Can't install version 1.5 from conda #729
Description
Description of bug:
When I try to install from conda, it says that version 1.5 of MultiQC cannot be found.
** Error log:**
$ conda create -y -c bioconda -n multiqc-1.5 multiqc==1.5
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- multiqc==1.5
- lzstring
- multiqc==1.5
- spectra[version='>=0.0.10']
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
But when I search for the package, version 1.5 is listed:
$ conda search -c bioconda 'multiqc'
Loading channels: done
# Name Version Build Channel
...
...
multiqc 1.5a py27_0 bioconda
multiqc 1.5a py35_0 bioconda
multiqc 1.5a py36_0 bioconda
multiqc 1.5 py27_0 bioconda
multiqc 1.5 py35_0 bioconda
multiqc 1.5 py36_0 bioconda
I eventually got it to install, by not specifying which version I wanted:
$ conda create -y -c bioconda -n multiqc multiqc
Solving environment: done
## Package Plan ##
environment location: /ifs/home/kellys04/conda3/envs/multiqc
added / updated specs:
- multiqc
The following packages will be downloaded:
package | build
---------------------------|-----------------
functools32-3.2.3.2 | py27h4ead58f_1 22 KB
icu-58.2 | h9c2bf20_1 22.5 MB
libgfortran-ng-7.2.0 | hdf63c60_3 1.2 MB
simplejson-3.8.1 | py27_0 131 KB bioconda
multiqc-0.9.1a0 | py27_4 760 KB bioconda
pyparsing-2.2.0 | py27hf1513f8_1 93 KB
click-6.7 | py27h4225b90_0 103 KB
backports_abc-0.5 | py27h7b3c97b_0 12 KB
jinja2-2.10 | py27h4114e70_0 177 KB
intel-openmp-2018.0.0 | 8 620 KB
python-2.7.14 | h1571d57_31 11.8 MB
certifi-2018.1.18 | py27_0 143 KB
expat-2.2.5 | he0dffb1_0 186 KB
pyyaml-3.12 | py27h2d70dd7_1 159 KB
cycler-0.10.0 | py27hc7354d3_0 13 KB
subprocess32-3.2.7 | py27h373dbce_0 40 KB
backports.functools_lru_cache-1.5| py27_1 9 KB
wheel-0.31.0 | py27_0 61 KB
numpy-1.14.2 | py27hdbf6ddf_1 4.1 MB
kiwisolver-1.0.1 | py27hc15e7b5_0 86 KB
pyqt-5.9.2 | py27h751905a_0 5.7 MB
singledispatch-3.4.0.3 | py27h9bcb476_0 15 KB
sip-4.19.8 | py27hf484d3e_0 291 KB
six-1.11.0 | py27h5f960f1_1 21 KB
fontconfig-2.12.6 | h49f89f6_0 283 KB
git-2.17.0 | pl526hb75a9fb_0 12.2 MB
gst-plugins-base-1.12.4 | h33fb286_0 4.8 MB
backports-1.0 | py27h63c9359_1 3 KB
pytz-2018.3 | py27_0 211 KB
libssh2-1.8.0 | h9cfc8f7_4 243 KB
mkl-2018.0.2 | 1 205.2 MB
mkl_fft-1.0.1 | py27h3010b51_0 137 KB
perl-5.26.0 | hae598fd_0 15.8 MB
libgcc-ng-7.2.0 | hdf63c60_3 6.1 MB
pcre-8.42 | h439df22_0 251 KB
python-dateutil-2.3 | py27_0 213 KB bioconda
libcurl-7.59.0 | h1ad7b7a_0 491 KB
qt-5.9.4 | h4e5bff0_0 86.6 MB
libxcb-1.13 | h1bed415_1 502 KB
mkl_random-1.0.1 | py27h629b387_0 361 KB
futures-3.2.0 | py27h7b459c0_0 25 KB
libstdcxx-ng-7.2.0 | hdf63c60_3 2.5 MB
libpng-1.6.34 | hb9fc6fc_0 334 KB
pip-9.0.3 | py27_0 2.4 MB
freetype-2.8 | hab7d2ae_1 804 KB
jpeg-9b | h024ee3a_2 248 KB
markupsafe-1.0 | py27h97b2822_1 24 KB
matplotlib-2.2.2 | py27h0e671d2_1 6.5 MB
libxml2-2.9.8 | hf84eae3_0 2.0 MB
gstreamer-1.12.4 | hb53b477_0 3.6 MB
tornado-5.0.1 | py27_1 617 KB
glib-2.53.6 | h5d9569c_2 8.4 MB
dbus-1.13.2 | hc3f9b76_0 554 KB
setuptools-39.0.1 | py27_0 582 KB
------------------------------------------------------------
Total: 410.1 MB
The following NEW packages will be INSTALLED:
backports: 1.0-py27h63c9359_1
backports.functools_lru_cache: 1.5-py27_1
backports_abc: 0.5-py27h7b3c97b_0
ca-certificates: 2018.03.07-0
certifi: 2018.1.18-py27_0
click: 6.7-py27h4225b90_0
cycler: 0.10.0-py27hc7354d3_0
dbus: 1.13.2-hc3f9b76_0
expat: 2.2.5-he0dffb1_0
fontconfig: 2.12.6-h49f89f6_0
freetype: 2.8-hab7d2ae_1
functools32: 3.2.3.2-py27h4ead58f_1
futures: 3.2.0-py27h7b459c0_0
git: 2.17.0-pl526hb75a9fb_0
glib: 2.53.6-h5d9569c_2
gst-plugins-base: 1.12.4-h33fb286_0
gstreamer: 1.12.4-hb53b477_0
icu: 58.2-h9c2bf20_1
intel-openmp: 2018.0.0-8
jinja2: 2.10-py27h4114e70_0
jpeg: 9b-h024ee3a_2
kiwisolver: 1.0.1-py27hc15e7b5_0
libcurl: 7.59.0-h1ad7b7a_0
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-hdf63c60_3
libgfortran-ng: 7.2.0-hdf63c60_3
libpng: 1.6.34-hb9fc6fc_0
libssh2: 1.8.0-h9cfc8f7_4
libstdcxx-ng: 7.2.0-hdf63c60_3
libxcb: 1.13-h1bed415_1
libxml2: 2.9.8-hf84eae3_0
markupsafe: 1.0-py27h97b2822_1
matplotlib: 2.2.2-py27h0e671d2_1
mkl: 2018.0.2-1
mkl_fft: 1.0.1-py27h3010b51_0
mkl_random: 1.0.1-py27h629b387_0
multiqc: 0.9.1a0-py27_4 bioconda
ncurses: 6.0-h9df7e31_2
numpy: 1.14.2-py27hdbf6ddf_1
openssl: 1.0.2o-h20670df_0
pcre: 8.42-h439df22_0
perl: 5.26.0-hae598fd_0
pip: 9.0.3-py27_0
pyparsing: 2.2.0-py27hf1513f8_1
pyqt: 5.9.2-py27h751905a_0
python: 2.7.14-h1571d57_31
python-dateutil: 2.3-py27_0 bioconda
pytz: 2018.3-py27_0
pyyaml: 3.12-py27h2d70dd7_1
qt: 5.9.4-h4e5bff0_0
readline: 7.0-ha6073c6_4
setuptools: 39.0.1-py27_0
simplejson: 3.8.1-py27_0 bioconda
singledispatch: 3.4.0.3-py27h9bcb476_0
sip: 4.19.8-py27hf484d3e_0
six: 1.11.0-py27h5f960f1_1
sqlite: 3.22.0-h1bed415_0
subprocess32: 3.2.7-py27h373dbce_0
tk: 8.6.7-hc745277_3
tornado: 5.0.1-py27_1
wheel: 0.31.0-py27_0
xz: 5.2.3-h55aa19d_2
yaml: 0.1.7-had09818_2
zlib: 1.2.11-ha838bed_2
...
...
...
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate multiqc
#
# To deactivate an active environment, use
#
# $ conda deactivate
But, it is only installing version 1.0 with Python 2.7 even though I am using Python 3 in this conda installation:
$ source conda3/bin/activate && python --version
Python 3.6.4 :: Anaconda, Inc.
$ source conda3/bin/activate multiqc && multiqc --version
multiqc, version 1.0.dev0 (2986bf4)
$ source conda3/bin/activate multiqc && python --version
Python 2.7.14 :: Anaconda, Inc.
Any idea what is going on here?
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ewels commentedon Apr 16, 2018
Hi @stevekm,
This is very strange, no idea I'm sorry. I tried copying and pasting the first command that you used and it worked perfectly for me.
I don't think this is really a MultiQC issue, but rather something strange happening with conda. I'd recommend posting this issue over on https://github.com/bioconda/bioconda-recipes/ and perhaps asking on their Gitter channel.
Let me know if there's anything that I can do to help..
Phil
stevekm commentedon Apr 18, 2018
Thanks I actually figured out that I had to run this first, as per the Bioconda docs:
ewels commentedon Apr 18, 2018
Interesting, thanks for letting me know! I would have thought that as you had
-c biocondaon the command line then it would have been ok. Will keep this in mind for the future 👍Kronopt commentedon Nov 12, 2018
I can confirm this problem.
I tried the fix by @stevekm and it worked, although most package dependencies come from conda-forge.
I tried to install multiqc without relying on the conda-forge channel and it didn't work, multiqc version 0.9 was installed again...