Closed gubrins closed 1 year ago
Seems like that version of r-base is not available anymore. I tried removing the specification and it installed correctly. Can you try the same? You can use the new yaml https://github.com/gf777/mitoVGP/blob/master/mitoVGP_conda_env_pacbio.yml
Let me know. Thanks
Giulio
Thanks Giulio for your fast reply. It did not work, a lot of conflicts were raised, here some examples:
Package biopython conflicts for:
genomicconsensus==2.3.3=py27_0 -> pbcore[version='>=1.6.5'] -> biopython[version='>=1.74']
pbcoretools==0.2.4=py27_4 -> pbcore[version='>=1.6.5'] -> biopython[version='>=1.74']
Package glib-tools conflicts for:
r-base -> glib[version='>=2.69.1,<3.0a0'] -> glib-tools[version='2.66.4|2.66.4|2.66.4|2.66.4|2.66.5|2.66.5|2.66.5|2.66.5|2.66.6|2.66.6|2.66.6|2.66.6|2.66.6|2.66.7|2.66.7|2.68.0|2.68.0|2.68.1|2.68.2|2.68.2|2.68.2|2.68.3|2.68.4|2.68.4|2.70.0|2.70.0|2.70.1|2.70.2|2.70.2|2.70.2|2.70.2|2.70.2|2.72.1',build='h709712a_2|hc4f0c31_2|h709712a_2|hc4f0c31_2|ha03b18c_2|hcd2ae1e_2|hc4f0c31_2|h9c3ff4c_0|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h780b84a_1|h780b84a_2|h780b84a_4|h6239696_0|h780b84a_3|h780b84a_1|h780b84a_0|h780b84a_0|h780b84a_0|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_3|ha03b18c_2|h709712a_2|hcd2ae1e_2|hcd2ae1e_2|ha03b18c_2']
cairo==1.16.0=hfb77d84_1002 -> glib[version='>=2.58.3,<3.0a0'] -> glib-tools[version='2.66.4|2.66.4|2.66.4|2.66.4|2.66.5|2.66.5|2.66.5|2.66.5|2.66.6|2.66.6|2.66.6|2.66.6|2.66.6|2.66.7|2.66.7|2.68.0|2.68.0|2.68.1|2.68.2|2.68.2|2.68.2|2.68.3|2.68.4|2.68.4|2.70.0|2.70.0|2.70.1|2.70.2|2.70.2|2.70.2|2.70.2|2.70.2|2.72.1',build='h709712a_2|hc4f0c31_2|h709712a_2|hc4f0c31_2|ha03b18c_2|hcd2ae1e_2|hc4f0c31_2|h9c3ff4c_0|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h780b84a_1|h780b84a_2|h780b84a_4|h6239696_0|h780b84a_3|h780b84a_1|h780b84a_0|h780b84a_0|h780b84a_0|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_3|ha03b18c_2|h709712a_2|hcd2ae1e_2|hcd2ae1e_2|ha03b18c_2']
harfbuzz==2.4.0=h9f30f68_3 -> glib[version='>=2.58.3,<3.0a0'] -> glib-tools[version='2.66.4|2.66.4|2.66.4|2.66.4|2.66.5|2.66.5|2.66.5|2.66.5|2.66.6|2.66.6|2.66.6|2.66.6|2.66.6|2.66.7|2.66.7|2.68.0|2.68.0|2.68.1|2.68.2|2.68.2|2.68.2|2.68.3|2.68.4|2.68.4|2.70.0|2.70.0|2.70.1|2.70.2|2.70.2|2.70.2|2.70.2|2.70.2|2.72.1',build='h709712a_2|hc4f0c31_2|h709712a_2|hc4f0c31_2|ha03b18c_2|hcd2ae1e_2|hc4f0c31_2|h9c3ff4c_0|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h780b84a_1|h780b84a_2|h780b84a_4|h6239696_0|h780b84a_3|h780b84a_1|h780b84a_0|h780b84a_0|h780b84a_0|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_3|ha03b18c_2|h709712a_2|hcd2ae1e_2|hcd2ae1e_2|ha03b18c_2']
Package xorg-libxrender conflicts for:
r-base -> xorg-libxrender
openjdk==11.0.1=h46a85a0_1017 -> xorg-libxrender
pango==1.42.4=ha030887_1 -> cairo[version='>=1.16.0,<1.17.0a0'] -> xorg-libxrender
cairo==1.16.0=hfb77d84_1002 -> xorg-libxrender
picard==2.20.6=0 -> openjdk[version='>=8'] -> xorg-libxrender
harfbuzz==2.4.0=h9f30f68_3 -> cairo[version='>=1.16.0,<1.17.0a0'] -> xorg-libxrender
xorg-libxrender==0.9.10=h516909a_1002
Package boost conflicts for:
boost==1.70.0=py27h9de70de_1
blast==2.5.0=hc0b0e79_3 -> boost
Package python-consensuscore conflicts for:
genomicconsensus==2.3.3=py27_0 -> python-consensuscore[version='>=1.1.1']
python-consensuscore==1.1.1=py27h3f2a3d2_3
Package python-consensuscore2 conflicts for:
python-consensuscore2==3.4.1=py27_0
genomicconsensus==2.3.3=py27_0 -> python-consensuscore2[version='>=3.4.1']The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.31=0
- feature:/linux-64::__unix==0=0
- feature:|@/linux-64::__unix==0=0
- alsa-lib==1.1.5=h516909a_1001 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- bcftools==1.9=ha228f0b_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- blast==2.5.0=hc0b0e79_3 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
and at the end I have this:
Your installed version is: 2.31
Note that strict channel priority may have removed packages required for satisfiability.
But no new environment is created.
Ah I see what the problem likely is. You have your conda config file overriding channel priority. You need to edit your .condarc
. file (usually in the home directory) setting priority to flexible:
auto_activate_base: true
anaconda_upload: false
channels:
- conda-forge
- bioconda
- r
- bioconda/label/cf201901
- biobuilds
- yuxiang
- defaults
channel_priority: flexible
I just tested the installation again, and it works fine in my conda (version 4.13.0). See log below. Hope this helps!
(base) [gformenti@login04 gformenti]$ conda remove --name mitoVGP_pacbio --all
Remove all packages in environment ...:
## Package Plan ##
environment location: ...
The following packages will be REMOVED:
_libgcc_mutex-0.1-main
_r-mutex-1.0.1-anacondar_1
alsa-lib-1.1.5-h516909a_1001
avro-python2-1.9.0-py_0
awscli-1.16.225-py27_0
bam2fastq-1.1.0-0
bcftools-1.9-ha228f0b_4
blast-2.5.0-hc0b0e79_3
boost-1.70.0-py27h9de70de_1
boost-cpp-1.70.0-h8e57a91_2
botocore-1.12.215-py_0
bowtie2-2.3.4.1-py27h2d50403_1
bzip2-1.0.8-h516909a_2
ca-certificates-2019.11.28-hecc5488_0
cairo-1.16.0-hfb77d84_1002
certifi-2019.11.28-py27_0
cffi-1.13.2-py27h8022711_0
chardet-3.0.4-py27_1003
colorama-0.3.9-py27_0
cryptography-2.8-py27h72c5cf5_1
curl-7.65.3-hf8cf82a_0
cython-0.29.14-py27he1b5a44_0
docutils-0.15.2-py27_0
enum34-1.1.6-py27_1002
fontconfig-2.13.1-h86ecdb6_1001
freebayes-1.0.2-0
freetype-2.10.0-he983fc9_1
fribidi-1.0.5-h516909a_1002
futures-3.3.0-py27_0
genomicconsensus-2.3.3-py27_0
gettext-0.19.8.1-hc5be6a0_1002
giflib-5.1.7-h516909a_1
glib-2.58.3-py27h6f030ca_1002
graphite2-1.3.13-hf484d3e_1000
h5py-2.10.0-nompi_py27h513d04c_100
harfbuzz-2.4.0-h9f30f68_3
hdf5-1.10.5-nompi_h3c11f04_1104
htslib-1.9-ha228f0b_7
icu-64.2-he1b5a44_1
idna-2.8-py27_1000
infernal-1.1.2-h14c3975_2
ipaddress-1.0.23-py_0
iso8601-0.1.12-py_1
java-jdk-7.0.91-1
jmespath-0.9.4-py_0
jpeg-9c-h14c3975_1001
krb5-1.16.3-h05b26f9_1001
lcms2-2.9-hbd6801e_1
libblas-3.8.0-14_openblas
libcblas-3.8.0-14_openblas
libcurl-7.65.3-hda55be3_0
libdeflate-1.0-h14c3975_1
libedit-3.1.20170329-hf8c457e_1001
libffi-3.2.1-he1b5a44_1006
libgcc-7.2.0-h69d50b8_2
libgcc-ng-9.2.0-hdf63c60_0
libgfortran-ng-7.3.0-hdf63c60_2
libiconv-1.15-h516909a_1005
liblapack-3.8.0-14_openblas
libopenblas-0.3.7-h5ec1e0e_5
libpng-1.6.37-hed695b0_0
libssh2-1.8.2-h22169c7_2
libstdcxx-ng-9.2.0-hdf63c60_0
libtiff-4.1.0-hc3755c2_1
libuuid-2.32.1-h14c3975_1000
libxcb-1.13-h14c3975_1002
libxml2-2.9.10-hee79883_0
linecache2-1.0.0-py_1
lz4-c-1.8.3-he1b5a44_1001
minimap2-2.17-h8b12597_1
mummer-3.23-pl526_8
muscle-3.8.1551-h6bb024c_4
ncurses-6.1-hf484d3e_1002
numpy-1.16.5-py27h95a1406_0
openjdk-11.0.1-h46a85a0_1017
openssl-1.1.1d-h516909a_0
pango-1.42.4-ha030887_1
pbbam-0.23.0-h88345a9_0
pbcommand-1.1.1-py_3
pbcopper-0.4.2-h3f2a3d2_1
pbcore-1.7.1-py27_0
pbcoretools-0.2.4-py27_4
pbgcpp-1.9.0-0
pbmm2-1.0.0-ha888412_0
pcre-8.43-he1b5a44_0
perl-5.26.2-h516909a_1006
picard-2.20.6-0
pip-19.3.1-py27_0
pixman-0.38.0-h516909a_1003
pthread-stubs-0.4-h14c3975_1001
pyasn1-0.4.8-py_0
pycparser-2.19-py27_1
pyopenssl-19.1.0-py27_0
pysam-0.15.3-py27hda2845c_1
pysocks-1.7.1-py27_0
python-2.7.15-h5a48372_1009
python-consensuscore-1.1.1-py27h3f2a3d2_3
python-consensuscore2-3.4.1-py27_0
python-dateutil-2.8.1-py_0
pytz-2019.3-py_0
pyyaml-5.2-py27h516909a_0
r-base-3.2.2-1
readline-8.0-hf8c457e_0
requests-2.22.0-py27_1
rsa-3.4.2-py_1
s3transfer-0.2.1-py27_0
samtools-1.9-h8571acd_11
setuptools-42.0.2-py27_0
six-1.13.0-py27_0
sqlite-3.30.1-hcee41ef_0
tbb-2019.9-hc9558a2_1
tk-8.6.10-hed695b0_0
traceback2-1.4.0-py27_0
trnascan-se-2.0-pl526h470a237_1
unittest2-1.1.0-py_0
urllib3-1.25.7-py27_0
wheel-0.33.6-py27_0
xorg-fixesproto-5.0-h14c3975_1002
xorg-inputproto-2.3.2-h14c3975_1002
xorg-kbproto-1.0.7-h14c3975_1002
xorg-libice-1.0.10-h516909a_0
xorg-libsm-1.2.3-h84519dc_1000
xorg-libx11-1.6.9-h516909a_0
xorg-libxau-1.0.9-h14c3975_0
xorg-libxdmcp-1.1.3-h516909a_0
xorg-libxext-1.3.4-h516909a_0
xorg-libxfixes-5.0.3-h516909a_1004
xorg-libxi-1.7.10-h516909a_0
xorg-libxrender-0.9.10-h516909a_1002
xorg-libxtst-1.2.3-h516909a_1002
xorg-recordproto-1.14.2-h516909a_1002
xorg-renderproto-0.11.1-h14c3975_1002
xorg-xextproto-7.3.0-h14c3975_1002
xorg-xproto-7.0.31-h14c3975_1007
xz-5.2.4-h14c3975_1001
yaml-0.2.2-h516909a_1
zlib-1.2.11-h516909a_1006
zstd-1.4.4-h3b9ef0a_1
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(base) [gformenti@login04 gformenti]$ wget https://raw.githubusercontent.com/gf777/mitoVGP/master/mitoVGP_conda_env_pacbio.yml
--2022-09-16 08:47:30-- https://raw.githubusercontent.com/gf777/mitoVGP/master/mitoVGP_conda_env_pacbio.yml
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 4273 (4.2K) [text/plain]
Saving to: ‘mitoVGP_conda_env_pacbio.yml’
100%[=====================================================================================================>] 4,273 --.-K/s in 0.002s
2022-09-16 08:47:30 (2.55 MB/s) - ‘mitoVGP_conda_env_pacbio.yml’ saved [4273/4273]
(base) [gformenti@login04 gformenti]$ conda env create -f mitoVGP_conda_env_pacbio.yml
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.13.0
latest version: 4.14.0
Please update conda by running
$ conda update -n base conda
Preparing transaction: done
Verifying transaction: done
Executing transaction: \
amazing! Thanks Giulio!!
Heys,
So I am trying to set up a new environment:
conda env create -f mitoVGP_conda_env_pacbio.yml
And I am getting this error:
ResolvePackageNotFound:
- r-base==3.2.2=0
Did anybody has a similar issue? Thanks in advance!