Failed to install SubPhaser

[Galaxy-228]

Hi~
When i type 'conda env create -f SubPhaser.yaml', an error showed:

Do u known how to solve this?
Best wishes.

[zhangrengang]

@Galaxy-228 Please try to install packages one by one referring to #10 (comment). It is the same error.

[Galaxy-228]

Dear Dr Zhang,
Thanks for replying, after installed packages one by one, when i type 'python setup.py install', another error showed：

I have check my python version is '3.8.8'.
Thanks so much.

[zhangrengang]

@Galaxy-228 It is strange. Can you execute the following commands and share me the yaml file? I will make a comparison.

conda activate SubPhaser
conda env export > SubPhaser2.yaml

[zhangrengang]

@Galaxy-228 Alternatively, you can comment the line python_requires='>=3.6:', in setup.py and retry. It should work. However, I appreciate you if you can share me your yaml file for debug purpose.

[Galaxy-228]

Dear Dr Zhang,
Thanks so much for your kindly reply, after execute 'conda env export > SubPhaser2.yaml', the content of SubPhaser2.yaml followed:
(SubPhaser) ug0981@gs100:~/liujie/workspace/SubPhaser$ cat SubPhaser2.yaml
name: SubPhaser
channels:

• conda-forge
• r
• bioconda
• defaults
  dependencies:
• _libgcc_mutex=0.1=conda_forge
• _openmp_mutex=4.5=2_gnu
• _r-mutex=1.0.1=anacondar_1
• appdirs=1.4.4=pyh9f0ad1d_0
• binpacking=1.5.0=pyh6c4a22f_0
• binutils_impl_linux-64=2.39=he00db2b_1
• binutils_linux-64=2.39=h5fc0e48_11
• bioconductor-ggtree=2.4.1=r40hdfd78af_0
• bioconductor-treeio=1.14.3=r40hdfd78af_0
• biopython=1.80=py38h0a891b7_0
• blast=2.5.0=hc0b0e79_3
• boost=1.77.0=py38h2b96118_0
• boost-cpp=1.77.0=h312852a_0
• brotli=1.0.9=h166bdaf_8
• brotli-bin=1.0.9=h166bdaf_8
• brotlipy=0.7.0=py38h0a891b7_1005
• bwidget=1.9.14=ha770c72_1
• bzip2=1.0.8=h7f98852_4
• c-ares=1.18.1=h7f98852_0
• ca-certificates=2022.12.7=ha878542_0
• cairo=1.16.0=h6cf1ce9_1008
• certifi=2022.12.7=pyhd8ed1ab_0
• cffi=1.14.6=py38ha65f79e_0
• charset-normalizer=2.1.1=pyhd8ed1ab_0
• circos=0.69.2=0
• contourpy=1.0.7=py38hfbd4bf9_0
• cryptography=39.0.0=py38h1724139_0
• cssselect2=0.2.1=pyh9f0ad1d_1
• curl=7.76.1=h979ede3_1
• cycler=0.11.0=pyhd8ed1ab_0
• dbus=1.13.6=h48d8840_2
• dill=0.3.6=pyhd8ed1ab_1
• drmaa=0.7.9=py_1000
• expat=2.5.0=h27087fc_0
• fasttree=2.1.11=hec16e2b_1
• fisher=0.1.9=py38hb5d20a5_2
• font-ttf-dejavu-sans-mono=2.37=hab24e00_0
• font-ttf-inconsolata=3.000=h77eed37_0
• font-ttf-source-code-pro=2.038=h77eed37_0
• font-ttf-ubuntu=0.83=hab24e00_0
• fontconfig=2.14.2=h14ed4e7_0
• fonts-conda-ecosystem=1=0
• fonts-conda-forge=1=0
• fonttools=4.38.0=py38h0a891b7_1
• freetype=2.12.1=hca18f0e_1
• fribidi=1.0.10=h36c2ea0_0
• future=0.18.3=pyhd8ed1ab_0
• gcc_impl_linux-64=9.5.0=h99780fb_19
• gcc_linux-64=9.5.0=h4258300_11
• genometools-genometools=1.6.1=py38h23571c4_2
• gettext=0.21.1=h27087fc_0
• gfortran_impl_linux-64=9.5.0=hf1096a2_19
• gfortran_linux-64=9.5.0=hdb51d14_11
• giflib=5.2.1=h36c2ea0_2
• glib=2.68.4=h9c3ff4c_0
• glib-tools=2.68.4=h9c3ff4c_0
• graphite2=1.3.13=h58526e2_1001
• gsl=2.6=he838d99_2
• gst-plugins-base=1.18.4=h29181c9_0
• gstreamer=1.18.5=h76c114f_0
• gxx_impl_linux-64=9.5.0=h99780fb_19
• gxx_linux-64=9.5.0=h43f449f_11
• harfbuzz=2.9.1=h83ec7ef_1
• hmmer=3.3.2=h87f3376_2
• icu=68.2=h9c3ff4c_0
• idna=3.4=pyhd8ed1ab_0
• importlib-resources=5.10.2=pyhd8ed1ab_0
• importlib_resources=5.10.2=pyhd8ed1ab_0
• iqtree=1.6.12=he513fc3_1
• isa-l=2.30.0=ha770c72_4
• jellyfish=0.9.0=py38h0a891b7_2
• joblib=1.2.0=pyhd8ed1ab_0
• jpeg=9e=h0b41bf4_3
• k8=0.2.5=hd03093a_2
• kernel-headers_linux-64=2.6.32=he073ed8_15
• kiwisolver=1.4.4=py38h43d8883_1
• krb5=1.17.2=h926e7f8_0
• ld_impl_linux-64=2.39=hcc3a1bd_1
• lerc=4.0.0=h27087fc_0
• libblas=3.9.0=16_linux64_openblas
• libbrotlicommon=1.0.9=h166bdaf_8
• libbrotlidec=1.0.9=h166bdaf_8
• libbrotlienc=1.0.9=h166bdaf_8
• libcblas=3.9.0=16_linux64_openblas
• libclang=11.1.0=default_ha53f305_1
• libcurl=7.76.1=hc4aaa36_1
• libdeflate=1.14=h166bdaf_0
• libedit=3.1.20191231=he28a2e2_2
• libev=4.33=h516909a_1
• libevent=2.1.10=h9b69904_4
• libffi=3.3=h58526e2_2
• libgcc-devel_linux-64=9.5.0=h0a57e50_19
• libgcc-ng=12.2.0=h65d4601_19
• libgd=2.2.5=h8e06009_4
• libgfortran-ng=12.2.0=h69a702a_19
• libgfortran5=12.2.0=h337968e_19
• libglib=2.68.4=h3e27bee_0
• libgomp=12.2.0=h65d4601_19
• libiconv=1.17=h166bdaf_0
• liblapack=3.9.0=16_linux64_openblas
• libllvm11=11.1.0=he0ac6c6_5
• libnghttp2=1.51.0=hdcd2b5c_0
• libnsl=2.0.0=h7f98852_0
• libopenblas=0.3.21=pthreads_h78a6416_3
• libpng=1.6.39=h753d276_0
• libpq=13.2=hfd2b0eb_2
• libsanitizer=9.5.0=h2f262e1_19
• libsqlite=3.40.0=h753d276_0
• libssh2=1.10.0=haa6b8db_3
• libstdcxx-devel_linux-64=9.5.0=h0a57e50_19
• libstdcxx-ng=12.2.0=h46fd767_19
• libtiff=4.1.0=hecacb30_2
• libuuid=2.32.1=h7f98852_1000
• libwebp=1.0.2=h56121f0_5
• libxcb=1.13=h7f98852_1004
• libxkbcommon=1.0.3=he3ba5ed_0
• libxml2=2.9.12=h72842e0_0
• libxslt=1.1.33=h15afd5d_2
• libzlib=1.2.13=h166bdaf_4
• ltr_finder=1.07=h9f5acd7_2
• lxml=4.8.0=py38h0a891b7_2
• mafft=7.515=hec16e2b_0
• make=4.3=hd18ef5c_1
• matplotlib=3.7.0=py38h578d9bd_0
• matplotlib-base=3.7.0=py38hd6c3c57_0
• minimap2=2.24=h7132678_1
• multiprocess=0.70.14=py38h0a891b7_3
• munkres=1.1.4=pyh9f0ad1d_0
• mysql-common=8.0.32=h14678bc_0
• mysql-libs=8.0.32=h54cf53e_0
• ncurses=6.3=h27087fc_1
• newick_utils=1.6=hec16e2b_5
• nspr=4.35=h27087fc_0
• nss=3.88=he45b914_0
• numpy=1.24.2=py38h10c12cc_0
• olefile=0.46=pyh9f0ad1d_1
• openssl=1.1.1t=h0b41bf4_0
• packaging=23.0=pyhd8ed1ab_0
• pandas=1.5.3=py38hdc8b05c_0
• pango=1.42.4=h69149e4_5
• patsy=0.5.3=pyhd8ed1ab_0
• pbzip2=1.1.13=0
• pcre=8.45=h9c3ff4c_0
• pcre2=10.36=h032f7d1_1
• perl=5.26.2=h36c2ea0_1008
• perl-autoloader=5.74=pl526_2
• perl-carp=1.38=pl526_3
• perl-clone=0.42=pl526h516909a_0
• perl-config-general=2.63=pl526_0
• perl-digest-perl-md5=1.9=pl526_1
• perl-dynaloader=1.25=pl526_1
• perl-exporter=5.72=pl526_1
• perl-extutils-makemaker=7.36=pl526_1
• perl-font-ttf=1.06=pl526_0
• perl-gd=2.71=pl526he860b03_0
• perl-io-string=1.08=pl526_3
• perl-list-moreutils=0.15=pl526_1
• perl-math-bezier=0.01=pl526_1
• perl-math-round=0.07=pl526_1
• perl-math-vecstat=0.08=pl526_1
• perl-module-implementation=0.09=pl526_2
• perl-module-runtime=0.016=pl526_1
• perl-number-format=1.75=pl526_3
• perl-params-validate=1.29=pl526h14c3975_1
• perl-pathtools=3.75=pl526h14c3975_1
• perl-readonly=2.05=pl526_0
• perl-regexp-common=2017060201=pl526_0
• perl-scalar-list-utils=1.52=pl526h516909a_0
• perl-set-intspan=1.19=pl526_1
• perl-statistics-basic=1.6611=pl526_2
• perl-svg=2.84=pl526_0
• perl-text-format=0.59=pl526_2
• perl-threaded=5.32.1=hdfd78af_1
• perl-time-hires=1.9760=pl526h14c3975_1
• perl-try-tiny=0.30=pl526_1
• perl-xml-parser=2.44_01=pl5262hc3e0081_1002
• perl-xsloader=0.24=pl526_0
• pigz=2.6=h27826a3_0
• pillow=7.2.0=py38h9776b28_0
• pip=23.0=pyhd8ed1ab_0
• pixman=0.40.0=h36c2ea0_0
• pooch=1.6.0=pyhd8ed1ab_0
• pp=1.6.4.4=py_0
• psutil=5.9.4=py38h0a891b7_0
• pthread-stubs=0.4=h36c2ea0_1001
• pycparser=2.21=pyhd8ed1ab_0
• pyopenssl=23.0.0=pyhd8ed1ab_0
• pyparsing=3.0.9=pyhd8ed1ab_0
• pyqt=5.12.3=py38ha8c2ead_4
• pysocks=1.7.1=pyha2e5f31_6
• python=3.8.8=hffdb5ce_0_cpython
• python-dateutil=2.8.2=pyhd8ed1ab_0
• python-isal=1.1.0=py38h0a891b7_1
• python_abi=3.8=3_cp38
• pytz=2022.7.1=pyhd8ed1ab_0
• qt=5.12.9=hda022c4_4
• r-ape=5.6_2=r40h43535f1_0
• r-aplot=0.1.7=r40hc72bb7e_0
• r-backports=1.4.1=r40hcfec24a_0
• r-base=4.0.3=hd23ff56_6
• r-biocmanager=1.30.18=r40hc72bb7e_0
• r-bitops=1.0_7=r40h06615bd_0
• r-brio=1.1.3=r40hcfec24a_0
• r-callr=3.7.2=r40hc72bb7e_0
• r-catools=1.18.2=r40h7525677_0
• r-cli=3.4.1=r40h7525677_0
• r-colorspace=2.0_3=r40h06615bd_0
• r-crayon=1.5.1=r40hc72bb7e_0
• r-desc=1.4.2=r40hc72bb7e_0
• r-diffobj=0.3.5=r40hcfec24a_0
• r-digest=0.6.29=r40h03ef668_0
• r-dplyr=1.0.5=r40h03ef668_0
• r-ellipsis=0.3.2=r40hcfec24a_0
• r-evaluate=0.16=r40hc72bb7e_0
• r-fansi=1.0.3=r40h06615bd_0
• r-farver=2.1.1=r40h7525677_0
• r-fs=1.5.2=r40h7525677_1
• r-generics=0.1.3=r40hc72bb7e_0
• r-ggfun=0.0.7=r40hc72bb7e_0
• r-ggplot2=3.3.6=r40hc72bb7e_0
• r-ggplotify=0.1.0=r40hc72bb7e_0
• r-glue=1.6.2=r40h06615bd_0
• r-gplots=3.1.1=r40hc72bb7e_0
• r-gridgraphics=0.5_1=r40hc72bb7e_0
• r-gtable=0.3.1=r40hc72bb7e_0
• r-gtools=3.9.3=r40h06615bd_0
• r-isoband=0.2.5=r40h03ef668_0
• r-jsonlite=1.8.0=r40h06615bd_0
• r-kernsmooth=2.23_20=r40h742201e_0
• r-labeling=0.4.2=r40hc72bb7e_1
• r-lattice=0.20_45=r40hcfec24a_0
• r-lazyeval=0.2.2=r40hcfec24a_2
• r-lifecycle=1.0.2=r40hc72bb7e_0
• r-magrittr=2.0.3=r40h06615bd_0
• r-mass=7.3_58.1=r40h06615bd_0
• r-matrix=1.4_1=r40h0154571_0
• r-mgcv=1.8_40=r40h0154571_0
• r-munsell=0.5.0=r40hc72bb7e_1004
• r-nlme=3.1_159=r40h8da6f51_0
• r-patchwork=1.1.2=r40hc72bb7e_0
• r-pillar=1.8.1=r40hc72bb7e_0
• r-pkgconfig=2.0.3=r40hc72bb7e_1
• r-pkgload=1.3.0=r40hc72bb7e_0
• r-praise=1.0.0=r40hc72bb7e_1005
• r-processx=3.7.0=r40h06615bd_0
• r-ps=1.7.1=r40h06615bd_0
• r-purrr=0.3.4=r40hcfec24a_1
• r-r6=2.5.1=r40hc72bb7e_0
• r-rcolorbrewer=1.1_3=r40h785f33e_0
• r-rcpp=1.0.9=r40h7525677_1
• r-rematch2=2.1.2=r40hc72bb7e_1
• r-rlang=1.0.6=r40h7525677_0
• r-rprojroot=2.0.3=r40hc72bb7e_0
• r-rvcheck=0.2.1=r40hc72bb7e_0
• r-scales=1.2.1=r40hc72bb7e_0
• r-testthat=3.1.4=r40h7525677_0
• r-tibble=3.1.8=r40h06615bd_0
• r-tidyr=1.2.1=r40h7525677_0
• r-tidyselect=1.1.2=r40hc72bb7e_0
• r-tidytree=0.4.1=r40hc72bb7e_0
• r-utf8=1.2.2=r40hcfec24a_0
• r-vctrs=0.4.1=r40h7525677_0
• r-viridislite=0.4.1=r40hc72bb7e_0
• r-waldo=0.4.0=r40hc72bb7e_0
• r-withr=2.5.0=r40hc72bb7e_0
• r-yulab.utils=0.0.5=r40hc72bb7e_0
• readline=8.1.2=h0f457ee_0
• reportlab=3.5.68=py38hadf75a6_1
• requests=2.28.2=pyhd8ed1ab_0
• scikit-learn=1.2.1=py38h1e1a916_0
• scipy=1.10.0=py38h10c12cc_2
• sed=4.8=he412f7d_0
• setuptools=67.3.2=pyhd8ed1ab_0
• six=1.16.0=pyh6c4a22f_0
• sqlite=3.40.0=h4ff8645_0
• statsmodels=0.13.5=py38h26c90d9_2
• svglib=1.5.1=pyhd8ed1ab_0
• sysroot_linux-64=2.12=he073ed8_15
• tesorter=1.3.0=py_0
• threadpoolctl=3.1.0=pyh8a188c0_0
• tinycss2=1.2.1=pyhd8ed1ab_0
• tk=8.6.12=h27826a3_0
• tktable=2.10=hb7b940f_3
• tornado=6.2=py38h0a891b7_1
• trimal=1.4.1=h9f5acd7_6
• unicodedata2=15.0.0=py38h0a891b7_0
• unimap=0.1=h7132678_2
• urllib3=1.26.14=pyhd8ed1ab_0
• webencodings=0.5.1=py_1
• wheel=0.38.4=pyhd8ed1ab_0
• xopen=1.1.0=py38h578d9bd_3
• xorg-kbproto=1.0.7=h7f98852_1002
• xorg-libice=1.0.10=h7f98852_0
• xorg-libsm=1.2.3=hd9c2040_1000
• xorg-libx11=1.7.2=h7f98852_0
• xorg-libxau=1.0.9=h7f98852_0
• xorg-libxdmcp=1.1.3=h7f98852_0
• xorg-libxext=1.3.4=h7f98852_1
• xorg-libxrender=0.9.10=h7f98852_1003
• xorg-libxt=1.2.1=h7f98852_2
• xorg-renderproto=0.11.1=h7f98852_1002
• xorg-xextproto=7.3.0=h7f98852_1002
• xorg-xproto=7.0.31=h7f98852_1007
• xz=5.2.6=h166bdaf_0
• zipp=3.13.0=pyhd8ed1ab_0
• zlib=1.2.13=h166bdaf_4
• zstandard=0.19.0=py38h5945529_1
• zstd=1.5.2=h3eb15da_6
• pip:
  • colorama==0.4.6
  • halo==0.0.31
  • log-symbols==0.0.14
  • pyqt5-sip==4.19.18
  • pyqtchart==5.12
  • pyqtwebengine==5.12.1
  • spinners==0.0.24
  • termcolor==2.2.0
    prefix: /home/ug0981/.conda/envs/SubPhaser

[Galaxy-228]

Dear Dr Zhang,
after comment the line 'python_requires='>=3.6:', i have secceed installed SubPhaser, however, when i type 'subphaser -h', a warning message showed:

Will it matter?
thanks again.

[zhangrengang]

@Galaxy-228 It can be ignored.

[mynoleon]

Dear Dr Zhang,
l have installed packages one by one, but when i type 'python setup.py install ,the error showed:
ModuleNotFoundError: No moddle named 'sysconfigdata_x86 64_conda_linux_gnu'
I would be especially happy if you could tell me how to fix it.

[zhangrengang]

I may have fixed the bugs in installing the envirionment via conda, by removing the build versions in SubPhaser.yaml. If anyone have not installed successfully with issues of conda, you can try the updated version.