[conda] Unable to create environment

[c***@gmail.com]

Greetings.

I preformed a fresh install on conda. In order to do so, I deleted the
conda & .conda directory as well as .condarc. I downloaded
Miniconda3-latest-Linux-x86_64.sh and installed it with the following
command.

bash Miniconda3-latest-Linux-x86_64.sh $HOME

Specs on the Linux environment are below

LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.4.1708 (Core)
Release: 7.4.1708
Codename: Core

Linux l-0-01 3.10.0-514.2.2.el7.x86_64 #1 SMP Tue Dec 6 23:06:41 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux

conda -V
conda4.5.5

I tried to create an environment with the aid of the attached file
(python3_requirements.txt) with the following command:

/home/myDirectoryName/miniconda/bin/conda create --name py35 --file
python3_requirements.txt python=3.5

And I received a message stating that an error had occurred and the
following report is created.



# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<




Traceback (most recent call last):
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/exceptions.py"
, line 819, in __call__
return func(*args, **kwargs)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/main.py"
, line 78, in _main
exit_code = do_call(args, p)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/conda_argparse.py"
, line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/main_create.py"
, line 11, in execute
install(args, parser, 'create')
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/install.py"
, line 184, in install
explicit(specs, prefix, verbose=not context.quiet, index_args=
index_args)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/misc.py",
line 78, in explicit
assert not any(spec_pcrec[1] is None for spec_pcrec in specs_pcrecs)
AssertionError


`$ /home/myDirectoryName/miniconda/bin/conda create --name py35 --file
python3_requirements.txt python=3.5`


environment variables:
CIO_TEST=<not set>
CONDA_ROOT=/home/myDirectoryName/miniconda
CPATH=/cm/shared/apps/uge/8.5.3/include
LD_LIBRARY_PATH=/cm/shared/apps/uge/8.5.3/lib/lx-amd64
MANPATH=/cm/shared/apps/uge/8.5.3/man:/usr/local/share/man
:/usr/share/man/over
rides:/usr/share/man:/cm/local/apps/environment-
modules/current/share/man
MODULEPATH=/cm/local/modulefiles:/cm/shared/modulefiles:/cm/
shared/modulefiles_ch
op
PATH=/home/myDirectoryName/miniconda/bin:/home/
myDirectoryName/miniconda/bin:/home/myDirectoryName/miniconda/bin:/cm/shared
/apps/uge/8.5.3/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/
sbin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/opt/dell
/srvadmin/bin:/home/myDirectoryName/.local/bin:/home/myDirectoryName/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>


active environment : None
user config file : /home/myDirectoryName/.condarc
populated config files :
conda version : 4.5.4
conda-build version : not installed
python version : 3.6.5.final.0
base environment : /home/myDirectoryName/miniconda (writable)
channel URLs : 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
package cache : /home/myDirectoryName/miniconda/pkgs
/home/myDirectoryName/.conda/pkgs
envs directories : /home/myDirectoryName/miniconda/envs
/home/myDirectoryName/.conda/envsplatform : linux-
64
user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/
3.10.0-514.2.2.el7.x86_64 centos/7 glibc/2.17
UID:GID : 988541:85000002
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

There is no .condarc file created and I am not certain what the error
actually is. I do know that I do not have any permission rights outside of
my directory. Any assistance is deeply appreciated.

C

[Paul Madden]

I hacked the contents of your python3_requirements.txt into a single conda
create command:

conda create -n foo -c defaults -c bioconda -c r -c leipzig -c drramki -c
conda-forge -c bioconda-legacy -c biobuilds awscli=1.11.21 bcdoc=0.16.0
bcftools=1.3.1 vcftools=0.1.15 bioconductor-annotationdbi=1.34.4
bioconductor-biobase=2.32.0 bioconductor-biocgenerics=0.18.0 bioconductor-
biocparallel=1.6.6 bioconductor-biomart=2.28.0 bioconductor-biostrings=2.40.
2 bioconductor-bsgenome=1.40.1 bioconductor-genomeinfodb=1.8.3 bioconductor-
genomicalignments=1.8.4 bioconductor-genomicfeatures=1.24.5 bioconductor-
genomicranges=1.24.2 bioconductor-geoquery=2.38.4 bioconductor-graph=1.50.0
bioconductor-iranges=2.6.1 bioconductor-rsamtools=1.24.0 bioconductor-
rtracklayer=1.32.2 bioconductor-s4vectors=0.10.3 bioconductor-sradb=1.28.0
bioconductor-summarizedexperiment=1.1.22 bioconductor-variantannotation=1.16
.4 bioconductor-xvector=0.12.0 bioconductor-zlibbioc=1.18.0 boost=1.60.0
boto=2.39.0 boto3=1.4.0 botocore=1.4.78 bwa=0.7.15 bzip2=1.0.6 cairo=1.12.18
cffi=1.8.3 click=6.6 cmake=3.3.1 colorama=0.3.7 cryptography=1.5.2 curl=7.49
.0 cycler=0.10.0 cyvcf2=0.5.5 decorator=4.0.10 deeptools=2.3.5 denovogear=
1.1.1 docutils=0.12 drmaa=0.7.6 dropbox=5.2.1 ecdsa=0.13 eigen=3.2 expat=2.1
.0 fastqc=0.11.5 filechunkio=1.6 flake8=2.5.1 fontconfig=2.11.1 freetype=2.5
.5 ftputil=3.2 gatk=3.8 gettext=0.19.7 glib=2.43.0 gmp=5.1.2 graphviz=2.38.0
gsl=2.1 harfbuzz=0.9.39 htslib=1.3.2 icu=54.1 idna=2.1 igv=2.3.72 java-jdk=
8.0.45 jbig=2.1 jinja2=2.8 jmespath=0.9.0 jpeg=8d libdb=6.1.26 libffi=3.2.1
libgcc=5.2.0 libgd=2.2.4 libgfortran=3.0.0 libiconv=1.14 libpng=1.6.22
libtiff=4.0.6 libxml2=2.9.3 libxslt=1.1.28 markupsafe=0.23 matplotlib=1.5.1
mccabe=0.3.1 mkl=11.3.3 mkl-rt=11.1 multiqc=0.8 mysql-connector-c=6.1.6
mysqlclient=1.3.7 ncurses=5.9 networkx=1.11 novoalign=3.04.04 numexpr=2.6.1
numpy=1.11.2 openblas=0.2.14 openssl=1.0.2j pandas=0.19.1 pandoc=1.17.2
pango=1.39.0 paramiko=2.0.2 pcre=8.39 peddy=0.2.7 pep8=1.7.0 perl=5.22.0.1
perl-aceperl=1.92 perl-algorithm-diff=1.1903 perl-algorithm-munkres=0.08
perl-appconfig=1.71 perl-archive-extract=0.76 perl-archive-tar=2.18 perl-
archive-zip=1.55 perl-array-compare=2.11 perl-bio-asn1-entrezgene=1.72 perl-
bio-db-hts=2.4 perl-bio-featureio=1.6.905 perl-bio-phylo=0.58 perl-bio-
samtools=1.43 perl-bioperl=1.6.924 perl-bioperl-core=1.6.924 perl-bioperl-
run=1.006900 perl-capture-tiny=0.36 perl-cgi=4.22 perl-class-data-
inheritable=0.08 perl-class-method-modifiers=2.11 perl-clone=0.38 perl-
common-sense=3.74 perl-compress-raw-bzip2=2.069 perl-compress-raw-zlib=2.069
perl-convert-binary-c=0.78 perl-crypt-rc4=2.02 perl-data-stag=0.14 perl-db-
file=1.835 perl-dbd-mysql=4.033 perl-dbd-pg=3.5.3 perl-dbd-sqlite=1.50 perl-
dbi=1.636 perl-devel-globaldestruction=0.13 perl-devel-stacktrace=2.00 perl-
digest-hmac=1.03 perl-digest-perl-md5=1.9 perl-encode-locale=1.05 perl-error
=0.17024 perl-exception-class=1.40 perl-exporter-tiny=0.042 perl-extutils-
makemaker=6.66 perl-extutils-manifest=1.70 perl-file-copy-recursive=0.38
perl-file-fetch=0.48 perl-file-listing=6.04 perl-file-sharedir=1.102 perl-
file-sharedir-install=0.10 perl-file-slurp-tiny=0.004 perl-file-sort=1.01
perl-file-which=1.20 perl-font-afm=1.20 perl-gd=2.56 perl-graph=0.9704 perl-
graphviz=2.20 perl-html-element-extended=1.18 perl-html-entities-numbered=
0.04 perl-html-formatter=2.14 perl-html-parser=3.72 perl-html-tableextract=
2.13 perl-html-tagset=3.20 perl-html-tidy=1.56 perl-html-tree=5.03 perl-html
-treebuilder-xpath=0.14 perl-http-cookies=6.01 perl-http-daemon=6.01 perl-
http-date=6.02 perl-http-message=6.11 perl-http-negotiate=6.01 perl-image-
info=1.38 perl-image-size=3.300 perl-inline=0.80 perl-inline-c=0.76 perl-io-
all=0.86 perl-io-compress=2.069 perl-io-html=1.001 perl-io-socket-ssl=2.024
perl-io-string=1.08 perl-io-stringy=2.111 perl-io-tty=1.12 perl-ipc-run=0.94
perl-ipc-system-simple=1.25 perl-jcode=2.07 perl-json=2.90 perl-json-xs=2.34
perl-libwww-perl=6.15 perl-libxml-perl=0.08 perl-list-moreutils=0.413 perl-
lwp-mediatypes=6.02 perl-lwp-protocol-https=6.06 perl-lwp-simple=6.15 perl-
math-cdf=0.1 perl-math-derivative=0.04 perl-math-random=0.72 perl-math-
spline=0.02 perl-memoize=1.03 perl-mldbm=2.05 perl-module-build=0.4214 perl-
module-runtime=0.014 perl-moo=2.001000 perl-net-http=6.09 perl-net-ssleay=
1.74 perl-ntlm=1.09 perl-ole-storage_lite=0.19 perl-parse-recdescent=
1.967013 perl-pdf-api2=2.025 perl-pegex=0.61 perl-postscript=0.06 perl-role-
tiny=2.000001 perl-scalar-list-utils=1.45 perl-set-scalar=1.29 perl-sort-
naturally=1.03 perl-spreadsheet-parseexcel=0.65 perl-spreadsheet-writeexcel=
2.40 perl-statistics-descriptive=3.0612 perl-statistics-frequency=0.04 perl-
sub-exporter-progressive=0.001011 perl-sub-uplevel=0.25 perl-svg=2.64 perl-
svg-graph=0.02 perl-template-toolkit=2.26 perl-test-deep=1.120 perl-test-
differences=0.64 perl-test-exception=0.43 perl-test-leaktrace=0.15 perl-test
-most=0.34 perl-test-pod=1.51 perl-test-simple=1.302052 perl-test-warn=0.30
perl-text-diff=1.44 perl-text-parsewords=3.29 perl-threaded=5.22.0 perl-tie-
cacher=0.09 perl-tie-ixhash=1.23 perl-time-hires=1.9728 perl-tree-dag_node=
1.29 perl-type-tiny=1.000005 perl-unicode-map=0.112 perl-uri=1.71 perl-www-
robotrules=6.02 perl-xml-dom=1.45 perl-xml-dom-xpath=0.14 perl-xml-filter-
buffertext=1.01 perl-xml-libxml=2.0124 perl-xml-libxslt=1.94 perl-xml-
namespacesupport=1.11 perl-xml-parser=2.44 perl-xml-regexp=0.04 perl-xml-sax
=0.99 perl-xml-sax-base=1.08 perl-xml-sax-expat=0.51 perl-xml-sax-writer=
0.56 perl-xml-simple=2.22 perl-xml-twig=3.49 perl-xml-writer=0.625 perl-xml-
xpath=1.33 perl-xml-xpathengine=0.14 perl-yaml=1.18 perl-yaml-libyaml=0.63
picard=2.3.0 pip=8.1.2 pixman=0.32.6 postgresql=9.5.4 pyasn1=0.1.9 pybigwig=
0.2.8 pycparser=2.14 pycrypto=2.6.1 pyflakes=1.1.0 pyparsing=2.1.1 pyqt=4.11
.4 pysam=0.9.0 pysftp=0.2.8 python=3.5.2 python-dateutil=2.3 pytz=2016.7
pyyaml=3.12 qt=4.8.7 qualimap=2.2 r=3.3.1 r-aod=1.3 r-assertthat=0.1 r-base=
3.3.1 r-bh=1.60.0_2 r-bitops=1.0_6 r-boot=1.3_18 r-cairo=1.5_9 r-catools=
1.17.1 r-class=7.3_14 r-cluster=2.0.4 r-codetools=0.2_14 r-curl=0.9.7 r-dbi=
0.4_1 r-devtools=1.11.1 r-digest=0.6.9 r-doparallel=1.0.10 r-dplyr=0.4.3 r-
dt=0.2 r-evaluate=0.9 r-exomedepth=1.1.10 r-foreach=1.4.3 r-foreign=0.8_66 r
-formatr=1.4 r-futile.logger=1.4.1 r-futile.options=1.0.0 r-git2r=0.15.0 r-
highr=0.6 r-htmltools=0.3.5 r-htmlwidgets=0.6 r-httr=1.2.0 r-iterators=1.0.8
r-jsonlite=0.9.22 r-kernsmooth=2.23_15 r-knitr=1.13 r-lambda.r=1.1.7 r-
lattice=0.20_33 r-lazyeval=0.2.0 r-lme4=1.1_12 r-magrittr=1.5 r-markdown=0.7
.7 r-mass=7.3_45 r-matrix=1.2_6 r-memoise=1.0.0 r-mgcv=1.8_12 r-mime=0.4 r-
minqa=1.2.4 r-nlme=3.1_128 r-nloptr=1.0.4 r-nnet=7.3_12 r-openssl=0.9.4 r-
plyr=1.8.4 r-png=0.1_7 r-r6=2.1.2 r-rcpp=0.12.5 r-rcppeigen=0.3.2.8.1 r-
rcurl=1.95_4.8 r-recommended=3.3.1 r-reshape2=1.4.1 r-rmarkdown=0.9.6 r-
rpart=4.1_10 r-rsqlite=1.0.0 r-rstudioapi=0.5 r-snow=0.4_1 r-spatial=7.3_11
r-stringi=1.1.1 r-stringr=1.0.0 r-survival=2.39_4 r-vgam=1.0_2 r-whisker=0.3_2
r-withr=1.0.2 r-xml=3.98_1.4 r-yaml=2.1.13 readline=6.2 requests=2.11.1 rpy2
=2.8.1 rsa=3.1.4 s3transfer=0.1.9 samtools=1.3.1 scikit-learn=0.18.1 scipy=
0.18.1 seaborn=0.7.1 setuptools=27.2.0 simplejson=3.8.2 sip=4.16.9 six=1.10.
0 snakemake=3.9.0 snpeff=4.3 snpsift=4.3 sqlite=3.13.0 system=5.8 tidyp=1.04
tk=8.5.18 toolshed=0.4.6 twobitreader=3.1.4 urllib3=1.12 variant-effect-
predictor=86 vcfanno=0.1.0 vt=2015.11.10 wheel=0.29.0 wrapt=1.10.8 xz=5.2.2
yaml=0.1.6 zlib=1.2.8 python=3.5


This omits the build numbers, but otherwise specifies the same package
versions. When I run this command:

Solving environment: failed


UnsatisfiableError: The following specifications were found to be in
conflict:
- libgd=2.2.4 -> libpng[version='>=1.6.28,<1.7']
- libpng=1.6.22
Use "conda info <package>" to see the dependencies for each package.


I'm not sure how the order of the -c channel options affects package
selection -- I don't know whether conda will try lower-priority channels
when there are conflicts, or only when it simply cannot find packages with
the specified versions in a higher-priority channel.

In any case, simplifying the problem:

% conda create -n foo -c defaults -c conda-forge libgd=2.2.4 libpng=1.6.22
Solving environment: failed


UnsatisfiableError: The following specifications were found to be in
conflict:
- libgd=2.2.4 -> libpng[version='>=1.6.28,<1.7']
- libpng=1.6.22
Use "conda info <package>" to see the dependencies for each package.


When I remove the version pinning from libgd and libpng in the (big) conda
create command above, I'm able to successfully create an environment.

I don't know if that helps, but maybe it's at least a clue.

FWIW, I get the best results from conda by not over-specifying my
environment: I try to specify only those packages that supply modules
directly named in Python import statements, or that provide executable
programs that I need to call directly in my environment. I suspect that
most of the packages in your big list are dependencies of the (handful of?)
packages you actually want to directly use. I leave it to conda to provide
all the dependency packages, and rely on the package maintainers to specify
dependency chains correctly. Every now and then there's a problem with
dependency definitions, but it's rare, and usually fixed quickly --
especially for the conda-forge packages.

[c***@gmail.com]

Paul,

Thank you for creating the command, I can only hope you have a script that
assisted in creating it.

It is more than a handful, but you are correct about many of the tools not
being used directly. The pipeline that employs these tools is long and
finicky so when you finally get it to work, you don't want to touch
anything. ....but curiosity got the better of me...

Let me see if I can get this working, I'll post again if I need anything
clarified. Thank you again Paul.

C

Post by c***@gmail.com
Greetings.
I preformed a fresh install on conda. In order to do so, I deleted the
conda & .conda directory as well as .condarc. I downloaded
Miniconda3-latest-Linux-x86_64.sh and installed it with the following
command.
bash Miniconda3-latest-Linux-x86_64.sh $HOME
Specs on the Linux environment are below
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.4.1708 (Core)
Release: 7.4.1708
Codename: Core
Linux l-0-01 3.10.0-514.2.2.el7.x86_64 #1 SMP Tue Dec 6 23:06:41 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux
conda -V
conda4.5.5
I tried to create an environment with the aid of the attached file
/home/myDirectoryName/miniconda/bin/conda create --name py35 --file
python3_requirements.txt python=3.5
And I received a message stating that an error had occurred and the
following report is created.
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/exceptions.py"
, line 819, in __call__
return func(*args, **kwargs)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/main.py"
, line 78, in _main
exit_code = do_call(args, p)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/conda_argparse.py"
, line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/main_create.py"
, line 11, in execute
install(args, parser, 'create')
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/install.py"
, line 184, in install
explicit(specs, prefix, verbose=not context.quiet, index_args=
index_args)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/misc.py"
, line 78, in explicit
assert not any(spec_pcrec[1] is None for spec_pcrec in
specs_pcrecs)
AssertionError
`$ /home/myDirectoryName/miniconda/bin/conda create --name py35 --file
python3_requirements.txt python=3.5`
CIO_TEST=<not set>
CONDA_ROOT=/home/myDirectoryName/miniconda
CPATH=/cm/shared/apps/uge/8.5.3/include
LD_LIBRARY_PATH=/cm/shared/apps/uge/8.5.3/lib/lx-amd64
MANPATH=/cm/shared/apps/uge/8.5.3/man:/usr/local/share/
man:/usr/share/man/over
rides:/usr/share/man:/cm/local/apps/environment-
modules/current/share/man
/cm/shared/modulefiles_ch
op
PATH=/home/myDirectoryName/miniconda/bin:/home/
myDirectoryName/miniconda/bin:/home/myDirectoryName/miniconda/bin:/cm/
shared/apps/uge/8.5.3/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin
/opt/dell/srvadmin/bin:/home/myDirectoryName/.local/bin:/home/
myDirectoryName/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : None
user config file : /home/myDirectoryName/.condarc
conda version : 4.5.4
conda-build version : not installed
python version : 3.6.5.final.0
base environment : /home/myDirectoryName/miniconda (writable)
channel URLs : 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
package cache : /home/myDirectoryName/miniconda/pkgs
/home/myDirectoryName/.conda/pkgs
envs directories : /home/myDirectoryName/miniconda/envs
linux-64
user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/
3.10.0-514.2.2.el7.x86_64 centos/7 glibc/2.17
UID:GID : 988541:85000002
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
There is no .condarc file created and I am not certain what the error
actually is. I do know that I do not have any permission rights outside of
my directory. Any assistance is deeply appreciated.
C

[c***@gmail.com]

(Thumbs Way UP) Thank you Paul, it worked.

Post by c***@gmail.com
Paul,
Thank you for creating the command, I can only hope you have a script that
assisted in creating it.
It is more than a handful, but you are correct about many of the tools not
being used directly. The pipeline that employs these tools is long and
finicky so when you finally get it to work, you don't want to touch
anything. ....but curiosity got the better of me...
Let me see if I can get this working, I'll post again if I need anything
clarified. Thank you again Paul.
C

Post by c***@gmail.com
Greetings.
I preformed a fresh install on conda. In order to do so, I deleted the
conda & .conda directory as well as .condarc. I downloaded
Miniconda3-latest-Linux-x86_64.sh and installed it with the following
command.
bash Miniconda3-latest-Linux-x86_64.sh $HOME
Specs on the Linux environment are below
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.4.1708 (Core)
Release: 7.4.1708
Codename: Core
Linux l-0-01 3.10.0-514.2.2.el7.x86_64 #1 SMP Tue Dec 6 23:06:41 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux
conda -V
conda4.5.5
I tried to create an environment with the aid of the attached file
/home/myDirectoryName/miniconda/bin/conda create --name py35 --file
python3_requirements.txt python=3.5
And I received a message stating that an error had occurred and the
following report is created.
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/exceptions.py"
, line 819, in __call__
return func(*args, **kwargs)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/main.py"
, line 78, in _main
exit_code = do_call(args, p)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/conda_argparse.py"
, line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/main_create.py"
, line 11, in execute
install(args, parser, 'create')
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/cli/install.py"
, line 184, in install
explicit(specs, prefix, verbose=not context.quiet, index_args=
index_args)
File
"/home/myDirectoryName/miniconda/lib/python3.6/site-packages/conda/misc.py"
, line 78, in explicit
assert not any(spec_pcrec[1] is None for spec_pcrec in specs_pcrecs)
AssertionError
`$ /home/myDirectoryName/miniconda/bin/conda create --name py35 --file
python3_requirements.txt python=3.5`
CIO_TEST=<not set>
CONDA_ROOT=/home/myDirectoryName/miniconda
CPATH=/cm/shared/apps/uge/8.5.3/include
LD_LIBRARY_PATH=/cm/shared/apps/uge/8.5.3/lib/lx-amd64
MANPATH=/cm/shared/apps/uge/8.5.3/man:/usr/local/share/
man:/usr/share/man/over
rides:/usr/share/man:/cm/local/apps/environment
-
modules/current/share/man
/cm/shared/modulefiles_ch
op
PATH=/home/myDirectoryName/miniconda/bin:/home/
myDirectoryName/miniconda/bin:/home/myDirectoryName/miniconda/bin:/cm/
shared/apps/uge/8.5.3/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/
sbin:/usr/sbin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/
bin:/opt/dell/srvadmin/bin:/home/myDirectoryName/.local/bin:/home/
myDirectoryName/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : None
user config file : /home/myDirectoryName/.condarc
conda version : 4.5.4
conda-build version : not installed
python version : 3.6.5.final.0
base environment : /home/myDirectoryName/miniconda (writable)
channel URLs : 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
package cache : /home/myDirectoryName/miniconda/pkgs
/home/myDirectoryName/.conda/pkgs
envs directories : /home/myDirectoryName/miniconda/envs
linux-64
user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux
/3.10.0-514.2.2.el7.x86_64 centos/7 glibc/2.17
UID:GID : 988541:85000002
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
There is no .condarc file created and I am not certain what the error
actually is. I do know that I do not have any permission rights outside of
my directory. Any assistance is deeply appreciated.
C

[Paul Madden]

I'm happy to hear it.

The way conda was failing for you seems possibly not correct, and it might
be worth opening a ticket with the developers
(https://github.com/conda/conda) if you have time to do so. It might be
worth paring down your python3_requirements.txt file to just those two
conflicting packages to see if "conda create" fails in the same way. If it
does, you'd have a nice minimal reproducer for a bug report.