Salmon gcc7 #10344

rob-p · 2018-08-09T03:03:31Z

I have read the guidelines for bioconda recipes.
This PR adds a new recipe.
AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
This PR updates an existing recipe.
This PR does something else (explain below).

This is a test to see if we can build salmon using the new compiler (gcc7) ... at least on linux. This works locally using the "bootstrap" method, so let's see what happens on Circle CI.

rob-p · 2018-08-09T03:31:43Z

Hrmm, this seemed to work .... not so sure what's different between this and before when it failed. Going to try uncommenting OSX now too.

Try building on OSX

rob-p · 2018-08-09T04:05:40Z

Hrmmm .. looks like this icu58 issue is still popping up on OSX, but has gone away under linux on the newer compiler. I'd really like to figure this out so I can provide a mac executable through bioconda.

bgruening · 2018-08-09T04:06:57Z

recipes/salmon/build_config.yaml

@@ -0,0 +1,6 @@
+c_compiler:
+  - gcc      # [linux]
+  - clang    # [osx]


Rob can you try to replace clang here with GCC as well?

Ok; just pushed. I didn't even know that building with GCC on OSX was an option here :).

trying GCC/GXX even on Mac

rob-p · 2018-08-09T04:36:40Z

It used clang anyway, it seems ....

rob-p

Ahhh, so it wasnt even fixed on linux yet. Well, at least the error seems the same in both cases! Is this affecting any other packages?

bgruening · 2018-08-09T12:15:15Z

Not really as we do not build many pkgs with the new compilers. My assumption is that we need to rebuild iuc with the new compilers before we build Salmon :(

rob-p · 2018-08-09T12:49:31Z

Can that be done here, or is that coming from conda-forge? Can we submit PRs there?

bgruening · 2018-08-09T13:09:07Z

Its a larger effort we are working on. The migration to the new compilers should happen soon. But it will take time, nothing we can influence right now. Its mainly CI build time dependent ... If someone want to buy more CI build-time - more then welcome :)

I will keep you posted, sorry.

rob-p · 2018-08-09T16:08:45Z

Ok, so I get it to build locally if I force the boost from anaconda cloud and not the one from conda-forge. The conda-forge ppl aren't building a c++11 enabled boost :(. Perhaps there is a more elegant way to do this.

revert to clang on OSX.

rob-p · 2018-08-09T17:49:20Z

ahh, so no we are getting something different popping up on OSX. Perhaps this one is solvable. Any thoughts @bioconda/osx ?

bump llvm_version

version

version again

acaprez · 2018-08-10T22:05:56Z

librt is part of glibc, so yeah, you'd need to remove that flag entirely. Hopefully you won't get an unresolved symbol error then...

change deployment target (10.9)

rob-p · 2018-08-28T16:38:02Z

Now it's back at a damn icu58 linker issue under OSX ... . But, the icu being pulled in is v58. From the build log:

   icu:             58.2-hfc679d8_0               conda-forge

why won't it link?

There are also some even stranger errors:

 NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)

and

  "std::__1::cout", referenced from:

etc. Perhaps this boost was not linked against libstdc++, given that it's on OSX?

ok, let's go all in on the new stuff and try to fix it from that direction

try different boost on osx?

this is a frustrated commit message ...

Try boost instead of libboost --- do we get the same error on OSX?

See if we can use boost instead of libboost on linux

nope ... `boost` instead of `libboost` fails under linux.

horrible, horrible, horrible ...

nope. nope, nope, nope --- we *need* `libboost` on linux for now. Why doesn't it work on OSX?

try this

update md5sum

50th time's a charm?

51st time's a charm ... I'm gonna guess not.

rob-p · 2018-08-29T21:20:22Z

Holy shit!

Ok --- last attempt *worked*! Now, try to make everything C++14, and re-enable linux build.

have to update md5sum

rob-p · 2018-08-29T22:17:36Z

Note : This is currently pulling from develop. I will be cutting a new release (tagged) imminently. Please don't merge this yet.

try and build tagged v0.11.3

bgruening

Holy cow! Amazing @rob-p. Thanks a lot for all the effort - very appreciated.

bgruening · 2018-08-31T02:27:02Z

recipes/salmon/meta.yaml

  host:
-    - boost
-    - icu
+    - libboost # [linux]


the selector is now not needed here ...

Thanks @bgruening --- yes, I agree that this is not needed (and probably the same with the libcxx below). Should I try to bump the version and remove these and see if it compiles?

That would be great, yes. Thanks.

bgruening · 2018-08-31T02:27:22Z

recipes/salmon/meta.yaml

-    - boost
-    - icu
+    - libcxx 
+    - libboost # [linux]


bgruening · 2018-08-31T02:27:40Z

recipes/salmon/meta.yaml

    - {{ compiler('cxx') }}
    - {{ compiler('c') }}
-    #- clangdev =={{ llvm_version }}  # [osx]
-    #- libcxx =={{ llvm_version }}  # [osx]
+    - libcxx 


is this needed?

Rob Patro added 2 commits August 8, 2018 22:15

try new compiler

6544cba

commit build_config.yaml

87c7098

Update meta.yaml

b29fe53

Try building on OSX

bgruening reviewed Aug 9, 2018

View reviewed changes

Update build_config.yaml

d1b55ec

trying GCC/GXX even on Mac

Rename build_config.yaml to conda_build_config.yaml

6cdd3f2

rob-p commented Aug 9, 2018

View reviewed changes

Rob Patro added 8 commits August 9, 2018 10:14

pinning

d6ab39b

pinning

fb1f1ef

boost => boost-cpp

2e07116

boost => boost-cpp

7e6bc87

boost => boost-cpp

d60a257

boost => boost-cpp

78f3005

boost => boost-cpp

1dc89f1

boost => boost-cpp

84f27bb

Update conda_build_config.yaml

641a70d

revert to clang on OSX.

Rob Patro and others added 5 commits August 9, 2018 14:13

osx build

f674233

osx build

80e2621

Update meta.yaml

233570b

bump llvm_version

Update meta.yaml

185d3b0

version

Update meta.yaml

98e4acb

version again

rob-p mentioned this pull request Aug 10, 2018

nanopolish out of blacklist #10368

Merged

5 tasks

Rob Patro and others added 6 commits August 28, 2018 11:31

try and remove librt on OSX build

59f92f1

try and remove librt on OSX build

e5b0efb

skip linux until we have OSX

97e0ad1

Update meta.yaml

28f74b1

Update meta.yaml

216286f

Update build.sh

b745f43

change deployment target (10.9)

rob-p added 15 commits August 28, 2018 21:37

Create conda_build_config.yaml

047202d

Update meta.yaml

0686f30

ok, let's go all in on the new stuff and try to fix it from that direction

Update meta.yaml

4219ff3

Update meta.yaml

507a07b

try different boost on osx?

Update meta.yaml

57a0bdf

this is a frustrated commit message ...

Update meta.yaml

e71f72f

Update meta.yaml

a3767e1

Try boost instead of libboost --- do we get the same error on OSX?

Update meta.yaml

2a15e50

See if we can use boost instead of libboost on linux

revert boost to libboost under linux.

40fc6e7

nope ... `boost` instead of `libboost` fails under linux.

Update meta.yaml

196118e

horrible, horrible, horrible ...

Update meta.yaml

f3cf3bf

nope. nope, nope, nope --- we *need* `libboost` on linux for now. Why doesn't it work on OSX?

Update meta.yaml

561fe92

try this

Update meta.yaml

2b01aea

update md5sum

Update meta.yaml

61543b8

50th time's a charm?

Update meta.yaml

90fc3b9

51st time's a charm ... I'm gonna guess not.

rob-p added 2 commits August 29, 2018 17:25

Update meta.yaml

47d5a68

Ok --- last attempt *worked*! Now, try to make everything C++14, and re-enable linux build.

Update meta.yaml

3d73d7b

have to update md5sum

Update meta.yaml

7606f5d

try and build tagged v0.11.3

rob-p merged commit c1a7153 into bioconda:master Aug 30, 2018

bgruening reviewed Aug 31, 2018

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Salmon gcc7 #10344

Salmon gcc7 #10344

rob-p commented Aug 9, 2018

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bgruening Aug 9, 2018

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Salmon gcc7 #10344

Salmon gcc7 #10344

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