Conda environment conflicts
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weedcentipede commented
Hey there,
I just ran Conda to install ViewBS and apparently there's some conflicts in the environment, listed below
Package snakemake-minimal conflicts for:
snakemake -> snakemake-minimal[version='5.10.0.*|5.9.1.*|5.8.2.*|5.8.1.*|5.7.4.*|5.7.1.*|5.7.0.*|5.6.0.*|5.5.4.*|5.5.3.*|5.5.2.*|5.5.1.*|5.5.0.*|5.4.5.*|5.4.4.*|5.4.3.*|5.4.2.*.2.2.*|5.2.1.*']
snakemake-minimal
Package datrie conflicts for:
snakemake -> datrie
snakemake-minimal -> datrie
datrie
Package markupsafe conflicts for:
jinja2 -> markupsafe[version='>=0.23']
snakemake -> jinja2 -> markupsafe[version='>=0.23']
markupsafe
Package liblapacke conflicts for:
r-base -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_openblas|5_openblas|9_openblas|11_openblas|15_openblas|14_openblas|13_openblas|12_openblas|10_openblas|8_openblas|
numpy -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_mkl|5_mkl|6_mkl|7_mkl|9_mkl|13_mkl|15_mkl|4_openblas|5_openblas|9_openblas|11_openblas|15_openblas|14_openblas|13_o|7_openblas|6_openblas|14_mkl|12_mkl|11_mkl|10_mkl|8_mkl']
Package perl-html-formatter conflicts for:
perl-html-formatter
perl-xml-twig -> perl-html-formatter
perl-bioperl-core -> perl-xml-twig -> perl-html-formatter
perl-bio-phylo -> perl-xml-twig -> perl-html-formatter
perl-graphviz -> perl-xml-twig -> perl-html-formatter
Package typing_extensions conflicts for:
typing_extensions
aiohttp -> typing_extensions[version='>=3.6.5']
aioeasywebdav -> aiohttp -> typing_extensions[version='>=3.6.5']
Package gitpython conflicts for:
gitpython
snakemake -> snakemake-minimal=5.10.0 -> gitpython
snakemake-minimal -> gitpython
Package perl-jcode conflicts for:
perl-spreadsheet-parseexcel -> perl-jcode
perl-jcode
perl-bioperl-core -> perl-spreadsheet-parseexcel -> perl-jcode
Package networkx conflicts for:
networkx
snakemake -> networkx[version='>=2.0']
Package multidict conflicts for:
aiohttp -> yarl[version='>=1.0,<2.0'] -> multidict[version='>=2.0|>=4.0']
multidict
aiohttp -> multidict[version='>=2.1.4|>=4.0,<5.0|>=4.5,<5.0|>=3.0.0']
aioeasywebdav -> aiohttp -> multidict[version='>=2.1.4|>=4.0,<5.0|>=4.5,<5.0|>=3.0.0']
yarl -> multidict[version='>=2.0|>=4.0']
Package r-colorspace conflicts for:
r-munsell -> r-colorspace
r-scales -> r-munsell[version='>=0.2'] -> r-colorspace
r-colorspace
Package r-ggplot2 conflicts for:
r-ggplot2
r-ggsci -> r-ggplot2[version='>=2.0.0']
Package xorg-libxcb conflicts for:
r-base -> xorg-libx11 -> xorg-libxcb=1
cairo -> xorg-libx11 -> xorg-libxcb=1
Package gitdb2 conflicts for:
gitdb2
snakemake-minimal -> gitpython -> gitdb2[version='<=3.0.0|>=3,<4']
gitpython -> gitdb2[version='<=3.0.0|>=3,<4']
Package perl-json conflicts for:
perl-json
perl-bioperl-core -> perl-bio-phylo -> perl-json
perl-bio-phylo -> perl-json
perl-data-stag -> perl-json
Package ftputil conflicts for:
ftputil
snakemake -> ftputil[version='>=3.2']
Package perl-xml-sax-expat conflicts for:
perl-xml-simple -> perl-xml-sax-expat
perl-bioperl-core -> perl-xml-simple -> perl-xml-sax-expat
perl-xml-sax-expat
Package perl-cache-cache conflicts for:
perl-bioperl-core -> perl-aceperl -> perl-cache-cache
perl-aceperl -> perl-cache-cache
Package perl-types-serialiser conflicts for:
perl-json-xs -> perl-types-serialiser
perl-json -> perl-json-xs[version='<3'] -> perl-types-serialiser
Package pycrypto conflicts for:
paramiko -> pycrypto[version='>=2.1,!=2.4,<3.0']
pysftp -> paramiko[version='>=1.7.7'] -> pycrypto[version='>=2.1,!=2.4,<3.0']
Package filechunkio conflicts for:
filechunkio
snakemake -> filechunkio[version='>=1.6']
Package perl-spreadsheet-writeexcel conflicts for:
perl-spreadsheet-parseexcel -> perl-spreadsheet-writeexcel
perl-bioperl-core -> perl-spreadsheet-parseexcel -> perl-spreadsheet-writeexcel
perl-spreadsheet-writeexcel
Package perl-template-toolkit conflicts for:
perl-bio-phylo -> perl-template-toolkit
perl-template-toolkit
perl-bioperl-core -> perl-bio-phylo -> perl-template-toolkit
Package boto3 conflicts for:
snakemake -> boto3
boto3
snakemake -> moto[version='>=0.4.14'] -> boto3[version='>=1.2.1|>=1.2.1,<1.8.0|>=1.6.15|>=1.9.201|>=1.9.86,<1.9.197|>=1.9.86,<=1.9.197|>=1.9.86']
Package httplib2 conflicts for:
google-cloud-core -> google-auth-httplib2 -> httplib2
google-cloud-core -> httplib2[version='>=0.9.1']
Package paramiko conflicts for:
pysftp -> paramiko[version='>=1.17.0|>=1.7.7']
snakemake -> pysftp[version='>=0.2.8'] -> paramiko[version='>=1.17.0|>=1.7.7']
paramiko
Package mkl_fft conflicts for:
pandas -> numpy[version='>=1.14.6,<2.0a0'] -> mkl_fft[version='>=1.0.4|>=1.0.6,<2.0a0']
numpy -> mkl_fft[version='>=1.0.4|>=1.0.6,<2.0a0']
EDIT:
Even installing a "mild" version of the environment the conflicts persist
(meths-illumina) larteagafi@bf2i-galaxy:~/meths/longipes$ conda create -n viewbs bioconda::htslib anaconda::perl r::r-ggplot2 bioconda::r-pheatmap r::r-reshape2 conda-forge::r-cowplot bioconda::perl-cpan-shell
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \
Found conflicts! Looking for incompatible packages. failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
return getattr(module, func_name)(args, parser)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/main_create.py", line 37, in execute
install(args, parser, 'create')
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/install.py", line 265, in install
should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
should_retry_solve)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
force_remove, should_retry_solve)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
ssc = self._run_sat(ssc)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 808, in _run_sat
should_retry_solve=ssc.should_retry_solve
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 1318, in solve
self.find_conflicts(specs, specs_to_add, history_specs)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 347, in find_conflicts
bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 507, in build_conflict_map
root, search_node, dep_graph, num_occurances)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 369, in breadth_first_search_for_dep_graph
last_spec = MatchSpec.union((path[-1], target_paths[-1][-1]))[0]
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 481, in union
return cls.merge(match_specs, union=True)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in merge
reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in <lambda>
reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 502, in _merge
final = this_component.union(that_component)
File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 764, in union
return '|'.join(options)
TypeError: sequence item 0: expected str instance, Channel found
`$ /home/data/larteagafi/miniconda3/bin/conda create -n viewbs bioconda::htslib anaconda::perl r::r-ggplot2 bioconda::r-pheatmap r::r-reshape2 conda-forge::r-cowplot bioconda::perl-cpan-shell`
environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_ADDR2LINE=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
addr2line
CONDA_BACKUP_AR=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ar
CONDA_BACKUP_AS=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-as
CONDA_BACKUP_CC=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_CMAKE_PREFIX_PATH=/home/data/larteagafi/miniconda3:/home/data/larteagafi/miniconda3/x86_
64-conda_cos6-linux-gnu/sysroot/usr
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/home/data/larteagafi/miniconda3/x86_64-conda_cos6-linux-gnu/sysroot
CONDA_BACKUP_CPP=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cpp
CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_CXX=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++
CONDA_BACKUP_CXXFILT=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-
gnu-c++filt
CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_ELFEDIT=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
elfedit
CONDA_BACKUP_F77=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
gfortran
CONDA_BACKUP_F90=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
gfortran
CONDA_BACKUP_F95=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-f95
CONDA_BACKUP_FC=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
gfortran
CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/data/larteagafi/miniconda3/include
CONDA_BACKUP_GCC=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_BACKUP_GCC_AR=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
ar
CONDA_BACKUP_GCC_NM=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
nm
CONDA_BACKUP_GCC_RANLIB=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
ranlib
CONDA_BACKUP_GFORTRAN=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
gfortran
CONDA_BACKUP_GPROF=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gprof
CONDA_BACKUP_GXX=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-g++
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
CONDA_BACKUP_JAVA_HOME=/usr/lib/jvm/java-8-oracle
CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=
CONDA_BACKUP_LD=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,
--disable-new-dtags -Wl,--gc-sections
-Wl,-rpath,/home/data/larteagafi/miniconda3/lib -Wl,-rpath-
link,/home/data/larteagafi/miniconda3/lib
-L/home/data/larteagafi/miniconda3/lib
CONDA_BACKUP_LD_GOLD=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
ld.gold
CONDA_BACKUP_NM=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_BACKUP_OBJCOPY=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
objcopy
CONDA_BACKUP_OBJDUMP=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
objdump
CONDA_BACKUP_RANLIB=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
ranlib
CONDA_BACKUP_READELF=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
readelf
CONDA_BACKUP_SIZE=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-size
CONDA_BACKUP_STRINGS=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
strings
CONDA_BACKUP_STRIP=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
CONDA_DEFAULT_ENV=meths-illumina
CONDA_EXE=/home/data/larteagafi/miniconda3/bin/conda
CONDA_PREFIX=/home/data/larteagafi/miniconda3/envs/meths-illumina
CONDA_PREFIX_1=/home/data/larteagafi/miniconda3
CONDA_PROMPT_MODIFIER=(meths-illumina)
CONDA_PYTHON_EXE=/home/data/larteagafi/miniconda3/bin/python
CONDA_ROOT=/home/data/larteagafi/miniconda3
CONDA_SHLVL=2
JAVA_LD_LIBRARY_PATH=/home/data/larteagafi/miniconda3/envs/meths-
illumina/jre/lib/amd64/server
PATH=/home/data/larteagafi/miniconda3/bin:/home/data/larteagafi/miniconda3/
envs/meths-illumina/bin:/home/data/larteagafi/miniconda3/bin:/home/dat
a/larteagafi/miniconda3/bin:/home/data/larteagafi/miniconda3/condabin:
/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/
java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-
8-oracle/jre/bin:/usr/local/bin/kentUtils:/home/data/larteagafi/apps/m
irdeep2-0.1.3/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : meths-illumina
active env location : /home/data/larteagafi/miniconda3/envs/meths-illumina
shell level : 2
user config file : /home/data/larteagafi/.condarc
populated config files : /home/data/larteagafi/.condarc
conda version : 4.8.2
conda-build version : not installed
python version : 3.7.4.final.0
virtual packages : __glibc=2.28
base environment : /home/data/larteagafi/miniconda3 (writable)
channel URLs : 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 : /home/data/larteagafi/miniconda3/pkgs
/home/data/larteagafi/.conda/pkgs
envs directories : /home/data/larteagafi/miniconda3/envs
/home/data/larteagafi/.conda/envs
platform : linux-64
user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.4 Linux/4.19.0-6-amd64 debian/10 glibc/2.28
UID:GID : 1016:1019
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Cheers,
Luis Alfonso.