hdf-ni / hdf5.node Goto Github PK

Thread model: posix
gcc version 4.9.3 (Homebrew gcc49 4.9.3) 
COLLECT_GCC_OPTIONS='-D' 'NODE_GYP_MODULE_NAME=h5im' '-D' '_DARWIN_USE_64_BIT_INODE=1' '-D' '_LARGEFILE_SOURCE' '-D' '_FILE_OFFSET_BITS=64' '-D' 'BUILDING_NODE_EXTENSION' '-I' '/Users/username/.node-gyp/4.2.0/include/node' '-I' '/Users/username/.node-gyp/4.2.0/src' '-I' '/Users/username/.node-gyp/4.2.0/deps/uv/include' '-I' '/Users/username/.node-gyp/4.2.0/deps/v8/include' '-I' '/usr/local/Cellar/hdf5/1.8.15/include' '-Os' '-gdwarf-2' '-mmacosx-version-min=10.5' '-m64' '-Wall' '-Wendif-labels' '-Wextra' '-Wno-unused-parameter' '-std=gnu++11' '-fno-rtti' '-fno-threadsafe-statics' '-fPIC' '-O4' '-std=c++11' '-fexceptions' '-v' '-MMD' '-MF' './Release/.deps/Release/obj.target/h5im/src/h5im.o.d.raw' '-c' '-o' 'Release/obj.target/h5im/src/h5im.o' '-mtune=core2'
 /usr/local/Cellar/gcc49/4.9.3/libexec/gcc/x86_64-apple-darwin14.4.0/4.9.3/cc1plus -quiet -v -I /Users/username/.node-gyp/4.2.0/include/node -I /Users/username/.node-gyp/4.2.0/src -I /Users/username/.node-gyp/4.2.0/deps/uv/include -I /Users/username/.node-gyp/4.2.0/deps/v8/include -I /usr/local/Cellar/hdf5/1.8.15/include -MMD Release/obj.target/h5im/src/h5im.d -MF ./Release/.deps/Release/obj.target/h5im/src/h5im.o.d.raw -MQ Release/obj.target/h5im/src/h5im.o -D__DYNAMIC__ -D NODE_GYP_MODULE_NAME=h5im -D _DARWIN_USE_64_BIT_INODE=1 -D _LARGEFILE_SOURCE -D _FILE_OFFSET_BITS=64 -D BUILDING_NODE_EXTENSION ../src/h5im.cc -fPIC -quiet -dumpbase h5im.cc -mmacosx-version-min=10.5 -m64 -mtune=core2 -auxbase-strip Release/obj.target/h5im/src/h5im.o -gdwarf-2 -Os -O4 -Wall -Wendif-labels -Wextra -Wno-unused-parameter -std=gnu++11 -std=c++11 -version -fno-rtti -fno-threadsafe-statics -fPIC -fexceptions -o /var/folders/gm/prk8pp4n6b3b4p82cpmdfssdykv292/T//ccY4bnzL.s
GNU C++ (Homebrew gcc49 4.9.3) version 4.9.3 (x86_64-apple-darwin14.4.0)
    compiled by GNU C version 4.9.3, GMP version 4.3.2, MPFR version 2.4.2, MPC version 0.8.1
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring nonexistent directory "/usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3/../../../../../../x86_64-apple-darwin14.4.0/include"
ignoring nonexistent directory "/Users/username/.node-gyp/4.2.0/src"
ignoring nonexistent directory "/Users/username/.node-gyp/4.2.0/deps/uv/include"
ignoring nonexistent directory "/Users/username/.node-gyp/4.2.0/deps/v8/include"
#include "..." search starts here:
#include <...> search starts here:
 /Users/username/.node-gyp/4.2.0/include/node
 /usr/local/Cellar/hdf5/1.8.15/include
 /usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3/../../../../../../include/c++/4.9.3
 /usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3/../../../../../../include/c++/4.9.3/x86_64-apple-darwin14.4.0
 /usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3/../../../../../../include/c++/4.9.3/backward
 /usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3/include
 /usr/local/include
 /usr/local/Cellar/gcc49/4.9.3/include
 /usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3/include-fixed
 /usr/include
 /System/Library/Frameworks
 /Library/Frameworks
End of search list.
GNU C++ (Homebrew gcc49 4.9.3) version 4.9.3 (x86_64-apple-darwin14.4.0)
    compiled by GNU C version 4.9.3, GMP version 4.3.2, MPFR version 2.4.2, MPC version 0.8.1
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 588f768c4156eb0b3065f0148fd605f3
In file included from ../src/h5im.cc:4:0:
../src/h5_im.hpp: In static member function 'static void NodeHDF5::H5im::read_image(const v8::FunctionCallbackInfo<v8::Value>&)':
../src/h5_im.hpp:104:132: error: call of overloaded 'New(v8::Isolate*, const char*, hsize_t)' is ambiguous
     v8::Local<v8::Object> buffer=node::Buffer::New(v8::Isolate::GetCurrent(), (const char*)contentBuffer.get(), planes*width*height);
                                                                                                                                    ^
../src/h5_im.hpp:104:132: note: candidates are:
In file included from ../src/h5_im.hpp:5:0,
                 from ../src/h5im.cc:4:
/Users/username/.node-gyp/4.2.0/include/node/node_buffer.h:31:40: note: v8::MaybeLocal<v8::Object> node::Buffer::New(v8::Isolate*, v8::Local<v8::String>, node::encoding) <near match>
 NODE_EXTERN v8::MaybeLocal<v8::Object> New(v8::Isolate* isolate,
                                        ^
/Users/username/.node-gyp/4.2.0/include/node/node_buffer.h:31:40: note:   no known conversion for argument 3 from 'hsize_t {aka long long unsigned int}' to 'node::encoding'
/Users/username/.node-gyp/4.2.0/include/node/node_buffer.h:43:40: note: v8::MaybeLocal<v8::Object> node::Buffer::New(v8::Isolate*, char*, size_t) <near match>
 NODE_EXTERN v8::MaybeLocal<v8::Object> New(v8::Isolate* isolate,
                                        ^
/Users/username/.node-gyp/4.2.0/include/node/node_buffer.h:43:40: note:   no known conversion for argument 2 from 'const char*' to 'char*'
In file included from ../src/h5im.cc:4:0:
../src/h5_im.hpp: In static member function 'static void NodeHDF5::H5im::make_palette(const v8::FunctionCallbackInfo<v8::Value>&)':
../src/h5_im.hpp:128:53: warning: narrowing conversion of 'rankValue.v8::Local<T>::operator-><v8::Value>()->v8::Value::ToInt32().v8::Local<T>::operator-><v8::Int32>()->v8::Int32::Value()' from 'int32_t {aka int}' to 'hsize_t {aka long long unsigned int}' inside { } [-Wnarrowing]
     hsize_t pal_dims[1]{rankValue->ToInt32()->Value()};
                                                     ^
../src/h5_im.hpp:129:12: warning: unused variable 'err' [-Wunused-variable]
     herr_t err=H5IMmake_palette ( args[0]->ToInt32()->Value(), *dset_name, pal_dims, (const unsigned char *)buffer->Buffer()->Externalize().Data());
            ^
make: *** [Release/obj.target/h5im/src/h5im.o] Error 1

var dataset = new Array(10000);
h5lt.makeDataset(file.id, '/dataset', dataset);

var dataset = new Array(100000);
h5lt.makeDataset(file.id, '/dataset', dataset);

HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
  #000: H5Dio.c line 271 in H5Dwrite(): can't prepare for writing data
    major: Dataset
    minor: Write failed
  #001: H5Dio.c line 352 in H5D__pre_write(): can't write data
    major: Dataset
    minor: Write failed
  #002: H5Dio.c line 769 in H5D__write(): unable to initialize storage
    major: Dataset
    minor: Unable to initialize object
  #003: H5Dint.c line 1836 in H5D__alloc_storage(): unable to initialize dataset with fill value
    major: Dataset
    minor: Unable to initialize object
  #004: H5Dint.c line 1898 in H5D__init_storage(): unable to allocate all chunks of dataset
    major: Dataset
    minor: Unable to initialize object
  #005: H5Dcontig.c line 315 in H5D__contig_fill(): unable to write fill value to dataset
    major: Dataset
    minor: Unable to initialize object
  #006: H5Dcontig.c line 618 in H5D__contig_write_one(): vector write failed
    major: Low-level I/O
    minor: Write failed
  #007: H5Dcontig.c line 1206 in H5D__contig_writevv(): can't perform vectorized sieve buffer write
    major: Dataset
    minor: Can't operate on object
  #008: H5VM.c line 1457 in H5VM_opvv(): can't perform operation
    major: Internal error (too specific to document in detail)
    minor: Can't operate on object
  #009: H5Dcontig.c line 952 in H5D__contig_writevv_sieve_cb(): block write failed
    major: Dataset
    minor: Write failed
  #010: H5Fio.c line 171 in H5F_block_write(): write through metadata accumulator failed
    major: Low-level I/O
    minor: Write failed
  #011: H5Faccum.c line 825 in H5F__accum_write(): file write failed
    major: Low-level I/O
    minor: Write failed
  #012: H5FDint.c line 260 in H5FD_write(): driver write request failed
    major: Virtual File Layer
    minor: Write failed
  #013: H5FDsec2.c line 802 in H5FD_sec2_write(): file write failed: time = Sat Oct  8 00:58:40 2016
, filename = '/home/jacopo/data-backend/products/gistemp/gistemp.h5', file descriptor = 12, errno = 14, error message = 'Bad address', buf = 0x55c61fcac378, total write size = 422496, bytes this sub-write = 422496, bytes actually written = 18446744073709551615, offset = 1179648
    major: Low-level I/O
    minor: Write failed
Unhandled rejection SyntaxError: failed to make var len dataset
    at SyntaxError (native)
    at createHDF5Product (/home/jacopo/data-backend/scripts/gistemp-process.js:111:8)
    at tryCatcher (/home/jacopo/data-backend/node_modules/bluebird/js/release/util.js:16:23)

PRETTY_NAME="Debian GNU/Linux 8 (jessie)"
NAME="Debian GNU/Linux"
VERSION_ID="8"
VERSION="8 (jessie)"
ID=debian

Node v4.7.0
NPM v2.15.11
HDF5 v1.8.18
gcc (Debian 4.9.2-10) 4.9.2

> var hdf5 = require('hdf5');
Error: libhdf5.so.100: cannot open shared object file: No such file or directory
    at Error (native)
    at Object.Module._extensions..node (module.js:434:18)
    at Module.load (module.js:343:32)
    at Function.Module._load (module.js:300:12)
    at Module.require (module.js:353:17)
    at require (internal/module.js:12:17)
    at Object.<anonymous> (/root/test-app/node_modules/hdf5/index.js:4:25)
    at Module._compile (module.js:409:26)
    at Object.Module._extensions..js (module.js:416:10)
    at Module.load (module.js:343:32)

  g++: error: unrecognized command line option ‘-std=c++14’

const hdf5 = require('hdf5').hdf5;
const h5lt = require('hdf5').h5lt;
const Access = require('hdf5/lib/globals').Access;
const H5Type = require('hdf5/lib/globals').H5Type;

var file = new hdf5.File('t.h5', Access.ACC_CREAT);
var data = new Float32Array(10);
data.type = H5Type.H5T_NATIVE_FLOAT;
data.rank = 3;
data.sections = 1;
// create dataset with data
h5lt.makeDataset(file.id, 'data', data);

data[3] = 5;

// reuse typed array to overwrite content
h5lt.writeDataset(file.id, 'data', data);

file.close();

$ mocha test
module.js:328
    throw err;
    ^

Error: Cannot find module './build/Release/hdf5'

SyntaxError: expected id, name
    at SyntaxError (native)
    at /Users/jacopo/Code/iseechange-v2/indexer/index.js:72:18
    at Array.forEach (native)
    at Object.<anonymous> (/Users/jacopo/Code/iseechange-v2/indexer/index.js:70:17)
    at Module._compile (module.js:409:26)
    at Object.Module._extensions..js (module.js:416:10)
    at Module.load (module.js:343:32)
    at Function.Module._load (module.js:300:12)
    at Function.Module.runMain (module.js:441:10)
    at startup (node.js:139:18)

h5lt.readDataset(id, name [, options])
   id → the group or file id location. Every group and the file return with an id attribute
   name → a string naming the dataset.
   [options] → start, stride and count.
   return ← A typed array or string
h5lt.readDatasetAsBuffer(id, name [, options])
    id → the group or file id location. Every group and the file return with an id attribute
    name → a string naming the dataset.
    [options] → start, stride and count.
    return ← A node::Buffer with the data and attributes for its shape and type.

var hdf5 = require('hdf5').hdf5;
var h5lt = require('hdf5').h5lt;
var Access = require('hdf5/lib/globals').Access;
var file = new hdf5.File('hgForebrainGlut.loom', Access.ACC_RDONLY);
var dim = file.getDatasetDimensions('matrix');
for (var i = 0; i < dim[0]; i++) {
  var buffer = h5lt.readDatasetAsBuffer(file.id, 'matrix', {
    start: [i, 0],
    stride: [1, 1],
    count: [1, dim[1]]
  });
}

C:\Users\jabba\icpdashboard>npm install hdf5 --fallback-to-build

> [email protected] install C:\Users\jabba\icpdashboard\node_modules\hdf5
> node-pre-gyp install --fallback-to-build

Building the projects in this solution one at a time. To enable parallel build, please add the "/m" switch.
  hdf5.cc
  h5_file.cc
  h5_group.cc
  win_delay_load_hook.cc
c:\program files\microsoft sdks\windows\v7.1\include\sal_supp.h(57): warning C4005: '__useHeader' : macro redefinition (C:\Users\jabba\icpdashboard\node_module
s\node-gyp\src\win_delay_load_hook.cc) [C:\Users\jabba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2886) : see previous definition of '__useHeader'
c:\program files\microsoft sdks\windows\v7.1\include\specstrings_supp.h(77): warning C4005: '__on_failure' : macro redefinition (C:\Users\jabba\icpdashboard\no
de_modules\node-gyp\src\win_delay_load_hook.cc) [C:\Users\jabba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2896) : see previous definition of '__on_failure'
c:\program files\microsoft sdks\windows\v7.1\include\sal_supp.h(57): warning C4005: '__useHeader' : macro redefinition (..\src\hdf5.cc) [C:\Users\jabba\icpdash
board\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2886) : see previous definition of '__useHeader'
c:\program files\microsoft sdks\windows\v7.1\include\specstrings_supp.h(77): warning C4005: '__on_failure' : macro redefinition (..\src\hdf5.cc) [C:\Users\jabb
a\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2896) : see previous definition of '__on_failure'
c:\program files\microsoft sdks\windows\v7.1\include\sal_supp.h(57): warning C4005: '__useHeader' : macro redefinition (..\src\h5_file.cc) [C:\Users\jabba\icpd
ashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2886) : see previous definition of '__useHeader'
c:\program files\microsoft sdks\windows\v7.1\include\specstrings_supp.h(77): warning C4005: '__on_failure' : macro redefinition (..\src\h5_file.cc) [C:\Users\j
abba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2896) : see previous definition of '__on_failure'
c:\program files\microsoft sdks\windows\v7.1\include\sal_supp.h(57): warning C4005: '__useHeader' : macro redefinition (..\src\h5_group.cc) [C:\Users\jabba\icp
dashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2886) : see previous definition of '__useHeader'
c:\program files\microsoft sdks\windows\v7.1\include\specstrings_supp.h(77): warning C4005: '__on_failure' : macro redefinition (..\src\h5_group.cc) [C:\Users\
jabba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
          C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\include\sal.h(2896) : see previous definition of '__on_failure'
c:\users\jabba\icpdashboard\node_modules\hdf5\src\file.h(11): fatal error C1083: Cannot open include file: 'hdf5.h': No such file or directory (..\src\h5_file.
cc) [C:\Users\jabba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
c:\users\jabba\icpdashboard\node_modules\hdf5\src\file.h(11): fatal error C1083: Cannot open include file: 'hdf5.h': No such file or directory (..\src\hdf5.cc)
 [C:\Users\jabba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
c:\users\jabba\icpdashboard\node_modules\hdf5\src\file.h(11): fatal error C1083: Cannot open include file: 'hdf5.h': No such file or directory (..\src\h5_group
.cc) [C:\Users\jabba\icpdashboard\node_modules\hdf5\build\hdf5.vcxproj]
gyp ERR! build error
gyp ERR! stack Error: `C:\Program Files (x86)\MSBuild\14.0\bin\msbuild.exe` failed with exit code: 1
gyp ERR! stack     at ChildProcess.onExit (C:\Users\jabba\icpdashboard\node_modules\node-gyp\lib\build.js:276:23)
gyp ERR! stack     at emitTwo (events.js:106:13)
gyp ERR! stack     at ChildProcess.emit (events.js:191:7)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:204:12)
gyp ERR! System Windows_NT 6.1.7601
gyp ERR! command "C:\\Program Files\\nodejs\\node.exe" "C:\\Users\\jabba\\icpdashboard\\node_modules\\node-gyp\\bin\\node-gyp.js" "build" "--fallback-to-build"
"--module=C:\\Users\\jabba\\icpdashboard\\node_modules\\hdf5\\lib\\binding\\hdf5.node" "--module_name=hdf5" "--module_path=C:\\Users\\jabba\\icpdashboard\\node_
modules\\hdf5\\lib\\binding"
gyp ERR! cwd C:\Users\jabba\icpdashboard\node_modules\hdf5
gyp ERR! node -v v6.2.2
gyp ERR! node-gyp -v v3.4.0
gyp ERR! not ok
node-pre-gyp ERR! build error
node-pre-gyp ERR! stack Error: Failed to execute 'C:\Program Files\nodejs\node.exe C:\Users\jabba\icpdashboard\node_modules\node-gyp\bin\node-gyp.js build --fal
lback-to-build --module=C:\Users\jabba\icpdashboard\node_modules\hdf5\lib\binding\hdf5.node --module_name=hdf5 --module_path=C:\Users\jabba\icpdashboard\node_mo
dules\hdf5\lib\binding' (1)
node-pre-gyp ERR! stack     at ChildProcess.<anonymous> (C:\Users\jabba\icpdashboard\node_modules\hdf5\node_modules\node-pre-gyp\lib\util\compile.js:83:29)
node-pre-gyp ERR! stack     at emitTwo (events.js:106:13)
node-pre-gyp ERR! stack     at ChildProcess.emit (events.js:191:7)
node-pre-gyp ERR! stack     at maybeClose (internal/child_process.js:852:16)
node-pre-gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:215:5)
node-pre-gyp ERR! System Windows_NT 6.1.7601
node-pre-gyp ERR! command "C:\\Program Files\\nodejs\\node.exe" "C:\\Users\\jabba\\icpdashboard\\node_modules\\hdf5\\node_modules\\node-pre-gyp\\bin\\node-pre-g
yp" "install" "--fallback-to-build"
node-pre-gyp ERR! cwd C:\Users\jabba\icpdashboard\node_modules\hdf5
node-pre-gyp ERR! node -v v6.2.2
node-pre-gyp ERR! node-pre-gyp -v v0.6.11
node-pre-gyp ERR! not ok
Failed to execute 'C:\Program Files\nodejs\node.exe C:\Users\jabba\icpdashboard\node_modules\node-gyp\bin\node-gyp.js build --fallback-to-build --module=C:\User
s\jabba\icpdashboard\node_modules\hdf5\lib\binding\hdf5.node --module_name=hdf5 --module_path=C:\Users\jabba\icpdashboard\node_modules\hdf5\lib\binding' (1)
[email protected] C:\Users\jabba\icpdashboard
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
+-- [email protected]
`-- [email protected]

npm WARN optional Skipping failed optional dependency /chokidar/fsevents:
npm WARN notsup Not compatible with your operating system or architecture: [email protected]
npm WARN Failed to parse json
npm WARN Unexpected token '?' at 1:1
npm WARN ??t??♫►♂&?Z??}???K7?}???♂?+?[?P?J????;???1?i??V^?a???G►↕♦?{?X?u§?S`?i\??p?\l??u
npm WARN ^
npm WARN File: C:\Users\jabba\icpdashboard\node_modules\convert-source-map\package.json
npm WARN [email protected] license should be a valid SPDX license expression
npm ERR! Windows_NT 6.1.7601
npm ERR! argv "C:\\Program Files\\nodejs\\node.exe" "C:\\Program Files\\nodejs\\node_modules\\npm\\bin\\npm-cli.js" "install" "hdf5" "--fallback-to-build"
npm ERR! node v6.2.2
npm ERR! npm  v3.9.5
npm ERR! code ELIFECYCLE

npm ERR! [email protected] install: `node-pre-gyp install --fallback-to-build`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] install script 'node-pre-gyp install --fallback-to-build'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the hdf5 package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-pre-gyp install --fallback-to-build
npm ERR! You can get information on how to open an issue for this project with:
npm ERR!     npm bugs hdf5
npm ERR! Or if that isn't available, you can get their info via:
npm ERR!     npm owner ls hdf5
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     C:\Users\jabba\icpdashboard\npm-debug.log

const hdf5 = require('hdf5').hdf5;
const Access = require('hdf5/lib/globals').Access;

const file = new hdf5.File('rich_sparse_otu_table_hdf5.biom', Access.ACC_RDONLY);
console.log(file);
console.log(file.getNumAttrs());
file.refresh();

const hdf5        = require('hdf5').hdf5;
const file        = new hdf5.File('NEONDSTowerTemperatureData.hdf5', Access.ACC_RDONLY);
const members     = file.getMemberNames();
const firstMember = members[0];
const group       = file.openGroup(firstMember);

// not populated, so unable to retrieve group datasets
console.log(file.id);
console.log(group.id);

../src/h5_im.hpp:104:128: error: 'class v8::Local<v8::Object>' has no member named 'ToLocalChecked'
     v8::Local<v8::Object> buffer=node::Buffer::New(v8::Isolate::GetCurrent(), (char*)contentBuffer.get(), planes*width*height).ToLocalChecked();

/Volumes/Coruscant/project/routes/index.js:17
var dataset = h5lt.readDataset(group.id,'Events');
                   ^
SyntaxError: unsupported data type
    at SyntaxError (native)
    at Object.<anonymous> (/Volumes/Coruscant/project/routes/ind
ex.js:17:20)
    at Module._compile (module.js:556:32)
    at Object.Module._extensions..js (module.js:565:10)
    at Module.load (module.js:473:32)
    at tryModuleLoad (module.js:432:12)
    at Function.Module._load (module.js:424:3)
    at Module.require (module.js:483:17)
    at require (internal/module.js:20:19)
    at Object.<anonymous> (/Volumes/Coruscant/project/app.js:8:1
3)

HDF5 "file1.fast5" {
DATASET "/Analyses/Basecall_1D_001/BaseCalled_template/Events" {
   DATATYPE  H5T_COMPOUND {
      H5T_IEEE_F32LE "mean";
      H5T_IEEE_F32LE "stdv";
      H5T_IEEE_F32LE "start";
      H5T_IEEE_F32LE "length";
      H5T_STRING {
         STRSIZE 5;
         STRPAD H5T_STR_NULLPAD;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      } "model_state";
      H5T_STD_I32LE "move";
      H5T_IEEE_F32LE "weights";
      H5T_IEEE_F32LE "p_model_state";
      H5T_STRING {
         STRSIZE 5;
         STRPAD H5T_STR_NULLPAD;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      } "mp_state";
      H5T_IEEE_F32LE "p_mp_state";
      H5T_IEEE_F32LE "p_A";
      H5T_IEEE_F32LE "p_C";
      H5T_IEEE_F32LE "p_G";
      H5T_IEEE_F32LE "p_T";
   }
   DATASPACE  SIMPLE { ( 12771 ) / ( 12771 ) }
   DATA {
   (0): {
         137.778,
         0.528982,
         218.686,
         0.001,
         "CTGTT",
         1,
         0.0343166,
         0.262244,
         "CTGTT",
         0.262244,
         0.16503,
         0.079916,
         0.679372,
         0.075683
      },
   (1): {
         110.178,
         2.62537,
         218.687,
         0.001,
         "CTGTT",
         0,
         0.420341,
         0.0162997,
         "TATTT",
         0.219776,
         0.301549,
         0.0163437,
         0.0578457,
         0.624261
      },
   ...
   .... {hidden items} ....
   ...
(12770): {
         116.651,
         5.52655,
         234.834,
         0.001,
         "TTCGC",
         0,
         1,
         0.0477271,
         "TTTAA",
         0.080599,
         0.4063,
         0.25599,
         0.16818,
         0.16953
      }
   }
}
}

npm i hdf5 --hdf5_home_linux=/usr/lib/x86_64-linux-gnu/hdf5/serial

var express = require('express');
var hdf5 = require('hdf5').hdf5;
var router = express.Router();

var Access = require('hdf5/lib/globals').Access;
var file = new hdf5.File('filename.fast5', Access.ACC_RDONLY);
var group = file.openGroup('/Raw/Reads/Read_53');

./
├── README.md
├── app.js
├── bin
│   └── www
├── d3
│   ├── API.md
│   ├── CHANGES.md
│   ├── LICENSE
│   ├── README.md
│   ├── d3.js
│   └── d3.min.js
├── includes
│   ├── css
│   ├── data
│   └── js
├── index.html
├── node_modules
│   
|      .... 
│   ├── hdf5
|     ....
├── package.json
├── routes
│   ├── filename.fast5
│   ├── index.js
│   └── users.js
└── views
    ├── error.ejs
    └── index.ejs

╭─tayabsoomro
╰─$ npm start                                                                                                                                                1 ↵

> [email protected] start /Volumes/Coruscant/project
> node ./bin/www

HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0:
  #000: H5F.c line 586 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 1236 in H5F_open(): unable to open file: time = Fri Aug 25 10:06:39 2017
, name = 'filename.fast5', tent_flags = 0
    major: File accessibilty
    minor: Unable to open file
  #002: H5FD.c line 809 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #003: H5FDsec2.c line 346 in H5FD_sec2_open(): unable to open file: name = 'filename.fast5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
    major: File accessibilty
    minor: Unable to open file
/Volumes/Coruscant/project/routes/index.js:6
var file = new hdf5.File('filename.fast5', Access.ACC_RDONLY);
           ^

TypeError: Failed to open file, filename.fast5 and flags 0 with return: -1.

    at TypeError (native)
    at Object.<anonymous> (/Volumes/Coruscant/project/routes/index.js:6:12)
    at Module._compile (module.js:556:32)
    at Object.Module._extensions..js (module.js:565:10)
    at Module.load (module.js:473:32)
    at tryModuleLoad (module.js:432:12)
    at Function.Module._load (module.js:424:3)
    at Module.require (module.js:483:17)
    at require (internal/module.js:20:19)
    at Object.<anonymous> (/Volumes/Coruscant/project/app.js:8:13)
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] start: `node ./bin/www`
npm ERR! Exit status 1

'conditions': [
              [ 'OS=="mac"', {
                "xcode_settings": {
                    'OTHER_CPLUSPLUSFLAGS' : ['-std=c++1y','-stdlib=libc++'],
                    'OTHER_LDFLAGS': ['-stdlib=libc++'],
                    'MACOSX_DEPLOYMENT_TARGET': '10.7'
                }
              }]
            ],

gyp info spawn args [ 'BUILDTYPE=Release', '-C', 'build' ]
  CXX(target) Release/obj.target/h5im/src/h5im.o
In file included from ../src/h5im.cc:2:
In file included from ../src/file.h:14:
../src/attributes.hpp:39:13: error: no matching function for call to 'H5Aiterate2'
            H5Aiterate(group->id,H5_INDEX_NAME, H5_ITER_INC, &index, [&](hid_t loc, const char* attr_name, const H5...
            ^~~~~~~~~~
/usr/local/include/H5version.h:169:20: note: expanded from macro 'H5Aiterate'
#define H5Aiterate H5Aiterate2
                   ^~~~~~~~~~~
/usr/local/include/H5Apublic.h:74:16: note: candidate function not viable: no known conversion from '<lambda at
      ../src/attributes.hpp:39:70>' to 'H5A_operator2_t'
      (aka 'herr_t (*)(hid_t, const char *, const H5A_info_t *, void *)') for 5th argument
H5_DLL herr_t  H5Aiterate2(hid_t loc_id, H5_index_t idx_type,
               ^
1 error generated.
make: *** [Release/obj.target/h5im/src/h5im.o] Error 1

'use strict';
const h5 = require('hdf5');
const h5var = require('hdf5/lib/globals');

var file = new h5.hdf5.File('./test.h5', h5var.Access.ACC_TRUNC);
//file id is 72057594037927940
var gp = file.createGroup('test');
//group id is 144115188075855870

var buf = Buffer.alloc(8*10*8,0);
buf.rank=2;
buf.rows=8;
buf.columns=10;
buf.type=H5Type.H5T_NATIVE_DOUBLE;

h5.h5lt.makeDataset(gp.id,'test',buf);

var hdf5 = require('hdf5').hdf5;
var h5lt = require('hdf5').h5lt;

var Access = require('hdf5/lib/globals').Access;
var file = new hdf5.File('inchies_1.h5');

var dataset = h5lt.readDataset(file.id, "inchies", {start: [0], stride: [2]});

h5lt.makeDataset(id, name, buffer , {dimensions: [2,2,2,2]});