Comments (9)
@Galaxy-228 Please try to install packages one by one referring to #10 (comment). It is the same error.
from subphaser.
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.
from subphaser.
@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
from subphaser.
@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.
from subphaser.
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
from subphaser.
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.
from subphaser.
@Galaxy-228 It can be ignored.
from subphaser.
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.
from subphaser.
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.
from subphaser.
Related Issues (20)
- Error in os.link(figfile, dstfig) HOT 3
- IndexError: cannot do a non-empty take from an empty axes. HOT 10
- ModuleNotFoundError: No module named 'TEsorter' HOT 4
- The output subgenomes are not paired HOT 4
- Changing mutation rate HOT 1
- Invalid specifier: '>=3.6:' HOT 1
- Only one pair of homologous chromosomes were not phased HOT 5
- matplotlib raise RuntimeError ('Invalid DISPLAY variable') HOT 2
- Unbalanced of chromosomes number and differential kmers number among subgenomes HOT 1
- `TEsorter` cannot find `rexdb` in Singularity container HOT 3
- Singularity container fails if environmental variable `R_LIBS_USER` is set HOT 2
- No differential kmers HOT 2
- ValueError: All singletons are not allowed HOT 1
- ValueError: 0 kmer with fold > 2. Please reset the filter options. HOT 1
- cannot allocate memory HOT 13
- 亚基因组分析 HOT 2
- Getting location of subgenome specific TEs HOT 2
- Suggestion for specific settings to improve subphasing HOT 3
- kmer 13 or less gives a lot of broken pipe errors HOT 5
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