Install trouble: Write permissions?

[eacattle]

Hi there, thanks for your patience in advance, I'm a novice just trying to do my Master's thesis. I haven't been able to find out how to fix the install error I keep getting:

echo PEWO installer: Cannot create environment. Write permissions ?

It makes sense to me that write permissions need to be enabled in order for the installer to finish, but I'm having trouble figuring out where the write permission needs to be enabled. I tried downloading and installing PEWO from a folder I have full permissions for and got the same result.
I'm just running it from a Mac terminal with miniconda 3. Any advice would be much appreciated, I don't have anyone in my lab that will help me and I'm hoping to use PEWO for my main project.

[nromashchenko]

Hello,

Can you please provide the full error log and the exact versions of python and conda?

[eacattle]

Hi, thanks for your patience. I'm on python 3.11.4 and conda 23.5.2. Here is the full text of the error:

Solving environment: failed

ResolvePackageNotFound: 
  - biopython==1.76=py36h516909a_0
  - protobuf==3.8.0=py36he1b5a44_2
  - ant==1.10.0=0
  - libgcc-ng==9.2.0=h24d8f2e_2
  - libtool==2.4.6=h14c3975_1002
  - lz4-c==1.8.3=he1b5a44_1001
  - ld_impl_linux-64==2.33.1=h53a641e_8
  - r-plyr==1.8.5=r36h0357c0b_0
  - make==4.2.1=h14c3975_2004
  - xorg-inputproto==2.3.2=h14c3975_1002
  - r-utf8==1.1.4=r36hcdcec82_1001
  - xorg-libxrender==0.9.10=h516909a_1002
  - r-ellipsis==0.3.0=r36hcdcec82_0
  - _openmp_mutex==4.5=0_gnu
  - gobject-introspection==1.58.2=py36h5503ade_1002
  - xorg-xextproto==7.3.0=h14c3975_1002
  - bzip2==1.0.8=h516909a_2
  - hmmer==3.3=he1b5a44_0
  - libstdcxx-ng==9.2.0=hdf63c60_2
  - aiohttp==3.6.2=py36h516909a_0
  - r-rcpp==1.0.3=r36h0357c0b_0
  - graphviz==2.42.3=h0511662_0
  - r-base==3.6.1=h3a67422_6
  - graphite2==1.3.13=hf484d3e_1000
  - yaml==0.2.2=h516909a_1
  - gcc_impl_linux-64==7.3.0=hd420e75_5
  - psutil==5.6.7=py36h516909a_0
  - cairo==1.16.0=hfb77d84_1002
  - openssl==1.1.1d=h516909a_0
  - sed==4.7=h1bed415_1000
  - r-farver==2.0.3=r36h0357c0b_0
  - paml==4.9=h516909a_5
  - tk==8.6.10=hed695b0_0
  - libxml2==2.9.10=hee79883_0
  - pixman==0.38.0=h516909a_1003
  - r-nlme==3.1_144=r36h9bbef5b_0
  - wrapt==1.12.0=py36h516909a_0
  - lcms2==2.9=hbd6801e_1
  - zstd==1.4.4=h3b9ef0a_1
  - alsa-lib==1.1.5=h516909a_1002
  - fribidi==1.0.5=h516909a_1002
  - r-glue==1.3.1=r36hcdcec82_1
  - r-mgcv==1.8_31=r36hcdcec82_0
  - gxx_impl_linux-64==7.3.0=hdf63c60_5
  - xorg-libxt==1.1.5=h516909a_1003
  - cryptography==2.8=py36h72c5cf5_1
  - freetype==2.10.0=he983fc9_1
  - libtiff==4.1.0=hc3755c2_3
  - pthread-stubs==0.4=h14c3975_1001
  - r-cairo==1.5_10=r36hcdcec82_1
  - raxml-ng==0.9.0=h192cbe9_1
  - gettext==0.19.8.1=hc5be6a0_1002
  - r-matrix==1.2_18=r36hcdcec82_1
  - xorg-libxdmcp==1.1.3=h516909a_0
  - cffi==1.13.2=py36h8022711_0
  - libiconv==1.15=h516909a_1005
  - _libgcc_mutex==0.1=conda_forge
  - binutils_linux-64==2.33.1=h9595d00_16
  - libffi==3.2.1=he1b5a44_1006
  - expat==2.2.9=he1b5a44_2
  - xorg-libxpm==3.5.13=h516909a_0
  - fontconfig==2.13.1=h86ecdb6_1001
  - icu==64.2=he1b5a44_1
  - gcc_linux-64==7.3.0=h553295d_16
  - glib==2.58.3=py36h6f030ca_1002
  - openjpeg==2.3.1=h981e76c_3
  - gxx_linux-64==7.3.0=h553295d_16
  - tktable==2.10=h555a92e_3
  - jpeg==9c=h14c3975_1001
  - r-colorspace==1.4_1=r36hcdcec82_1
  - libcurl==7.68.0=hda55be3_0
  - gsl==2.5=h294904e_1
  - xorg-libxi==1.7.10=h516909a_0
  - ghostscript==9.22=hf484d3e_1001
  - yarl==1.3.0=py36h516909a_1000
  - r-lazyeval==0.2.2=r36hcdcec82_1
  - gfortran_linux-64==7.3.0=h553295d_16
  - openjdk==11.0.1=h600c080_1018
  - sqlalchemy==1.3.13=py36h516909a_0
  - multidict==4.7.4=py36h516909a_0
  - pyrsistent==0.15.7=py36h516909a_0
  - zlib==1.2.11=h516909a_1006
  - libedit==3.1.20170329=hf8c457e_1001
  - imagemagick==7.0.9_24=pl526ha9fe49d_0
  - numpy==1.18.1=py36h95a1406_0
  - libgfortran-ng==7.3.0=hdf63c60_5
  - libxcb==1.13=h14c3975_1002
  - libgomp==9.2.0=h24d8f2e_2
  - fftw==3.3.8=nompi_h7f3a6c3_1110
  - libssh2==1.8.2=h22169c7_2
  - curl==7.68.0=hf8cf82a_0
  - readline==8.0=hf8c457e_0
  - jbig==2.1=h14c3975_2001
  - r-fansi==0.4.1=r36hcdcec82_0
  - xorg-libxfixes==5.0.3=h516909a_1004
  - pkg-config==0.29.2=h516909a_1006
  - gdk-pixbuf==2.38.2=h3f25603_0
  - r-tibble==2.1.3=r36hcdcec82_1
  - xorg-libxau==1.0.9=h14c3975_0
  - datrie==0.8=py36h516909a_0
  - sqlite==3.30.1=hcee41ef_0
  - python==3.6.7=h357f687_1006
  - r-backports==1.1.5=r36hcdcec82_0
  - libopenblas==0.3.7=h5ec1e0e_6
  - xz==5.2.4=h14c3975_1001
  - xorg-kbproto==1.0.7=h14c3975_1002
  - r-rlang==0.4.4=r36hcdcec82_0
  - xorg-xproto==7.0.31=h14c3975_1007
  - binutils_impl_linux-64==2.33.1=h53a641e_8
  - libcroco==0.6.13=h8d621e5_0
  - r-reshape2==1.4.3=r36h0357c0b_1004
  - raxml==8.2.12=h14c3975_1
  - r-digest==0.6.24=r36h0357c0b_0
  - xorg-libxext==1.3.4=h516909a_0
  - xorg-fixesproto==5.0=h14c3975_1002
  - openmpi==4.0.2=hb1b8bf9_1
  - r-mass==7.3_51.5=r36hcdcec82_0
  - markupsafe==1.1.1=py36h516909a_0
  - pango==1.42.4=ha030887_1
  - libprotobuf==3.8.0=h8b12597_0
  - libwebp==1.0.2=h56121f0_5
  - pcre==8.44=he1b5a44_0
  - gmp==6.2.0=he1b5a44_1
  - librsvg==2.46.4=h33a7fed_0
  - pandas==1.0.1=py36hb3f55d8_0
  - pynacl==1.3.0=py36h516909a_1001
  - xorg-recordproto==1.14.2=h516909a_1002
  - xorg-libx11==1.6.9=h516909a_0
  - r-lattice==0.20_38=r36hcdcec82_1002
  - giflib==5.2.1=h516909a_1
  - gfortran_impl_linux-64==7.3.0=hdf63c60_5
  - bcrypt==3.1.7=py36h516909a_0
  - ncurses==6.1=hf484d3e_1002
  - xorg-libsm==1.2.3=h84519dc_1000
  - phyml==3.3.20190909=h516909a_0
  - r-stringi==1.4.6=r36h0e574ca_0
  - r-vctrs==0.2.2=r36hcdcec82_0
  - xorg-libice==1.0.10=h516909a_0
  - xorg-renderproto==0.11.1=h14c3975_1002
  - libuuid==2.32.1=h14c3975_1000
  - r-data.table==1.12.8=r36hcdcec82_0
  - krb5==1.16.4=h2fd8d38_0
  - perl==5.26.2=h516909a_1006
  - harfbuzz==2.4.0=h9f30f68_3
  - xorg-libxtst==1.2.3=h516909a_1002
  - libpng==1.6.37=hed695b0_0
  - pyyaml==5.3=py36h516909a_0

echo PEWO installer: Cannot create environment. Write permissions ?

[blinard-BIOINFO]

Hi. The last line indicates that the conda environment cannot be created. This command fails:
conda env create --file envs/environment.yaml

The message is misleading. You use Python 3.11 which is very old... if you read carefully requirements on our main repository page, you will see that you need Python >=3.5.

Please update your python setup or manually associate your conda installation to a more recent python version. Then, delete all pewo directories and try again installation from scratch.

[eacattle]

Ahh, thank you very very much. I will do that and report back! :) That's very helpful.

[nromashchenko]

@blinard-BIOINFO I don't think it's that. First you probably confused 3.11 and 3.1.1; 3.11 is actually quite new. But that's actually not even relevant as in our envs/environment.yml we specify every version of dependencies including python, which has to be 3.6.7. So conda env create should be able to work with the version PEWO needs. Let me look into this

[nromashchenko]

@eacattle So the issue is likely is in the channel priority policy that Conda changed. We have some quite old (python 3.6) dependencies that are troublesome now.

For the moment, try this:

conda config --set channel_priority flexible

# or in the case of mamba:
# conda config set channel_priority flexible

conda env create --file envs/environment.yaml   

as a temporary measure, which should do the installation. We will update the dependencies later so that the installation works for the default strict policy, too.

Also, if you experiment with phylogenetic placement, try EPIK which is also supported by PEWO.

[eacattle]

Hmm. It looks like the same issue.

Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

• sqlalchemy==1.3.13=py36h516909a_0
• glib==2.58.3=py36h6f030ca_1002
• lcms2==2.9=hbd6801e_1
• ant==1.10.0=0
• libpng==1.6.37=hed695b0_0
• pcre==8.44=he1b5a44_0
• r-utf8==1.1.4=r36hcdcec82_1001
• fontconfig==2.13.1=h86ecdb6_1001
• libgcc-ng==9.2.0=h24d8f2e_2
• pthread-stubs==0.4=h14c3975_1001
• ghostscript==9.22=hf484d3e_1001
• r-digest==0.6.24=r36h0357c0b_0
• raxml==8.2.12=h14c3975_1
• gfortran_impl_linux-64==7.3.0=hdf63c60_5
• r-fansi==0.4.1=r36hcdcec82_0
• libedit==3.1.20170329=hf8c457e_1001
• binutils_impl_linux-64==2.33.1=h53a641e_8
• r-colorspace==1.4_1=r36hcdcec82_1
• libxcb==1.13=h14c3975_1002
• imagemagick==7.0.9_24=pl526ha9fe49d_0
• r-nlme==3.1_144=r36h9bbef5b_0
• expat==2.2.9=he1b5a44_2
• graphviz==2.42.3=h0511662_0
• gobject-introspection==1.58.2=py36h5503ade_1002
• r-lazyeval==0.2.2=r36hcdcec82_1
• jpeg==9c=h14c3975_1001
• openssl==1.1.1d=h516909a_0
• gcc_linux-64==7.3.0=h553295d_16
• r-farver==2.0.3=r36h0357c0b_0
• r-cairo==1.5_10=r36hcdcec82_1
• cffi==1.13.2=py36h8022711_0
• r-stringi==1.4.6=r36h0e574ca_0
• graphite2==1.3.13=hf484d3e_1000
• gxx_linux-64==7.3.0=h553295d_16
• libopenblas==0.3.7=h5ec1e0e_6
• openmpi==4.0.2=hb1b8bf9_1
• r-data.table==1.12.8=r36hcdcec82_0
• pyrsistent==0.15.7=py36h516909a_0
• fribidi==1.0.5=h516909a_1002
• xorg-libice==1.0.10=h516909a_0
• libcroco==0.6.13=h8d621e5_0
• tktable==2.10=h555a92e_3
• xorg-libxtst==1.2.3=h516909a_1002
• xorg-libsm==1.2.3=h84519dc_1000
• bzip2==1.0.8=h516909a_2
• libcurl==7.68.0=hda55be3_0
• aiohttp==3.6.2=py36h516909a_0
• _libgcc_mutex==0.1=conda_forge
• gdk-pixbuf==2.38.2=h3f25603_0
• xorg-libx11==1.6.9=h516909a_0
• alsa-lib==1.1.5=h516909a_1002
• r-ellipsis==0.3.0=r36hcdcec82_0
• xorg-libxrender==0.9.10=h516909a_1002
• readline==8.0=hf8c457e_0
• xorg-libxext==1.3.4=h516909a_0
• libgomp==9.2.0=h24d8f2e_2
• gfortran_linux-64==7.3.0=h553295d_16
• r-backports==1.1.5=r36hcdcec82_0
• perl==5.26.2=h516909a_1006
• paml==4.9=h516909a_5
• datrie==0.8=py36h516909a_0
• gmp==6.2.0=he1b5a44_1
• zstd==1.4.4=h3b9ef0a_1
• yaml==0.2.2=h516909a_1
• ld_impl_linux-64==2.33.1=h53a641e_8
• gettext==0.19.8.1=hc5be6a0_1002
• gcc_impl_linux-64==7.3.0=hd420e75_5
• wrapt==1.12.0=py36h516909a_0
• r-plyr==1.8.5=r36h0357c0b_0
• phyml==3.3.20190909=h516909a_0
• libprotobuf==3.8.0=h8b12597_0
• r-matrix==1.2_18=r36hcdcec82_1
• libssh2==1.8.2=h22169c7_2
• jbig==2.1=h14c3975_2001
• python==3.6.7=h357f687_1006
• zlib==1.2.11=h516909a_1006
• giflib==5.2.1=h516909a_1
• _openmp_mutex==4.5=0_gnu
• r-tibble==2.1.3=r36hcdcec82_1
• r-mgcv==1.8_31=r36hcdcec82_0
• r-rcpp==1.0.3=r36h0357c0b_0
• xz==5.2.4=h14c3975_1001
• openjpeg==2.3.1=h981e76c_3
• pkg-config==0.29.2=h516909a_1006
• freetype==2.10.0=he983fc9_1
• gsl==2.5=h294904e_1
• xorg-libxt==1.1.5=h516909a_1003
• xorg-xextproto==7.3.0=h14c3975_1002
• xorg-libxdmcp==1.1.3=h516909a_0
• openjdk==11.0.1=h600c080_1018
• libgfortran-ng==7.3.0=hdf63c60_5
• multidict==4.7.4=py36h516909a_0
• libtiff==4.1.0=hc3755c2_3
• pynacl==1.3.0=py36h516909a_1001
• xorg-libxi==1.7.10=h516909a_0
• librsvg==2.46.4=h33a7fed_0
• bcrypt==3.1.7=py36h516909a_0
• psutil==5.6.7=py36h516909a_0
• raxml-ng==0.9.0=h192cbe9_1
• xorg-libxpm==3.5.13=h516909a_0
• pixman==0.38.0=h516909a_1003
• ncurses==6.1=hf484d3e_1002
• numpy==1.18.1=py36h95a1406_0
• make==4.2.1=h14c3975_2004
• fftw==3.3.8=nompi_h7f3a6c3_1110
• xorg-renderproto==0.11.1=h14c3975_1002
• yarl==1.3.0=py36h516909a_1000
• libiconv==1.15=h516909a_1005
• xorg-inputproto==2.3.2=h14c3975_1002
• r-base==3.6.1=h3a67422_6
• libstdcxx-ng==9.2.0=hdf63c60_2
• libuuid==2.32.1=h14c3975_1000
• pandas==1.0.1=py36hb3f55d8_0
• sed==4.7=h1bed415_1000
• binutils_linux-64==2.33.1=h9595d00_16
• gxx_impl_linux-64==7.3.0=hdf63c60_5
• r-lattice==0.20_38=r36hcdcec82_1002
• xorg-xproto==7.0.31=h14c3975_1007
• pyyaml==5.3=py36h516909a_0
• cryptography==2.8=py36h72c5cf5_1
• sqlite==3.30.1=hcee41ef_0
• biopython==1.76=py36h516909a_0
• krb5==1.16.4=h2fd8d38_0
• xorg-libxau==1.0.9=h14c3975_0
• icu==64.2=he1b5a44_1
• cairo==1.16.0=hfb77d84_1002
• libxml2==2.9.10=hee79883_0
• r-reshape2==1.4.3=r36h0357c0b_1004
• libffi==3.2.1=he1b5a44_1006
• r-glue==1.3.1=r36hcdcec82_1
• libtool==2.4.6=h14c3975_1002
• pango==1.42.4=ha030887_1
• r-mass==7.3_51.5=r36hcdcec82_0
• xorg-recordproto==1.14.2=h516909a_1002
• curl==7.68.0=hf8cf82a_0
• markupsafe==1.1.1=py36h516909a_0
• xorg-libxfixes==5.0.3=h516909a_1004
• tk==8.6.10=hed695b0_0
• xorg-kbproto==1.0.7=h14c3975_1002
• libwebp==1.0.2=h56121f0_5
• harfbuzz==2.4.0=h9f30f68_3
• protobuf==3.8.0=py36he1b5a44_2
• r-vctrs==0.2.2=r36hcdcec82_0
• lz4-c==1.8.3=he1b5a44_1001
• r-rlang==0.4.4=r36hcdcec82_0
• xorg-fixesproto==5.0=h14c3975_1002
• hmmer==3.3=he1b5a44_0

I'm not sure what the issue could be. I'll check out EPIK too, though, thanks.

[nromashchenko]

What I suggest is to run conda env create --file envs/environment.yaml manually after setting channel_priority, instead of running the installer as you did. I reproduced the issue with the installer but running manually solved it. Can you please run both commands from the previous comment?

[eacattle]

I was able to set the channel priority to flexible, but it appears running that exact suggested command yielded the same error.

[nromashchenko]

Hi @eacattle,

We're updating dependencies for a new version that will come soon. In the meantime you can update to the latest master and try running the install script again. It should work regardless of what your channel_priority is now (which can be strict or flexible).

Keep in mind that this is a dev version that is not released, and eval_resources pipeline will not work correctly (although the accuracy pipelines and examples should all work fine). We'll update it too and release a new version soon

Let me know if the issue is solved by the latest master version.