ResolvePackageNotFound - Githubissues

dmi229 commented 2 years ago

Hello,

I saw someone had posted a similar issue, but I believe I'm working off the latest version that was fixed. I still see this error, eventually I think I linked it to a PC <> Mac issue (https://stackoverflow.com/questions/55554431/conda-fails-to-create-environment-from-yml/55576493#55576493). If it matters, this is a M1 mac. Hope for a fix!

This is my error, thanks in advance!:

ResolvePackageNotFound:

r-r6==2.4.1=r35h6115d3f_0
mintmap==2.0.0a0=pypi_0
_openmp_mutex==4.5=1_gnu
kernel-headers_linux-64==2.6.32=he073ed8_15
libuuid==1.0.3=h7f8727e_2
r-tidyselect==1.0.0=r35h6115d3f_0
lz4-c==1.9.3=h9c3ff4c_1
libcblas==3.9.0=8_openblas
r-cli==2.0.2=r35h6115d3f_0
xlsxwriter==3.0.2=pypi_0
biopython==1.79=pypi_0
r-farver==2.0.3=r35h0357c0b_0
colormath==3.0.0=pypi_0
libblas==3.9.0=8_openblas
libgfortran4==7.5.0=h14aa051_19
pip==21.0.1=py37h06a4308_0
htslib==1.12=h9093b5e_1
xyzservices==2021.11.0=pypi_0
freetype==2.10.4=h0708190_1
r-purrr==0.3.4=r35hcdcec82_0
libwebp-base==1.2.0=h7f98852_2
libstdcxx-devel_linux-64==7.5.0=hb016644_19
ca-certificates==2021.10.8=ha878542_0
r-glue==1.4.0=r35hcdcec82_0
bzip2==1.0.8=h7f98852_4
r-stringi==1.4.3=r35h0357c0b_2
c-ares==1.17.1=h7f98852_1
pcre==8.45=h9c3ff4c_0
r-rlang==0.4.5=r35hcdcec82_2
tk==8.6.11=h1ccaba5_0
multiqc==1.11=pypi_0
glib-tools==2.68.3=h9c3ff4c_0
lerc==2.2.1=h9c3ff4c_0
r-fansi==0.4.1=r35hcdcec82_0
fribidi==1.0.10=h36c2ea0_0
r-dplyr==0.8.5=r35h0357c0b_0
markupsafe==2.0.1=pypi_0
libedit==3.1.20191231=he28a2e2_2
jbig==2.1=h7f98852_2003
tornado==6.1=pypi_0
r-zeallot==0.1.0=r35h6115d3f_1001
pygments==2.10.0=pypi_0
xorg-libsm==1.2.2=h470a237_5
libstdcxx-ng==9.3.0=hd4cf53a_17
xorg-xextproto==7.3.0=h7f98852_1002
isal==0.11.1=pypi_0
jpeg==9d=h36c2ea0_0
libssh2==1.9.0=ha56f1ee_6
gxx_impl_linux-64==7.3.0=hdf63c60_1
xz==5.2.5=h7b6447c_0
libev==4.33=h516909a_1
xorg-libxdmcp==1.1.3=h7f98852_0
bwidget==1.9.14=ha770c72_1
r-scales==1.1.0=r35h6115d3f_0
make==4.3=hd18ef5c_1
pthread-stubs==0.4=h36c2ea0_1001
xorg-renderproto==0.11.1=h7f98852_1002
charset-normalizer==2.0.7=pypi_0
gfortran_impl_linux-64==7.3.0=hdf63c60_1
pyyaml==5.4.1=pypi_0
curl==7.76.1=h979ede3_1
networkx==2.6.3=pypi_0
r-assertthat==0.2.1=r35h6115d3f_1
krb5==1.17.2=h926e7f8_0
zipp==3.6.0=pypi_0
cairo==1.16.0=h18b612c_1001
cutadapt==3.5=pypi_0
r-tibble==3.0.1=r35hcdcec82_0
fontconfig==2.13.1=h6c09931_0
pillow==8.4.0=pypi_0
glib==2.68.3=h9c3ff4c_0
humanfriendly==10.0=pypi_0
r-pkgconfig==2.0.3=r35h6115d3f_0
six==1.16.0=pypi_0
patool==1.12=pypi_0
importlib-metadata==4.8.2=pypi_0
numpy==1.21.4=pypi_0
typing-extensions==3.10.0.2=pypi_0
future==0.18.2=pypi_0
r-munsell==0.5.0=r35h6115d3f_1002
r-optparse==1.6.6=r35h6115d3f_0
r-crayon==1.3.4=r35h6115d3f_1002
r-viridislite==0.3.0=r35h6115d3f_1002
libnghttp2==1.43.0=h812cca2_0
packaging==21.3=pypi_0
openssl==1.1.1k=h7f98852_0
libgcc-ng==9.3.0=h5101ec6_17
samtools==1.12=h9aed4be_1
r-rcpp==1.0.4.6=r35h0357c0b_0
r-plogr==0.2.0=r35h6115d3f_1002
pixman==0.38.0=h516909a_1003
mirtop==0.4.23=pypi_0
r-ellipsis==0.3.0=r35hcdcec82_0
r-backports==1.1.6=r35hcdcec82_1
python-dateutil==2.8.2=pypi_0
xicra==1.2.6=dev_0
click==8.0.3=pypi_0
python_abi==3.7=2_cp37m
libopenblas==0.3.12=pthreads_hb3c22a3_1
_r-mutex==1.0.1=anacondar_1
r-colorspace==1.4_1=r35hcdcec82_1
commonmark==0.9.1=pypi_0
libxcb==1.13=h7f98852_1003
r-rcolorbrewer==1.1_2=r35h6115d3f_1002
python==3.7.11=h12debd9_0
xopen==1.2.1=pypi_0
coloredlogs==15.0.1=pypi_0
binutils_linux-64==2.33.1=h9595d00_15
pandas==1.3.4=pypi_0
scipy==1.7.2=pypi_0
r-base==3.5.3=h26b83e4_0
zstd==1.5.0=ha95c52a_0
cycler==0.11.0=pypi_0
xorg-xproto==7.0.31=h7f98852_1007
pysam==0.17.0=pypi_0
binutils_impl_linux-64==2.33.1=he6710b0_7
r-xicra.stats==0.0.1=r35_0
jinja2==2.11.3=pypi_0
gsl==2.4=h294904e_1006
gettext==0.19.8.1=h0b5b191_1005
xorg-libxext==1.3.4=h7f98852_1
libgfortran-ng==7.5.0=h14aa051_19
rich==10.13.0=pypi_0
bokeh==3.0.0.dev1=pypi_0
seaborn==0.11.2=pypi_0
libtiff==4.3.0=hf544144_1
gcc_linux-64==7.3.0=h553295d_15
gxx_linux-64==7.3.0=h553295d_15
ncurses==6.2=he6710b0_1
kiwisolver==1.3.2=pypi_0
libgomp==9.3.0=h5101ec6_17
pybedtools==0.8.2=pypi_0
libgcc-devel_linux-64==7.5.0=hda03d7c_19
graphite2==1.3.13=h58526e2_1001
hcgb==0.5.4=dev_0
r-vctrs==0.2.4=r35hcdcec82_0
gfortran_linux-64==7.3.0=h553295d_15
readline==8.1=h27cfd23_0
r-getopt==1.20.3=r35_1
requests==2.26.0=pypi_0
libffi==3.3=he6710b0_2
libdeflate==1.7=h7f98852_5
libgcc==7.2.0=h69d50b8_2
ld_impl_linux-64==2.33.1=h53a641e_7
urllib3==1.26.7=pypi_0
setuptools==58.0.4=py37h06a4308_0
certifi==2021.10.8=py37h89c1867_1
colorama==0.4.4=pypi_0
libxml2==2.9.12=h03d6c58_0
libpng==1.6.37=h21135ba_2
xorg-libxau==1.0.9=h7f98852_0
lzstring==1.0.4=pypi_0
libcurl==7.76.1=hc4aaa36_1
xorg-libxrender==0.9.10=h7f98852_1003
r-utf8==1.1.4=r35hcdcec82_1002
matplotlib==3.4.3=pypi_0
xorg-libice==1.0.10=h7f98852_0
spectra==0.0.11=pypi_0
gcc_impl_linux-64==7.3.0=habb00fd_1
r-lifecycle==0.2.0=r35h6115d3f_0
pyparsing==3.0.5=pypi_0
tesmall==1.0.0=pypi_0
zlib==1.2.11=h7b6447c_3
xorg-libx11==1.7.2=h7f98852_0
dnaio==0.6.0=pypi_0
markdown==3.3.4=pypi_0
icu==58.2=hf484d3e_1000
r-tidyr==1.0.2=r35h0357c0b_0
harfbuzz==2.4.0=h37c48d4_1
libiconv==1.16=h516909a_0
simplejson==3.17.5=pypi_0
pytz==2021.3=pypi_0
sqlite==3.36.0=hc218d9a_0
tktable==2.10=hb7b940f_3
wget==3.2=pypi_0
r-magrittr==1.5=r35h6115d3f_1002
r-pillar==1.4.3=r35h6115d3f_0
r-labeling==0.3=r35h6115d3f_1002
r-digest==0.6.25=r35h0357c0b_1
idna==3.3=pypi_0
sysroot_linux-64==2.12=he073ed8_15
pango==1.42.4=h7062337_4
libglib==2.68.3=h3e27bee_0
star==2.7.9a=h9ee0642_0
xorg-kbproto==1.0.7=h7f98852_1002
termcolor==1.1.0=pypi_0

JFsanchezherrero commented 2 years ago

Hi there, I am not able to test in Mac whether XICRA works or not. But I guess it should work if conda works fine. I will be updating soon the package. I will let you know so that you can fresh install it.

Regards

JFsanchezherrero commented 2 years ago

Hi there, I have been working on the new installation.

Please do as follows and let me know it it worked.

Best regards,

1) Get requirements file from XICRA git repo

wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml

2) Create environment named XICRA and install required packages using conda:

conda env create -f environment.yml

3) Activate environment and install XICRA

## activate
conda activate XICRA

## install latest python code
pip install XICRA

4) Install missing software: Unfortunately, a couple of executables are not available neither as a conda or pip packages. These packages are miraligner, sRNAbench and 'MINTmap'. We have generated a bash script to retrieve and include within your conda environment.

## install missing software
wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
sh installer.sh

To check everything is fine, try executing the config module:

XICRA config

HCGB-IGTP / XICRA

ResolvePackageNotFound #33