Cannot install or rebuild module on OSX 10.10 about hdf5.node HOT 8 CLOSED

Hi @paologf , you need the environment variable HDF5_HOME=/home/roger/NodeProjects/hdf5 set to your native hdf5 distribution. the include of their hdf5.h will then get picked up

the legacy folder isn't involved, compatible with v0.12.x or supported anymore.

Also check the #4 about building on darwin and getting the right gcc compiler version on your computer with homebrew. the version should be g++ 4.9 at least:
g++ --version

Some details at
http://rycole.com/hdf5.node/doc/install-setup.html

from hdf5.node.

Ok, thank you for the reply (and sorry for the delay..).

I follow the link instruction, I download and install the hdf5, then I set my HDF5_HOME variable to the installed hdf5 path.

I had some compiler error so I also do :

brew install gcc49
export CXX=/usr/local/bin/gcc-4.9

as suggest in #4 by @dasantonym .

Then I install hdf5 module using npm install hdf5 .

If I do a require from node the module works.
If I try to do the require from Electron I have the following message error :

Uncaught Error: dlopen(app/node_modules/hdf5/build/Release/hdf5.node, 1): Symbol not found: __ZNSs4_Rep20_S_empty_rep_storageE
Referenced from: app/node_modules/hdf5/build/Release/hdf5.node
Expected in: dynamic lookup

Referenced from: app/node_modules/hdf5/build/Release/hdf5.node
Expected in: dynamic lookup

at Error (native)
at Object.module.(anonymous function) (ATOM_SHELL_ASAR.js:134:20)
at Object.module.(anonymous function) as .node
at Module.load (module.js:343:32)
at Function.Module._load (module.js:298:12)
at Module.require (module.js:353:17)
at require (module.js:372:17)
at Object. (app/node_modules/hdf5/index.js:4:13)
at Module._compile (module.js:418:26)
at Object.Module._extensions..js (module.js:436:10)

Any (other) suggestion?

Thanks.

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I am also having trouble building on a Mac. I have tried using npm install hdf5 with HDF5_HOME=*path_to_hdf_directory*, which yields a fatal error due to too many errors being ommitted. The first error in the chain is:

In file included from ../src/file.h:14:
../src/attributes.hpp:24:40: error: no type named 'FunctionCallbackInfo' in namespace 'v8'
        static void Refresh (const v8::FunctionCallbackInfo<v8::Value>& args) {
                                   ~~~~^
../src/attributes.hpp:24:60: error: expected ')'
        static void Refresh (const v8::FunctionCallbackInfo<v8::Value>& args) {
                                                           ^
../src/attributes.hpp:24:29: note: to match this '('
        static void Refresh (const v8::FunctionCallbackInfo<v8::Value>& args) {
                            ^
../src/attributes.hpp:84:38: error: no type named 'FunctionCallbackInfo' in namespace 'v8'
        static void Flush (const v8::FunctionCallbackInfo<v8::Value>& args) {
                                 ~~~~^
../src/attributes.hpp:84:58: error: expected ')'
        static void Flush (const v8::FunctionCallbackInfo<v8::Value>& args) {
                                                         ^
../src/attributes.hpp:84:27: note: to match this '('
        static void Flush (const v8::FunctionCallbackInfo<v8::Value>& args) {
                          ^
../src/attributes.hpp:27:17: error: use of undeclared identifier 'args'; did you mean 'uv_process_options_s::args'?
            if (args.Length() >0 ) {
                ^~~~
                uv_process_options_s::args
/Users/jduckwor/.node-gyp/0.10.35/deps/uv/include/uv.h:1345:10: note: 'uv_process_options_s::args' declared here
  char** args;

I get the same errors when trying to build from the repo using node-gyp. I am a little unclear on what I should be setting my NODE_PATH variable too, since the example seems to suggest there should be a build directory in the main hdf5.node directory, but I don't see one, so this may be the root of the issue.

Any help is much appreciated. I am running OS Mavericks 10.9.5, node v0.10.35, node-gyp v2.0.2.

Thanks very much,

Jon

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Hi Jon,
you don't need to set the NODE_PATH as specify here http://rycole.com/hdf5.node/doc/install-setup.html .
I think I had the same problem before updating the gcc, try :

brew install gcc49
export CXX=/usr/local/bin/gcc-4.9

from hdf5.node.

Thanks for the help, that seemed to get me a bit farther along. It's now throwing an error related to the homebrew cellar:

make: /usr/local/Cellar/gcc/4.9.2_1: Permission denied
make: *** [Release/obj.target/h5ds/src/h5ds.o] Error 1

I tried using chmod to give read and write permissions to that directory, but still got the same error. I actually tried giving read and write permission to the whole chain up through /usr/local temporarily and changing the owner of /usr/local to my username, but still got the same thing.

I know this is kind of a separate issue from the node installation, but any thoughts?

Thanks a bunch,

Jon

from hdf5.node.

@jduckworth Hi, this project is nodejs v0.12.x based. v0.10.x isn't supported. Developer >=v0.11.14 will probably work but I would go to v0.13.x if in nodejs developer mode.

Your last is a permissions issue with the gcc install of course. At a terminal what does
which g++
g++ --version

give you?

from hdf5.node.

Note I am working on node-pre-gyp building yet for mac I'm not sure if all OS versions will get supported quickly seeing mac doesn't license well for developers on the cloud; but I'll try and also borrow some machines at work

from hdf5.node.

That's what I suspected for the gcc install...

The system I described above is my work setup, which I think is leading to the permission issues. I tried doing the install on my home computer (OS X Yosemite 10.10.4, Node v0.12.7, node-gyp v2.0.2) and it installed without an error. However, when I try to require it I get the error:

Error: dlopen(/Users/jduckwor/node_modules/hdf5/build/Release/hdf5.node, 1): Symbol not found: __ZN3MPI3Win4FreeEv
Referenced from: /Users/jduckwor/node_modules/hdf5/build/Release/hdf5.node
Expected in: dynamic lookup

It seems like others have had similar errors when installing Python modules and that it has to do with the MPI compiler being used. I'm going to play around with it and I'll let you know if I come up with a solution.

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