Installation problem on Linux

[nickjcroucher]

Installs smoothy on local Mac OSX with bioconda: conda install pp-sketchlib

Set up new python3.6 conda environment on Unix HPC, added bioconda channel and ran same command - did not work. Used the setup.py approach instead, hit a problem with CMake:

running build_ext -- The C compiler identification is GNU 7.4.0 -- The CXX compiler identification is GNU 7.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Error at CMakeLists.txt:7 (add_compile_definitions): Unknown CMake command "add_compile_definitions".

This is the conda environment, in case informative:

conda env export
name: py3
channels:
  - defaults
  - bioconda
dependencies:
  - _libgcc_mutex=0.1=main
  - ca-certificates=2019.11.27=0
  - certifi=2019.11.28=py36_0
  - ld_impl_linux-64=2.33.1=h53a641e_7
  - libedit=3.1.20181209=hc058e9b_0
  - libffi=3.2.1=hd88cf55_4
  - libgcc-ng=9.1.0=hdf63c60_0
  - libstdcxx-ng=9.1.0=hdf63c60_0
  - ncurses=6.1=he6710b0_1
  - openssl=1.1.1d=h7b6447c_3
  - pip=19.3.1=py36_0
  - python=3.6.10=h0371630_0
  - readline=7.0=h7b6447c_5
  - setuptools=44.0.0=py36_0
  - sqlite=3.30.1=h7b6447c_0
  - tk=8.6.8=hbc83047_0
  - wheel=0.33.6=py36_0
  - xz=5.2.4=h14c3975_4
  - zlib=1.2.11=h7b6447c_3

My cmake version is 3.10.2 - judging from this comment, the required cmake version may need to be updated? https://github.com/CppMicroServices/CppMicroServices/issues/412

[nickjcroucher]

Upgrading cmake to 3.14.0 removes this problem. However, I now get the report:

-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:20 (find_package):
  By not providing "Findpybind11.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "pybind11",
  but CMake did not find one.

  Could not find a package configuration file provided by "pybind11" with any
  of the following names:

    pybind11Config.cmake
    pybind11-config.cmake

  Add the installation prefix of "pybind11" to CMAKE_PREFIX_PATH or set
  "pybind11_DIR" to a directory containing one of the above files.  If
  "pybind11" provides a separate development package or SDK, be sure it has
  been installed.

[johnlees]

What was the error with the bioconda install on Linux?

Thanks for the cmake fix – I'll update that in both methods. For python setup.py install you need all the dependencies installed already, which is probably easiest in a conda env. The ones you might not have are pybind11 eigen hdf5 mkl

[nickjcroucher]

Yes, sorry, that was a bioconda install problem - seems to think there are a lot of conflicts:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Package ld_impl_linux-64 conflicts for:
python=3.6 -> ld_impl_linux-64
Package sqlite conflicts for:
python=3.6 -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.26.0,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
Package zlib conflicts for:
pp-sketchlib -> zlib[version='>=1.2.11,<1.3.0a0']
python=3.6 -> zlib[version='>=1.2.11,<1.3.0a0']
Package hdf5 conflicts for:
pp-sketchlib -> hdf5[version='>=1.10.5,<1.10.6.0a0']
Package ncurses conflicts for:
python=3.6 -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0']
Package mkl conflicts for:
pp-sketchlib -> mkl[version='>=2019.4,<2020.0a0']
Package bzip2 conflicts for:
pp-sketchlib -> bzip2[version='>=1.0.8,<2.0a0']
Package intel-openmp conflicts for:
pp-sketchlib -> intel-openmp
Package openssl conflicts for:
python=3.6 -> openssl[version='1.0.*|1.0.*,>=1.0.2l,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a']
Package xz conflicts for:
python=3.6 -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0']
Package pip conflicts for:
python=3.6 -> pip
Package libgcc-ng conflicts for:
python=3.6 -> libgcc-ng[version='>=7.2.0|>=7.3.0']
pp-sketchlib -> libgcc-ng[version='>=7.3.0']
Package libffi conflicts for:
python=3.6 -> libffi[version='3.2.*|>=3.2.1,<4.0a0']
Package tk conflicts for:
python=3.6 -> tk[version='8.6.*|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
Package h5py conflicts for:
pp-sketchlib -> h5py
Package libstdcxx-ng conflicts for:
python=3.6 -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
pp-sketchlib -> libstdcxx-ng[version='>=7.3.0']
Package readline conflicts for:
python=3.6 -> readline[version='7.*|>=7.0,<8.0a0']
Package numpy conflicts for:
pp-sketchlib -> numpy

This is a fresh conda environment, so there might just be something obvious missing.

[johnlees]

I ran (on the farm):

conda create -n ppsketch pp-sketchlib

which worked

This was with conda 4.5.11. I had noticed a similar problem with running conda-build with a newer version (4.8.0). Which version are you using?

[nickjcroucher]

conda 4.8.1. Running: conda create -n ppsketch pp-sketchlib Gives the following report:

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package bzip2 conflicts for:
pp-sketchlib -> bzip2[version='>=1.0.8,<2.0a0']
Package mkl conflicts for:
pp-sketchlib -> mkl[version='>=2019.4,<2020.0a0']
Package hdf5 conflicts for:
pp-sketchlib -> hdf5[version='>=1.10.5,<1.10.6.0a0']
Package python conflicts for:
pp-sketchlib -> python[version='>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
Package zlib conflicts for:
pp-sketchlib -> zlib[version='>=1.2.11,<1.3.0a0']
Package intel-openmp conflicts for:
pp-sketchlib -> intel-openmp
Package libgcc-ng conflicts for:
pp-sketchlib -> libgcc-ng[version='>=7.3.0']
Package h5py conflicts for:
pp-sketchlib -> h5py
Package libstdcxx-ng conflicts for:
pp-sketchlib -> libstdcxx-ng[version='>=7.3.0']
Package numpy conflicts for:
pp-sketchlib -> numpy

[johnlees]

Does adding --no-update-dependencies help?

[nickjcroucher]

I ran: conda install --no-update-deps pp-sketchlib But get a simiilar-looking error:

The following specifications were found to be incompatible with each other:

Package krb5 conflicts for:
pkgs/main/linux-64::libcurl==7.67.0=h20c2e04_0 -> krb5[version='>=1.16.1,<1.17.0a0']
Package sqlite conflicts for:
pkgs/main/linux-64::python==3.6.10=h0371630_0 -> sqlite[version='>=3.30.1,<4.0a0']

etc.

[johnlees]

Final thing I can find is the advice here: https://conda-forge.org/docs/user/tipsandtricks.html

What is the output of

conda config --describe channel_priority

If you set the channel priorities up as bioconda recommends:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

and set a strict channel order:

conda config --set channel_priority strict

does that work?

If this doesn't help, I am guessing this is a bug in newer versions of conda, as I can find a few similar issues there. I'll raise this as an issue with them if it still doesn't work.

[nickjcroucher]

Original setting is: # channel_priority: flexible. Then:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install --no-update-deps pp-sketchlib

But I still get:

The following specifications were found to be incompatible with each other:

Seems like a conda version problem?

[johnlees]

Yeah, I think it must be. I will raise an issue with them

You might want to downgrade conda to 4.5 (I'll include this in the install notes for now)

[johnlees]

Could you paste the return from the following commands so I can raise an issue with conda:

conda info
conda config --show-sources
conda list --show-channel-urls

I'll edit out any user-specifics before posing

[nickjcroucher]

conda info:

     active environment : py3
    active env location : /lustre/scratch118/infgen/team284/nc3/conda/envs/py3
            shell level : 2
       user config file : /nfs/users/nfs_n/nc3/.condarc
 populated config files : /nfs/users/nfs_n/nc3/.condarc
          conda version : 4.8.1
    conda-build version : not installed
         python version : 2.7.16.final.0
       virtual packages : __glibc=2.27
       base environment : /lustre/scratch118/infgen/team284/nc3/conda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          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/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /lustre/scratch118/infgen/team284/nc3/nc3/pkgs
       envs directories : /lustre/scratch118/infgen/team284/nc3/conda/envs
                          /nfs/users/nfs_n/nc3/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.1 requests/2.22.0 CPython/2.7.16 Linux/4.15.0-70-generic ubuntu/18.04.2 glibc/2.27
                UID:GID : 12303:14970
             netrc file : None
           offline mode : False

conda config --show-sources:

==> /nfs/users/nfs_n/nc3/.condarc <==
channels:
  - conda-forge
  - bioconda
  - defaults
pkgs_dirs:
  - /lustre/scratch118/infgen/team284/nc3/nc3/pkgs
channel_priority: strict

conda list --show-channel-urls

# packages in environment at /lustre/scratch118/infgen/team284/nc3/conda/envs/py3:
# 
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
blast                     2.9.0           pl526h3066fca_4    bioconda
boost-cpp                 1.70.0               h8e57a91_2    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
cairo                     1.16.0            hfb77d84_1002    conda-forge
cd-hit                    4.8.1                hdbcaa40_0    bioconda
certifi                   2019.11.28               py36_0    conda-forge
clustalw                  2.1                  hc9558a2_5    bioconda
cmake                     3.16.2               h28c56e5_1    conda-forge
curl                      7.65.3               hf8cf82a_0    conda-forge
diamond                   0.9.29               h56fc30b_0    bioconda
eigen                     3.3.7             hc9558a2_1001    conda-forge
entrez-direct             11.0                    pl526_1    bioconda
expat                     2.2.5             he1b5a44_1004    conda-forge
fasttree                  2.1.10               h14c3975_3    bioconda
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.0               he983fc9_1    conda-forge
fribidi                   1.0.5             h516909a_1002    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
giflib                    5.2.1                h516909a_1    conda-forge
glib                      2.58.3          py36h6f030ca_1002    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
graphviz                  2.42.3               h0511662_0    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
hdf5                      1.10.6          nompi_h3c11f04_100    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
intel-openmp              2019.4                      243    defaults
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_7    conda-forge
libcurl                   7.65.3               hda55be3_0    conda-forge
libdb                     6.1.26            he1b5a44_2001    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgd                     2.2.5             h307a58e_1007    conda-forge
libgfortran-ng            7.3.0                hdf63c60_4    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libtool                   2.4.6             h14c3975_1002    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libuv                     1.34.0               h516909a_0    conda-forge
libwebp                   1.0.2                h56121f0_5    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
libxslt                   1.1.33               h31b3aaa_0    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
mafft                     7.455                h516909a_0    bioconda
mcl                       14.137          pl526h516909a_5    bioconda
mkl                       2019.4                      243    defaults
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
paml                      4.9                  h516909a_5    bioconda
pango                     1.42.4               ha030887_1    conda-forge
parallel                  20191122                      0    conda-forge
pcre                      8.43                 he1b5a44_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-aceperl              1.92                    pl526_2    bioconda
perl-algorithm-diff       1.1903                  pl526_2    bioconda
perl-algorithm-munkres    0.08                    pl526_1    bioconda
perl-apache-test          1.40                    pl526_1    bioconda
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-appconfig            1.71                    pl526_1    bioconda
perl-archive-tar          2.32                    pl526_0    bioconda
perl-array-compare        3.0.1                   pl526_1    bioconda
perl-autoloader           5.74                    pl526_2    bioconda
perl-base                 2.23                    pl526_1    bioconda
perl-bio-asn1-entrezgene  1.73                    pl526_1    bioconda
perl-bio-coordinate       1.007001                pl526_1    bioconda
perl-bio-featureio        1.6.905                 pl526_2    bioconda
perl-bio-phylo            0.58                    pl526_2    bioconda
perl-bio-samtools         1.43            pl526h1341992_1    bioconda
perl-bio-tools-phylo-paml 1.7.3                   pl526_1    bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4                   pl526_1    bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4                   pl526_2    bioconda
perl-bioperl              1.7.2                  pl526_11    bioconda
perl-bioperl-core         1.007002                pl526_2    bioconda
perl-bioperl-run          1.007002                pl526_4    bioconda
perl-business-isbn        3.004                   pl526_0    bioconda
perl-business-isbn-data   20140910.003            pl526_0    bioconda
perl-cache-cache          1.08                    pl526_0    bioconda
perl-capture-tiny         0.48                    pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-cgi                  4.44            pl526h14c3975_1    bioconda
perl-class-data-inheritable 0.08                    pl526_1    bioconda
perl-class-inspector      1.34                    pl526_0    bioconda
perl-class-load           0.25                    pl526_0    bioconda
perl-class-load-xs        0.10            pl526h6bb024c_2    bioconda
perl-class-method-modifiers 2.12                    pl526_0    bioconda
perl-clone                0.42            pl526h516909a_0    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-bzip2   2.087           pl526he1b5a44_0    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-convert-binary-c     0.78            pl526h6bb024c_3    bioconda
perl-convert-binhex       1.125                   pl526_1    bioconda
perl-crypt-rc4            2.02                    pl526_1    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-data-optlist         0.110                   pl526_2    bioconda
perl-data-stag            0.14                    pl526_1    bioconda
perl-date-format          2.30                    pl526_2    bioconda
perl-db-file              1.852           pl526h14c3975_0    bioconda
perl-dbd-sqlite           1.64            pl526h516909a_0    bioconda
perl-dbi                  1.642                   pl526_0    bioconda
perl-devel-globaldestruction 0.14                    pl526_0    bioconda
perl-devel-overloadinfo   0.005                   pl526_0    bioconda
perl-devel-stacktrace     2.04                    pl526_0    bioconda
perl-digest-hmac          1.03                    pl526_3    bioconda
perl-digest-md5           2.55                    pl526_0    bioconda
perl-digest-perl-md5      1.9                     pl526_1    bioconda
perl-digest-sha1          2.13            pl526h6bb024c_1    bioconda
perl-dist-checkconflicts  0.11                    pl526_2    bioconda
perl-dynaloader           1.25                    pl526_1    bioconda
perl-email-date-format    1.005                   pl526_2    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-encode-locale        1.05                    pl526_6    bioconda
perl-error                0.17027                 pl526_1    bioconda
perl-eval-closure         0.14            pl526h6bb024c_4    bioconda
perl-exception-class      1.44                    pl526_0    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-listing         6.04                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-slurp-tiny      0.004                   pl526_1    bioconda
perl-file-sort            1.01                    pl526_2    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-file-which           1.23                    pl526_0    bioconda
perl-font-afm             1.20                    pl526_2    bioconda
perl-font-ttf             1.06                    pl526_0    bioconda
perl-gd                   2.71            pl526he860b03_0    bioconda
perl-getopt-long          2.50                    pl526_1    bioconda
perl-graph                0.9704                  pl526_1    bioconda
perl-graphviz             2.24            pl526h734ff71_0    bioconda
perl-html-element-extended 1.18                    pl526_1    bioconda
perl-html-entities-numbered 0.04                    pl526_1    bioconda
perl-html-formatter       2.16                    pl526_0    bioconda
perl-html-parser          3.72            pl526h6bb024c_5    bioconda
perl-html-tableextract    2.13                    pl526_2    bioconda
perl-html-tagset          3.20                    pl526_3    bioconda
perl-html-tidy            1.60                    pl526_0    bioconda
perl-html-tree            5.07                    pl526_1    bioconda
perl-html-treebuilder-xpath 0.14                    pl526_1    bioconda
perl-http-cookies         6.04                    pl526_0    bioconda
perl-http-daemon          6.01                    pl526_1    bioconda
perl-http-date            6.02                    pl526_3    bioconda
perl-http-message         6.18                    pl526_0    bioconda
perl-http-negotiate       6.01                    pl526_3    bioconda
perl-image-info           1.38                    pl526_1    bioconda
perl-image-size           3.300                   pl526_2    bioconda
perl-io-compress          2.087           pl526he1b5a44_0    bioconda
perl-io-html              1.001                   pl526_2    bioconda
perl-io-sessiondata       1.03                    pl526_1    bioconda
perl-io-socket-ssl        2.066                   pl526_0    bioconda
perl-io-string            1.08                    pl526_3    bioconda
perl-io-stringy           2.111                   pl526_1    bioconda
perl-io-tty               1.12                    pl526_1    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-ipc-run              20180523.0              pl526_0    bioconda
perl-ipc-sharelite        0.17            pl526h6bb024c_1    bioconda
perl-jcode                2.07                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-lib                  0.63                    pl526_1    bioconda
perl-libwww-perl          6.39                    pl526_0    bioconda
perl-libxml-perl          0.08                    pl526_2    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-lwp-mediatypes       6.04                    pl526_0    bioconda
perl-lwp-protocol-https   6.07                    pl526_4    bioconda
perl-lwp-simple           6.15            pl526h470a237_4    bioconda
perl-mailtools            2.21                    pl526_0    bioconda
perl-math-cdf             0.1             pl526h14c3975_5    bioconda
perl-math-derivative      1.01                    pl526_0    bioconda
perl-math-random          0.72            pl526h14c3975_2    bioconda
perl-math-spline          0.02                    pl526_2    bioconda
perl-mime-base64          3.15                    pl526_1    bioconda
perl-mime-lite            3.030                   pl526_1    bioconda
perl-mime-tools           5.508                   pl526_1    bioconda
perl-mime-types           2.17                    pl526_0    bioconda
perl-mldbm                2.05                    pl526_1    bioconda
perl-module-implementation 0.09                    pl526_2    bioconda
perl-module-runtime       0.016                   pl526_1    bioconda
perl-module-runtime-conflicts 0.003                   pl526_0    bioconda
perl-moo                  2.003004                pl526_0    bioconda
perl-moose                2.2011          pl526hf484d3e_1    bioconda
perl-mozilla-ca           20180117                pl526_1    bioconda
perl-mro-compat           0.13                    pl526_0    bioconda
perl-net-http             6.19                    pl526_0    bioconda
perl-net-ssleay           1.88            pl526h90d6eec_0    bioconda
perl-ntlm                 1.09                    pl526_4    bioconda
perl-ole-storage_lite     0.19                    pl526_3    bioconda
perl-package-deprecationmanager 0.17                    pl526_0    bioconda
perl-package-stash        0.38            pl526hf484d3e_1    bioconda
perl-package-stash-xs     0.28            pl526hf484d3e_1    bioconda
perl-params-util          1.07            pl526h6bb024c_4    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-parse-recdescent     1.967015                pl526_0    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-pdf-api2             2.035                   pl526_0    bioconda
perl-pod-escapes          1.07                    pl526_1    bioconda
perl-pod-usage            1.69                    pl526_1    bioconda
perl-postscript           0.06                    pl526_2    bioconda
perl-role-tiny            2.000008                pl526_0    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-set-scalar           1.29                    pl526_2    bioconda
perl-soap-lite            1.19                    pl526_1    bioconda
perl-socket               2.027                   pl526_1    bioconda
perl-sort-naturally       1.03                    pl526_2    bioconda
perl-spreadsheet-parseexcel 0.65                    pl526_2    bioconda
perl-spreadsheet-writeexcel 2.40                    pl526_2    bioconda
perl-statistics-descriptive 3.0702                  pl526_0    bioconda
perl-storable             3.15            pl526h14c3975_0    bioconda
perl-sub-exporter         0.987                   pl526_2    bioconda
perl-sub-exporter-progressive 0.001013                pl526_0    bioconda
perl-sub-identify         0.14            pl526h14c3975_0    bioconda
perl-sub-install          0.928                   pl526_2    bioconda
perl-sub-name             0.21                    pl526_1    bioconda
perl-sub-quote            2.006003                pl526_1    bioconda
perl-sub-uplevel          0.2800          pl526h14c3975_2    bioconda
perl-svg                  2.84                    pl526_0    bioconda
perl-svg-graph            0.02                    pl526_3    bioconda
perl-task-weaken          1.06                    pl526_0    bioconda
perl-template-toolkit     2.26                    pl526_1    bioconda
perl-test                 1.26                    pl526_1    bioconda
perl-test-deep            1.128                   pl526_1    bioconda
perl-test-differences     0.67                    pl526_0    bioconda
perl-test-exception       0.43                    pl526_2    bioconda
perl-test-harness         3.42                    pl526_0    bioconda
perl-test-leaktrace       0.16            pl526h14c3975_2    bioconda
perl-test-most            0.35                    pl526_0    bioconda
perl-test-requiresinternet 0.05                    pl526_0    bioconda
perl-test-warn            0.36                    pl526_1    bioconda
perl-text-diff            1.45                    pl526_0    bioconda
perl-tie-ixhash           1.23                    pl526_2    bioconda
perl-time-hires           1.9760          pl526h14c3975_1    bioconda
perl-time-local           1.28                    pl526_1    bioconda
perl-timedate             2.30                    pl526_1    bioconda
perl-tree-dag_node        1.31                    pl526_0    bioconda
perl-try-tiny             0.30                    pl526_1    bioconda
perl-type-tiny            1.004004                pl526_0    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-unicode-map          0.112           pl526h6bb024c_3    bioconda
perl-uri                  1.76                    pl526_0    bioconda
perl-www-robotrules       6.02                    pl526_3    bioconda
perl-xml-dom              1.46                    pl526_0    bioconda
perl-xml-dom-xpath        0.14                    pl526_1    bioconda
perl-xml-filter-buffertext 1.01                    pl526_2    bioconda
perl-xml-libxml           2.0132          pl526h7ec2d77_1    bioconda
perl-xml-libxslt          1.94                    pl526_1    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44_01         pl526ha1d75be_1002    conda-forge
perl-xml-regexp           0.04                    pl526_2    bioconda
perl-xml-sax              1.02                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_3    bioconda
perl-xml-sax-writer       0.57                    pl526_0    bioconda
perl-xml-simple           2.25                    pl526_1    bioconda
perl-xml-twig             3.52                    pl526_2    bioconda
perl-xml-writer           0.625                   pl526_2    bioconda
perl-xml-xpath            1.44                    pl526_0    bioconda
perl-xml-xpathengine      0.14                    pl526_2    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
perl-yaml                 1.29                    pl526_0    bioconda
pip                       19.3.1                   py36_0    conda-forge
pirate                    1.0.3                         2    bioconda
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
pybind11                  2.4.3            py36hc9558a2_0    conda-forge
python                    3.6.7             h357f687_1006    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
rhash                     1.3.6             h14c3975_1001    conda-forge
setuptools                45.0.0                   py36_1    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
t_coffee                  11.0.8           py36hea885bf_8    bioconda
tidyp                     1.04                          1    bioconda
tk                        8.6.10               hed695b0_0    conda-forge
unzip                     6.0                  h516909a_0    conda-forge
wheel                     0.33.6                   py36_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxpm               3.5.13               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.1.5             h516909a_1003    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h3b9ef0a_1    conda-forge

I just installed PIRATE, hence the extended list. And to check this hadn't affected pp-sketchlib, I re-ran conda install pp-sketchlib. And now it works fine. So it seems if another package installs the dependencies, there isn't a problem?

[johnlees]

Hmm, puzzling. I guess it's probably a bug, which may only be triggered by the order dependencies are getting brought in by pp-sketchlib (I saw it with hdf5, h5py and gfortran).

It may also be because there are packages installed in py3. Could you try activating your base environment/making a completely clean new environment with conda new --name=testenvand activating it, then running conda install pp-sketchlib from that one? If that fails, could you send me the output of conda list --show-channel-urls from that new env?

[nickjcroucher]

Created a new environment and it worked fine this time. No idea why.

[johnlees]

The only thing I can think of is packages in base. I'll add a link to that conda-forge page in the install.

Annoying though! Very difficult to diagnose what might be wrong. Hope this doesn't become an issue with conda going forwards...