debugging installing r-package

setup.py

@@ -3,74 +3,96 @@
 import os
 import io
 import subprocess
+
 if sys.version_info.major < 3 or sys.version_info.minor < 2:
     raise ValueError("genepy is only compatible with Python 3.5 and above")
 if sys.version_info.minor < 5:
     import warnings
+
     warnings.warn("genepy may not function properly on Python < 3.8")
 
-os.system('git submodule init && git submodule sync')
+os.system("git submodule init && git submodule sync")
 
-with open("README.md", 'r') as f:
-  long_description = f.read()
+with open("README.md", "r") as f:
+    long_description = f.read()
 
 print("trying to install R packages")
-subprocess.run(
-    'R -e \'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager", repos="http://cran.us.r-project.org")};BiocManager::install(c("GSEABase", "erccdashboard", "GSVA", "DESeq2"));\'',
-      shell=True, check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-print('if it did not work. please install R or check your R installation')
-print("once R is installed you need to install erccdashboard, GSEABase GSVA, DESeq2 to have access to all the functions")
+try:
+    subprocess.run(
+        'R -e \'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager", repos="http://cran.us.r-project.org")};BiocManager::install(c("GSEABase", "erccdashboard", "GSVA", "DESeq2"));\'',
+        shell=True,
+        check=True,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+    )
+except:
+    print("R packages not installed")
+print("if it did not work. please install R or check your R installation")
+print(
+    "once R is installed you need to install erccdashboard, GSEABase GSVA, DESeq2 to have access to all the functions"
+)
+
 
 def read(*paths, **kwargs):
-  """Read the contents of a text file safely.
-  >>> read("genepy", "VERSION")
-  '0.1.0'
-  >>> read("README.md")
-  ...
-  """
+    """Read the contents of a text file safely.
+    >>> read("genepy", "VERSION")
+    '0.1.0'
+    >>> read("README.md")
+    ...
+    """
 
-  content = ""
-  with io.open(
-    os.path.join(os.path.dirname(__file__), *paths),
-    encoding=kwargs.get("encoding", "utf8"),
-  ) as open_file:
-    content = open_file.read().strip()
-  return content
+    content = ""
+    with io.open(
+        os.path.join(os.path.dirname(__file__), *paths),
+        encoding=kwargs.get("encoding", "utf8"),
+    ) as open_file:
+        content = open_file.read().strip()
+    return content
 
 
 def read_requirements(path):
-  return [
-    line.strip()
-    for line in read(path).split("\n")
-    if not line.startswith(('"', "#", "-", "git+"))
-  ]
+    return [
+        line.strip()
+        for line in read(path).split("\n")
+        if not line.startswith(('"', "#", "-", "git+"))
+    ]
+
 
 setup(
-  name='Broad-genepy',
-  version=read("genepy", "VERSION"),
-  description='A useful module for any CompBio',
-  long_description=long_description,
-  long_description_content_type="text/markdown",
-  author='Jeremie Kalfon',
-  author_email='[email protected]',
-  url="https://github.com/BroadInstitute/genepy",
-  packages=['genepy/cell_line_mapping-master/python/cell_line_mapper',
-            'genepy/epigenetics', 'genepy/mutations', 'genepy/google', 'genepy/sequencing/',
-            'genepy/terra', 'genepy/rna', 'genepy/utils'],
-  package_data={'genepy': ['data/*']},
-  python_requires='>=3.5',
-  install_requires=read_requirements("requirements.txt"),
-  classifiers=[
-    "Programming Language :: Python :: 3",
-    "Intended Audience :: Science/Research",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-  ],
+    name="Broad-genepy",
+    version=read("genepy", "VERSION"),
+    description="A useful module for any CompBio",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Jeremie Kalfon",
+    author_email="[email protected]",
+    url="https://github.com/BroadInstitute/genepy",
+    packages=[
+        "genepy/cell_line_mapping-master/python/cell_line_mapper",
+        "genepy/epigenetics",
+        "genepy/mutations",
+        "genepy/google",
+        "genepy/sequencing/",
+        "genepy/terra",
+        "genepy/rna",
+        "genepy/utils",
+    ],
+    package_data={"genepy": ["data/*"]},
+    python_requires=">=3.5",
+    install_requires=read_requirements("requirements.txt"),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
 )
 
 
-print("You might want to install Bowtie2, samtools, bwa and R to be able to use all functions of this package:\n\
+print(
+    "You might want to install Bowtie2, samtools, bwa and R to be able to use all functions of this package:\n\
   http://bowtie-bio.sourceforge.net/bowtie2/index.shtml\n\
   http://www.htslib.org/\n\
-  https://github.com/lh3/bwa\n")
+  https://github.com/lh3/bwa\n"
+)
 
 print("Finished!")