From 5a14a3ef9277687e270a682911bded08868ee362 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 23 Dec 2024 09:28:38 -0500
Subject: [PATCH] feat: Bioconductor skeleton updates (#1027)

- When running `bioconda-utils bioconductor-skeleton` on Bioconductor
data packages, I was getting self-signed SSL errors (@bgruening is this
expected?). This change allow such errors to be ignored, returning None
for the url.
- In this round of Bioconductor 3.20 updates, it seems like a lot of
packages are now missing `zlib`. I still haven't pinpointed the reason,
but I'm guessing it has something to do with the updates to pinnings. So
for BioC packages that are detected to be compiled, this adds `zlib` to
host dependencies.
---
 bioconda_utils/bioconductor_skeleton.py | 37 ++++++++++++++++---------
 1 file changed, 24 insertions(+), 13 deletions(-)

diff --git a/bioconda_utils/bioconductor_skeleton.py b/bioconda_utils/bioconductor_skeleton.py
index 9a98fedca1..15af50b91d 100755
--- a/bioconda_utils/bioconductor_skeleton.py
+++ b/bioconda_utils/bioconductor_skeleton.py
@@ -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):
@@ -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):
@@ -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')