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feat: Bioconductor skeleton updates #1027

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merged 2 commits into from
Dec 23, 2024
Merged

feat: Bioconductor skeleton updates #1027

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cbded24
ignore self-signed SSL errors and return None
daler Dec 22, 2024
98eff96
add zlib as host dep for compiled packages
daler Dec 22, 2024
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37 changes: 24 additions & 13 deletions bioconda_utils/bioconductor_skeleton.py
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Original file line number Diff line number Diff line change
Expand Up @@ -468,9 +468,12 @@ def bioarchive_url(self):
package, otherwise returns None.
"""
url = bioarchive_url(self.package, self.version, self.bioc_version)
response = requests.head(url)
if response.status_code == 200:
return url
try:
response = requests.head(url)
if response.status_code == 200:
return url
except requests.exceptions.SSLError:
pass

@property
def cargoport_url(self):
Expand All @@ -479,16 +482,19 @@ def cargoport_url(self):
it exists.
"""
url = cargoport_url(self.package, self.version, self.bioc_version)
response = requests.head(url)
if response.status_code == 404:
# This is expected if this is a new package or an updated version.
# Cargo Port will archive a working URL upon merging
return
elif response.status_code == 200:
return url
else:
raise PageNotFoundError(
"Unexpected error: {0.status_code} ({0.reason})".format(response))
try:
response = requests.head(url)
if response.status_code == 404:
# This is expected if this is a new package or an updated version.
# Cargo Port will archive a working URL upon merging
return
elif response.status_code == 200:
return url
else:
raise PageNotFoundError(
"Unexpected error: {0.status_code} ({0.reason})".format(response))
except requests.exceptions.SSLError:
pass

@property
def bioconductor_tarball_url(self):
Expand Down Expand Up @@ -937,6 +943,11 @@ def sub_placeholders(x):
additional_host_deps.append('libblas')
additional_host_deps.append('liblapack')

# During the BioC 3.20 builds, which also corresponded to updates
# in pinnings, there were quite a few issues where zlib was
# missing.
additional_host_deps.append('zlib')

additional_run_deps = []
if self.is_data_package:
additional_run_deps.append('curl')
Expand Down
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