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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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conda install -c bioconda phyluce #136

Closed lucper closed 5 years ago

lucper commented 5 years ago

Hello, I created an environment for Phyluce but when I try to install it running conda install -c bioconda phyluce I receive the following error. Any thoughts?


PackagesNotFoundError: The following packages are not available from current channels:

  - phyluce
  - itero
  - schwimmbad

Current channels:

  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-64
  - https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.
brantfaircloth commented 5 years ago

looks like you need to setup the correct channels. see the documentation for phyluce and/or follow the instructions here: https://bioconda.github.io/#set-up-channels

lucper commented 5 years ago

I thought that explicitly specifying the channel with the flag -c bioconda would avoid this issue, but indeed setting up the channels beforehand solved the problem. Thank you so much for your attention!

Although the package seems to have installed successfully, I received the following error:

Preparing transaction: done
Verifying transaction: \ 
SafetyError: The package for six located at /home/lucas/miniconda3/pkgs/six-1.11.0-py27_1001
appears to be corrupted. The path 'lib/python2.7/site-packages/six.pyc'
has a sha256 mismatch.
  reported sha256: a0f05ca8e73f03f2a9e0e1a0fda475e9057a9ccaff82fd700979adbcd049e79b
  actual sha256: b551b68054103947a43d8c3269be25f6bfce998a3e5a9ca86fccc410a67d2c1e

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/appletviewer'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/extcheck'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/idlj'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jarsigner'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/java'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/java-rmi.cgi'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/javac'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/javadoc'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/javah'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/javap'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jcmd'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jconsole'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jdb'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jdeps'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jhat'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jinfo'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jjs'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jmap'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jps'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jrunscript'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jsadebugd'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jstack'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jstat'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/jstatd'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/keytool'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/native2ascii'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/orbd'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/pack200'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/policytool'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/rmic'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/rmid'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/rmiregistry'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/schemagen'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/serialver'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/servertool'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/tnameserv'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/unpack200'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/wsgen'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/wsimport'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'bin/xjc'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/classfile_constants.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/jawt.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/jdwpTransport.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/jni.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/jvmti.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/jvmticmlr.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/linux/jawt_md.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'include/linux/jni_md.h'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/ASSEMBLY_EXCEPTION'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/LICENSE'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/THIRD_PARTY_README'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/java'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/jjs'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/keytool'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/orbd'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/pack200'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/policytool'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/rmid'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/rmiregistry'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/servertool'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/tnameserv'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/bin/unpack200'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/jli/libjli.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/jvm.cfg'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libattach.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libawt.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libawt_headless.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libawt_xawt.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libdt_socket.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libfontmanager.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libhprof.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libinstrument.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libj2gss.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libj2pcsc.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libj2pkcs11.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjaas_unix.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjava.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjava_crw_demo.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjawt.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjdwp.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjpeg.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjsdt.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjsig.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjsound.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libjsoundalsa.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/liblcms.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libmanagement.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libmlib_image.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libnet.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libnio.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libnpt.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libsaproc.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libsctp.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libsplashscreen.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libsunec.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libunpack.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libverify.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/libzip.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/server/Xusage.txt'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/server/libjsig.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/amd64/server/libjvm.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/calendars.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/charsets.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/classlist'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/cmm/CIEXYZ.pf'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/cmm/GRAY.pf'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/cmm/LINEAR_RGB.pf'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/cmm/PYCC.pf'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/cmm/sRGB.pf'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/content-types.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/currency.data'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/cldrdata.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/dnsns.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/jaccess.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/localedata.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/meta-index'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/nashorn.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/sunec.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/sunjce_provider.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/sunpkcs11.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/ext/zipfs.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/flavormap.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/fontconfig.bfc'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/fontconfig.properties.src'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/hijrah-config-umalqura.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/cursors.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/invalid32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/motif_CopyDrop32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/motif_CopyNoDrop32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/motif_LinkDrop32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/motif_LinkNoDrop32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/motif_MoveDrop32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/images/cursors/motif_MoveNoDrop32x32.gif'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/jce.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/jexec'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/jsse.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/jvm.hprof.txt'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/logging.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/management-agent.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/management/jmxremote.access'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/management/jmxremote.password.template'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/management/management.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/management/snmp.acl.template'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/meta-index'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/net.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/psfont.properties.ja'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/psfontj2d.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/resources.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/rt.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/security/blacklisted.certs'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/security/cacerts'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/security/java.policy'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/security/java.security'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/sound.properties'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'jre/lib/tzdb.dat'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/ct.sym'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/dt.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/ir.idl'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/jconsole.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/jexec'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/libjawt.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/libjli.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/libnet.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/orb.idl'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/sa-jdi.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda::java-jdk-8.0.92-1, defaults::openjdk-8.0.152-h46b5887_1
  path: 'lib/tools.jar'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge::libgfortran-3.0.0-1, conda-forge::libgcc-7.2.0-h69d50b8_2
  path: 'lib/libgfortran.so.3'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge::libgfortran-3.0.0-1, conda-forge::libgcc-7.2.0-h69d50b8_2
  path: 'lib/libgfortran.so.3.0.0'

done
Executing transaction: done
lucper commented 5 years ago

Seems to be a local problem with my miniconda3 installation.

brantfaircloth commented 5 years ago

these other issues appear to be related to packages already installed in the environment you are trying to create. it would be probably be easiest to delete that environment and start again.