execution of latest master fails on athyra

[ctb]

After a make clean all, 'nosetests' fails:

Failure: ImportError (/home/t/dev/khmer/khmer/_khmermodule.so: undefined symbol: __gcov_merge_add) ... ERROR

[ctb]

My guess is that this is caused by the -ftest-coverage and -pg options used in building the zlib files.

[mr-c]

I have a fix for this my #438 PR.

diff --git a/setup.py b/setup.py
index e0cc51f..4ff1e63 100755
--- a/setup.py
+++ b/setup.py
@@ -148,9 +148,8 @@ class KhmerBuildExt(_build_ext):  # pylint:
disable=R0904

     def run(self):
         if "z" and "bz2" not in self.libraries:
-            zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( test Makefile
-nt'
-                    ' configure || bash ./configure --static ) && make -f '
-                    'Makefile.pic PIC']
+            zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( bash
./configure '
+                    '--static ) && make -f Makefile.pic PIC']
             spawn(cmd=zcmd, dry_run=self.dry_run)
             bz2cmd = ['bash', '-c', 'cd ' + BZIP2DIR + ' && make -f '
                       'Makefile-libbz2_so all']

On Sat, May 31, 2014 at 7:24 AM, C. Titus Brown notifications@github.com
wrote:

My guess is that this is caused by the -ftest-coverage and -pg options
used in building the zlib files.

—
Reply to this email directly or view it on GitHub
#442 (comment).

[ctb]

On Sat, May 31, 2014 at 04:04:00PM -0700, Michael R. Crusoe wrote:

I have a fix for this my #438 PR.

OK, let's cherry-pick this into a different PR and get it reviewed & merged,
unless we can expedite #438. khmer needs to work on athyra.

thanks,
--titus

diff --git a/setup.py b/setup.py
index e0cc51f..4ff1e63 100755
--- a/setup.py
+++ b/setup.py
@@ -148,9 +148,8 @@ class KhmerBuildExt(_build_ext):  # pylint:
disable=R0904

     def run(self):
         if "z" and "bz2" not in self.libraries:
-            zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( test Makefile
-nt'
-                    ' configure || bash ./configure --static ) && make -f '
-                    'Makefile.pic PIC']
+            zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( bash
./configure '
+                    '--static ) && make -f Makefile.pic PIC']
             spawn(cmd=zcmd, dry_run=self.dry_run)
             bz2cmd = ['bash', '-c', 'cd ' + BZIP2DIR + ' && make -f '
                       'Makefile-libbz2_so all']

On Sat, May 31, 2014 at 7:24 AM, C. Titus Brown notifications@github.com
wrote:

My guess is that this is caused by the -ftest-coverage and -pg options
used in building the zlib files.

???
Reply to this email directly or view it on GitHub
#442 (comment).

---

Reply to this email directly or view it on GitHub:

#442 (comment)

C. Titus Brown, ctb@msu.edu