[med-svn] [Git][med-team/python-biopython][master] 3 commits: overred makeblastdb memory allocation for mipsel

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / python-biopython


Commits:
58fbb4da by Étienne Mollier at 2020-10-04T22:15:06+02:00
overred makeblastdb memory allocation for mipsel

- - - - -
5aa1d374 by Étienne Mollier at 2020-10-04T22:16:49+02:00
updated run-unit-test to reflect that change

- - - - -
632894cb by Étienne Mollier at 2020-10-04T22:24:29+02:00
routine-update: Ready to upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-biopython (1.78+dfsg-3) unstable; urgency=medium
+
+  * mpisel build still failing on buildd (host arch mips64el, schroot mipsel)
+      - overred makeblastdb memory allocation for that arch on build and test;
+      - updated run-unit-test to reflect that change.
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Sun, 04 Oct 2020 22:18:45 +0200
+
 python-biopython (1.78+dfsg-2) unstable; urgency=medium
 
   * Bumped build requirement on ncbi-blast+ 2.10.1-2 and greater:


=====================================
debian/rules
=====================================
@@ -34,6 +34,14 @@ else
     EXCLUDEARCHamd64=raxml_tool
 endif
 
+# virtualized environment, esp. with schroot, may be too constrained for the
+# memory allocation required by the test_NCBI_BLAST_tools.  See #969608 for
+# more details:
+#     https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40
+ifeq ($(BUILD_ARCH),mipsel)
+    export BLASTDB_LMDB_MAP_SIZE = 3000000000
+endif
+
 # avoid tests requiring data base connections if no server is running while we are doing the build
 # This would not trigger a failure but bloats the build log with irrelevant noise
 EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2


=====================================
debian/tests/run-unit-test
=====================================
@@ -27,12 +27,12 @@ if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then
     rm -f test_BWA_tool.py
 fi
 
-# arm64 virtualized environment, esp. with schroot, may be too constrained for
-# the memory allocation required by the test_NCBI_BLAST_tools.  See #969608
-# following for more details:
+# virtualized environment, esp. with schroot, may be too constrained for the
+# memory allocation required by the test_NCBI_BLAST_tools.  See #969608 for
+# more details:
 #     https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40
-if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "arm64" ]; then
-    BLASTDB_LMDB_MAP_SIZE=20000000000
+if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "mipsel" ]; then
+    BLASTDB_LMDB_MAP_SIZE=3000000000
     export BLASTDB_LMDB_MAP_SIZE
 fi
 



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50...632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50...632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc
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