXTv2aFMp3EocRBSFOfkotPL93v7iUxgbtb8TzGytdZfdxot5I755BT57veMQECDBvL9zNa%2FkR9r4odIHl1CQ3PvO3grTURcacZcR4LRCGQxP9yNERlbjgdGeSHUwN21NuKcSXQFb2rSWFUSjtL2eswDBXvXyy3xIZG8J4lrqMAIAvuLt1VeEEMVuP1jHLalnHNcpzlCPOuUquF4YK061i70Q4jBapbpBrdyOKhuJUwwNattQY6mQGhud6r99CHskLqPNLpwMptnVQQvAdIPiyFhZQ%2FV9Q2BckG9LRqbP9TZxGRa%2B39MtANTEPa8eCTSqj1FGrdOXPmfsbx0H8W5DWhDkF%2FBc8zankRCKmwkKOffuK6ssx3FNt7Le2T5pdjwZiWQmbpP9xMKiYSXwnXV5KlqF5vkDE9SmTWeKRCyTG0VxTz0oMh4DwazR7UHbcryTA%3D&X-Amz-Signature=013b315a74e824e96ef1f7841d05153620cd698b39347aec89c477da71d9bbee
Resolving binstar-cio-packages-prod.s3.amazonaws.com (binstar-cio-packages-prod.s3.amazonaws.com)... 52.216.61.193, 3.5.20.163, 3.5.22.1, ...
Connecting to binstar-cio-packages-prod.s3.amazonaws.com (binstar-cio-packages-prod.s3.amazonaws.com)|52.216.61.193|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 233899166 (223M) [application/x-tar]
Saving to: ‘cytoscape-3.10.2-he65b2d3_0.tar.bz2’

cytoscape-3.10.2-he65b2d3_0.tar.bz2                   100%[======================================================================================================================>] 223.06M  2.41MB/s    in 96s     

2024-08-01 14:05:22 (2.32 MB/s) - ‘cytoscape-3.10.2-he65b2d3_0.tar.bz2’ saved [233899166/233899166]


/tmp/cytoscape took 1m37s 
❯ tar xvf cytoscape-3.10.2-he65b2d3_0.tar.bz2 
info/test/run_test.sh
info/run_exports.json
info/test/run_test.bat
info/link.json
info/hash_input.json
info/recipe/response.varfile.template
info/index.json
info/recipe/build.sh
info/recipe/meta.yaml.template
info/has_prefix
info/recipe/cytoscape.sh.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/recipe/LICENSE
info/licenses/LICENSE0.txt
info/about.json
info/files
info/git
info/paths.json
share/cytoscape-3.10.2-0/framework/examples/karaf-docker-example/karaf-docker-example-static-dist/k8s/karaf-docker-example-static-dist.yaml
share/cytoscape-3.10.2-0/Cytoscape.desktop
share/cytoscape-3.10.2-0/.install4j/install4j_g9kxds-Cytoscape.desktop
share/cytoscape-3.10.2-0/sampleData/galFiltered.cys
share/cytoscape-3.10.2-0/sampleData/sessions/Yeast Perturbation.cys
share/cytoscape-3.10.2-0/sampleData/sessions/Import & Save.cys
share/cytoscape-3.10.2-0/sampleData/sessions/Affinity Purification.cys
share/cytoscape-3.10.2-0/sampleData/sessions/Yeast Gene Interactions.cys
share/cytoscape-3.10.2-0/sampleData/sessions/Ivacaftor Coauthor.cys
share/cytoscape-3.10.2-0/sampleData/sessions/TCGA Colorectal Cancer.cys
share/cytoscape-3.10.2-0/sampleData/sessions/Styles Demo.cys
share/cytoscape-3.10.2-0/.install4j/files.log
share/cytoscape-3.10.2-0/.install4j/installation.log
share/cytoscape-3.10.2-0/framework/etc/all.policy
share/cytoscape-3.10.2-0/.install4j/MessagesDefault
share/cytoscape-3.10.2-0/framework/etc/system.properties
share/cytoscape-3.10.2-0/framework/etc/startup.properties
share/cytoscape-3.10.2-0/framework/etc/java.util.logging.properties
share/cytoscape-3.10.2-0/framework/examples/karaf-branding-example/src/main/resources/org/apache/karaf/branding/branding.properties
share/cytoscape-3.10.2-0/framework/examples/karaf-itest-example/src/test/resources/etc/users.properties
share/cytoscape-3.10.2-0/framework/etc/users.properties
share/cytoscape-3.10.2-0/framework/etc/keys.properties
share/cytoscape-3.10.2-0/framework/etc/custom.properties
share/cytoscape-3.10.2-0/framework/etc/equinox-debug.properties
share/cytoscape-3.10.2-0/.install4j/stats.properties
share/cytoscape-3.10.2-0/framework/etc/config.properties
share/cytoscape-3.10.2-0/framework/etc/jre.properties
share/cytoscape-3.10.2-0/framework/bin/inc
share/cytoscape-3.10.2-0/framework/bin/karaf
share/cytoscape-3.10.2-0/Cytoscape.installoptions
share/cytoscape-3.10.2-0/sampleData/importNetworkFromFile.csv
share/cytoscape-3.10.2-0/sampleData/galExpData.csv
share/cytoscape-3.10.2-0/framework/lib/boot/README
bin/cytoscape.sh
bin/gen_vmoptions.sh
share/cytoscape-3.10.2-0/gen_vmoptions.sh
share/cytoscape-3.10.2-0/cytoscape.sh
share/cytoscape-3.10.2-0/.install4j/libi4jinst2.dylib
share/cytoscape-3.10.2-0/.install4j/libi4jinst.dylib
var/cache/fontconfig/8ca779ffb261dcb9809701586eb031a8-le64.cache-8
share/cytoscape-3.10.2-0/.install4j/autoUninstall.1
share/cytoscape-3.10.2-0/Cytoscape.vmoptions
share/cytoscape-3.10.2-0/framework/etc/org.cytoscape.cfg
share/cytoscape-3.10.2-0/.install4j/inst_jre.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.features.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/activemq/client.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/loanbroker/bank1.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/loanbroker/bank2.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/loanbroker/bank3.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/loanbroker/broker.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/loanbroker/base.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/activemq/broker.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/camel.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/default.profile/org.ops4j.pax.web.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/default.profile/version.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.felix.eventadmin.impl.EventAdmin.cfg
share/cytoscape-3.10.2-0/framework/etc/jmx.acl.java.lang.Memory.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.shell.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.feature.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.jaas.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.kar.cfg
share/cytoscape-3.10.2-0/framework/examples/karaf-profile-example/karaf-profile-example-registry/src/main/resources/default.profile/profile.cfg
share/cytoscape-3.10.2-0/framework/etc/jmx.acl.org.apache.karaf.security.jmx.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.kar.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.scope_bundle.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.system.cfg
share/cytoscape-3.10.2-0/framework/etc/profile.cfg
share/cytoscape-3.10.2-0/framework/etc/jmx.acl.org.apache.karaf.bundle.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.command.acl.bundle.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.log.cfg
share/cytoscape-3.10.2-0/framework/etc/org.apache.karaf.jaas.cfg
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share/cytoscape-3.10.2-0/framework/lib/openjfx/linux/javafx-controls-18.0.2-linux.jar
share/cytoscape-3.10.2-0/framework/system/org/apache/servicemix/bundles/org.apache.servicemix.bundles.xmlbeans/2.4.0_5/org.apache.servicemix.bundles.xmlbeans-2.4.0_5.jar
share/cytoscape-3.10.2-0/framework/system/org/apache/karaf/features/org.apache.karaf.features.core/4.3.7/org.apache.karaf.features.core-4.3.7.jar
share/cytoscape-3.10.2-0/framework/system/org/cytoscape/gui-cmdline-parser-impl/3.10.2/gui-cmdline-parser-impl-3.10.2.jar
share/cytoscape-3.10.2-0/apps/json-3.7.0.jar
share/cytoscape-3.10.2-0/apps/cx-support-2.8.3.jar
share/cytoscape-3.10.2-0/framework/system/org/ops4j/pax/url/pax-url-aether/2.6.10/pax-url-aether-2.6.10.jar
share/cytoscape-3.10.2-0/apps/enrichment-2.0.5.jar
share/cytoscape-3.10.2-0/apps/sbml-3.4.1.jar
share/cytoscape-3.10.2-0/framework/system/org/cytoscape/swing-application-impl/3.10.2/swing-application-impl-3.10.2.jar
share/cytoscape-3.10.2-0/framework/lib/openjfx/linux/javafx-graphics-18.0.2-linux.jar
share/cytoscape-3.10.2-0/apps/biopax-3.4.0.jar
share/cytoscape-3.10.2-0/apps/diffusion-1.6.4.jar
share/cytoscape-3.10.2-0/framework/system/org/bouncycastle/bcprov-jdk15on/1.69/bcprov-jdk15on-1.69.jar
share/cytoscape-3.10.2-0/apps/copycatLayout-1.3.1.jar
share/cytoscape-3.10.2-0/framework/system/org/cytoscape/search2-impl/3.10.2/search2-impl-3.10.2.jar
share/cytoscape-3.10.2-0/apps/cy-ndex-2-3.7.0.jar
share/cytoscape-3.10.2-0/apps/cy-rest-3.13.2.jar
share/cytoscape-3.10.2-0/framework/system/org/cytoscape/table-import-impl/3.10.2/table-import-impl-3.10.2.jar
share/cytoscape-3.10.2-0/framework/system/org/cytoscape/model-impl/3.10.2/model-impl-3.10.2.jar
share/cytoscape-3.10.2-0/framework/system/org/cytoscape/distribution/third-party/3.10.2/third-party-3.10.2.jar
share/cytoscape-3.10.2-0/framework/lib/openjfx/linux/javafx-web-18.0.2-linux.jar
share/cytoscape-3.10.2-0/framework/CytoscapeSplashScreen.svg

The package uncompresses without any issues here (Ubuntu 24.04).

@Mitmischer
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Interesting, so it works on Linux.
I downloaded the file from the URL you provided and it still won't decompress successfully.
I also m2w64-gcc-libs-5.3.0-7.tar.bz2(https://anaconda.org/conda-forge/m2w64-gcc-libs-core/5.3.0/download/win-64/m2w64-gcc-libs-core-5.3.0-7.tar.bz2) and it worked without issue. Is there something different between those archives' structure?

@martin-g
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martin-g commented Aug 1, 2024

/tmp/cytoscape 
❯ file *
cytoscape-3.10.2-he65b2d3_0.tar.bz2: bzip2 compressed data, block size = 900k
m2w64-gcc-libs-core-5.3.0-7.tar.bz2: bzip2 compressed data, block size = 900k

According to file they are similar bzip2 files.

/tmp/cytoscape 
❯ sha256sum *
b93ba198482d118be7391667c24810c96d6215ec30fa4db0da8161fcf4e14f34  cytoscape-3.10.2-he65b2d3_0.tar.bz2
58afdfe859ed2e9a9b1cc06bc408720cb2c3a6a132e59d4805b090d7574f4ee0  m2w64-gcc-libs-core-5.3.0-7.tar.bz2

Do you get the same SHA256 for cytoscape ? Maybe the download was not complete ?!

@Mitmischer
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Mitmischer commented Aug 1, 2024

Thank you for the quick reply!

Those are my checksums:

> Get-FileHash *.tar.bz2

Algorithm       Hash                                                                   Path
---------       ----                                                                   ----
SHA256          B93BA198482D118BE7391667C24810C96D6215EC30FA4DB0DA8161FCF4E14F34       C:\Users\Public\Downloads\cytoscape-3.10.2-he65b2d3_0.tar.bz2
SHA256          58AFDFE859ED2E9A9B1CC06BC408720CB2C3A6A132E59D4805B090D7574F4EE0       C:\Users\Public\Downloads\m2w64-gcc-libs-core-5.3.0-7.tar.bz2

I also noticed that I can extract the files using 7z just fine, also on Windows. Just not with Windows Explorer and I can't install the package (whereas I can install other packages using conda or extract other packages' archives just fine).

@Mitmischer
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As a sanity check, I just installed a small package into conda, that works. I'm really at a loss, but it looks like something in the cytoscape bz2 that only 7z and Linux archivers can understand, but the Windows decompression tools and whatever conda uses for compression can't.

>  conda install conda-forge::m2w64-gcc-libgfortran
Channels:
 - defaults
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: C:\Users\Public\miniconda3\envs\cytoscape_env

  added / updated specs:
    - conda-forge::m2w64-gcc-libgfortran


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    m2w64-gcc-libs-core-5.3.0  |                7         213 KB
    m2w64-gmp-6.1.0            |                2         689 KB
    m2w64-libwinpthread-git-5.0.0.4634.697f757|                2          30 KB
    msys2-conda-epoch-20160418 |                1           2 KB
    ------------------------------------------------------------
                                           Total:         934 KB

The following NEW packages will be INSTALLED:

  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
  m2w64-gcc-libs-co~ pkgs/msys2/win-64::m2w64-gcc-libs-core-5.3.0-7
  m2w64-gmp          pkgs/msys2/win-64::m2w64-gmp-6.1.0-2
  m2w64-libwinpthre~ pkgs/msys2/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
  msys2-conda-epoch  pkgs/msys2/win-64::msys2-conda-epoch-20160418-1


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(cytoscape_env)

@Mitmischer Mitmischer changed the title Cytoscape package corrupt on windows Cytoscape package corrupt on Windows Aug 1, 2024
@martin-g
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martin-g commented Aug 1, 2024

You may want to ask for more info at https://github.com/conda/conda-build

@Mitmischer
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Thank you for you ideas so far!
I've reraised the issue at the repo you recommended.

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