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aggregate's Introduction

About the AnacondaRecipes/aggregate repository

The aggregate repository contains:

  • The global conda-build variant config file: conda_build_config.yaml (similar to the conda-forge-pinnings-feedstock)
  • A central list of all public maintained feedstocks:
    • most feedstocks are separate feedstock repositories:
      • They are referenced as git submodule with relative repository URL and their release branches: .gitmodules. (similar to conda-forge feedstocks repository)
      • The quality on the referenced release branches is ensured via Pull Requests and Automated builds. The latest commit can be checked out via: git submodule update --init --remote $feedstock-folder (--remote is important as the submodule pinning to a specific sha1 of the referenced repository is often not updated.)
    • some feedstocks are normal directories checked into aggregate: aggregate serves here as staging area for recipes that eventually need to be submitted to conda-forge or for recipes that we think conda-forge will have no interest in.

How to add new recipes to the aggregate repository

Unfortunately, because of the structure of this organization, where each recipe has its own repository, there is no way to submit a PR that adds a new recipe, because PRs can’t create repositories, only modify existing ones. If you’d like to submit a recipe for us to build and make available on the default channel, you can either:

  • Submit your recipe to conda-forge’s staged-recipes repository (https://github.com/conda-forge/staged-recipes). There are directions in the readme here. When your recipe is merged and has become a feedstock repository, file an issue on the AnacondaRecipes/aggregate repo and we can fork that feedstock repository and build it.
  • Add your recipe in a folder on the aggregate repository. This is generally something we’d like to avoid. It does not benefit from the automated CI building that conda-forge does. It also mixes up the git history for your recipe with everything else that happens to the aggregate repository. We’ll still consider recipes submitted this way, but please consider it a last resort.

How to change recipes on the aggregate repository

Most recipes in the aggregate repository are submodules - essentially links to other repositories. To submit changes to recipes, it is best to fork those other repositories, submit PRs to them, and then we’ll update the aggregate’s link to the changed recipe. We prefer PRs to be submitted to conda-forge recipes, because their automatic CI builds help us know that your changes don’t cause any unintended breakage. Once your changes are incorporated at conda-forge, file an issue on the AnacondaRecipes/aggregate repo and we’ll pull them into our recipe on AnacondaRecipes.

For the few recipes that exist as folders on the aggregate repo, clone the aggregate repo, and issue PRs against it directly.

How to build python + packages once a new version of Python arrives (on ppc)

CONDA_ADD_PIP_AS_PYTHON_DEPENDENCY=0 \
  conda-build $(cat python-order.txt | \
      sed '/^python-feedstock/,$!d' | \
      grep -v '# \[not ppc\]' | \
      sed 's/[[:space:]].*$//' | tr '\n' ' ') \
    -c local \
    -c https://repo.anaconda.com/pkgs/main \
    --skip-existing --error-overlinking 2>&1 | \
  tee -a ~/conda/python-3.7.0-all-build-out.log

aggregate's People

Contributors

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aggregate's Issues

pytorch 0.4.1 c++/cuda extensions missing torch library symbols

Hello,

I've been fumbling with my own pytorch extensions for the past few days using the latest pkgs/main distribution of pytorch. It appears as though pytorch's c++ extension mechanism has been broken with this version. To reproduce, place the following meta.yaml file into the test/cpp_extensions directory of the pytorch GitHub repo (I also checked out tags/v0.4.1):

package:
  name: torch_test_cpp_extension
  version: 0.0.0

source:
  path: .

requirements:
  host:
    - pytorch 0.4.1
    - python {{ python }}
    - numpy
  build:
    - {{ compiler('cxx') }}
  run:
    - {{ pin_compatible('pytorch', exact=True) }}

build:
  script: python setup.py install --single-version-externally-managed --record=record.txt

test:
  commands:
    - python -c "import torch; import torch_test_cpp_extension.cpp as cpp_extension"
    # for 0.4.0 there's no wrapper module: python -c "import torch; import torch_test_cpp_extension"

Building with conda 4.5.10 gives the following error:

+ python -c 'import torch; import torch_test_cpp_extension.cpp as cpp_extension'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /u/sdrobert/.pyenv/versions/miniconda3-latest/conda-bld/torch_test_cpp_extension_1534377734852/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.6/site-packages/torch_test_cpp_extension/cpp.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZN2at5ErrorC1ENS_14SourceLocationESs
Tests failed for torch_test_cpp_extension-0.0.0-ha8d69ae_0.tar.bz2 - moving package to /u/sdrobert/.pyenv/versions/miniconda3-latest/conda-bld/broken
WARNING:conda_build.build:Tests failed for torch_test_cpp_extension-0.0.0-ha8d69ae_0.tar.bz2 - moving package to /u/sdrobert/.pyenv/versions/miniconda3-latest/conda-bld/broken
removing: torch_test_cpp_extension-0.0.0-ha8d69ae_0.tar.bz2
TESTS FAILED: torch_test_cpp_extension-0.0.0-ha8d69ae_0.tar.bz2

Change the pytorch version to 0.4.0 (you have to check out tags/v0.4.0 for this) or use pytorch 0.4.1 from pytorch's channel and the recipe successfully finishes.

@jjhelmus In your latest commit (fc96334), you excluded the cpp_extensions tests directly. Am I right to assume that this issue is known to you lot?

Thanks for your time,
Sean

sanitizer libs in ctng-compilers have wrong pinning

Take the example of let's say: libasan . On each compiler major bump, it bumps it's soname, making it incompatible with older versions. Right now, if I build a conda package with -fsanitize=address and gcc 7.3.0 and by run_exports I get a dependency of libgcc-ng >=7.3.0 and libstdcxx-ng >=7.3.0 which, on installation, will bring in latest versions of libgcc-ng and libstdcxx-ng, thereby breaking my package.

One solution could be to split the sanitizer libs into a separate conda package and restrict it's pinning.

Add enaml recipe

A new version of enaml supporting Python 3 and Qt5 has been published and is now available on conda-forge. Could please pull it in aggregate ?

Too many default CXXFLAGS

Since ctng-compilers inherit @CXXFLAGS apparently from build-time of the recipe, activating these compilers sets a lot of flags by default:

-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona
-mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
-pipe -I${PREFIX}/include
-fdebug-prefix-map=\${SRC_DIR}=/usr/local/src/conda/\${PKG_NAME}-\${PKG_VERSION}
-fdebug-prefix-map=\${PREFIX}=/usr/local/src/conda-prefix

In particular, setting the -std flag seems like an unexpected default behavior for a compiler, to me. Are all of these flags set on purpose, and is there a negative consequence to setting any of these by default? I'm debugging a build issue on nodejs right now, and my first hunch is that it may have to do with the fact that it has two flags for -std: -std=c++17 -std=gnu++1y.

Update arrow-cpp and pyarrow to 0.10

Is there any plan to update the arrow packages to the latest 0.10 release available in conda-forge? Moving my code to conda-forge would mean also changing all the gcc tool-sets, boost library and other changes and general trouble. Thanks in advance.

Updating Tensorflow/Tensorboard

Looks like Tensorflow/Tensorboard 1.4.1 (in its various incarnations) is included here. However since then 1.5.1, 1.6.0, and 1.7.0 have been released. Also a 1.8.0 RC0 is already out. Would be great to get this updated. Admittedly that may be a fair amount of work.

Side note: Tensorflow 1.8.0 will require CUDA 8.0+ and cuDNN 6.0+.

License

Is it okay to pull the commits from feedstocks here to conda-forge with the same license?

Windows Build of Redis?

I see a redis feedstock has been added, it doesn't support Windows.

Windows would be nice :-)

Here are some options:

There is the MS project:

https://github.com/MicrosoftArchive/redis

but:

  • it doesn't look like it's been touched in a while (a year)
  • the build instructions require point and click in VS -- annoying! though there is probably a way to script that if someone knows about Windows building...

The good part is that it is stand-alone, so doesn't have to use any particular run time environment...

Though maybe just copying binaries is easier, there are some online here:

https://github.com/dmajkic/redis/downloads

Update atom recipe

The new version of the atom package is online on conda-forge. As this release fixes a serious bug in the sortedmap implementation it would be great to update the recipe.

Strange result of the activate script inside conda-build

When I added env|grep CFLAGS in build.sh of a conda recipe, the following lines were shown. Notice how the environment variables, e.g. SRC_DIR, PREFIX are not expanded. Is it intended to be like this?

CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/home/yfeng1/anaconda3/install/conda-bld/mpich2_1522277866058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/home/yfeng1/anaconda3/install/conda-bld/mpich2_1522277866058/work=/usr/local/src/conda/mpich2-1.4.1p1 -fdebug-prefix-map=/home/yfeng1/anaconda3/install/conda-bld/mpich2_1522277866058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/home/yfeng1/anaconda3/install/conda-bld/mpich2_1522277866058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe

Numpy-feedstock patch to get compiler package name

Packages that rely on Numpy's distutils compiler bindings need the same compiler (at least in name it seems) as the compiler used to build (and baked at build time into) Numpy. In the case of conda build compilers it is not clear how to get from this compiler name to the name of a conda package to install, and indeed is likely impossible at present. As a result it would be helpful if a function or similar were patched into Numpy that yielded the name of the conda compiler packages needed to allow distutils to work. This arose from trying to get ahead of time compilation in Numba to work cleanly. CC @mingwandroid

Update basemap to 1.1.0

Can you please update basemap in Anaconda3 to the latest version already available in conda-forge (1.1.0)?

It still shows 1.0.7 as the latest version of basemap via normal conda, which requires an older version of numpy (1.13.3). So, trying to install basemap with Anaconda3 5.2.0 wants to REMOVE latest anaconda3 package (5.2.0) completely, since 5.2.0 requires numpy=1.14.3.

I would greatly appreciate basemap being updated to the latest version available in conda-forge (1.1.0) as soon as possible!

Thank you!

linux Fortran and cmake

Sorry, found another missing file from conda compilers. This one isn't bothering me, so consider it purely FYI.

In package gfortran_linux-64, there looks to be neither omp_lib.mod nor omp_lib.h, thus cmake's newest OpenMP detection, which looks for either for Fortran, fails. The recipe below should trigger the fail. Curiously, I haven't had problems actually building threaded Fortran programs with the conda compilers (at least compile-time), and I've seen these headers in older conda gfortran, hence my hope that it's a simple file inclusion fix.

fortomp/build.sh

${BUILD_PREFIX}/bin/cmake \
    -H${SRC_DIR} \
    -Bbuild \
    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_Fortran_COMPILER=${GFORTRAN} \
    -DCMAKE_Fortran_FLAGS="${FFLAGS}"

fortomp/src/CMakeLists.txt

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
project(fortomp
        LANGUAGES Fortran)

find_package(OpenMP REQUIRED)

fortomp/meta.yaml

package:
    name: fortomp
    version: 0.1

source:
    path: ./src

build:
    number: 0  # [linux]

requirements:
    build:
        - cmake 3.11*
        - {{ compiler('fortran') }}  # OpenMP not found, as no omp_lib header or module
                                     # https://github.com/Kitware/CMake/blob/master/Modules/FindOpenMP.cmake#L55-L60

Add libXMU in core dependency tree (CDT)

Hello,

I am trying to build an internal package with the new conda-build 3 with Anaconda compilers. After a lot trial and error, and by reading this ticket, https://github.com/conda/conda-docs/issues/607, I realized I need to find all system RPMs on which my tool is depending on.

Well, after identifying one by one (each time involving a conda build followed by a symbol resolution failure) all the required X libraries, and adding the corresponding - {{ cdt{'name-of-centos6-rpm-found-on-google') }}, I am blocked at libXmu-devel`. I think you didn't package that one. I have no idea on how this black magic works.

While I am at it, is this the expected workflow to identify all the CDT dependencies? It seems very clunky to me... I like the fact that I will be able to compile anything outside CentOS 6 and making sure that my package still works on CentOS 6. That is important for us.

Include cc/c++ in compilers

It's very common for builds to use cc or c++ as the executables to call compilers by. Would be very useful to have these executables included in the compilers so that they work smoothly in these cases.

Add PDAL feedstock (and dependencies) to Anaconda

The PDAL package (along with it's dependencies) are available as conda-forge feedstocks. It would be fabulous if we could get these added to Anaconda as well. I'm not sure if you would like an issue for each individual package, or if a list will do.

Adding -headerpad_max_install_names to LDFLAGS on macOS

Wasn't able to tell if this was already happening. So this could be a non-issue.

Thought it would be nice if the macOS compiler activation scripts added -headerpad_max_install_names to LDFLAGS on macOS to effectively get the longest prefix allowable on macOS to start with. We currently use this in conda-forge's toolchain package. Thoughts on using it here as well?

Missing libquadmath.so

readelf -d $CONDA_PREFIX/lib/libgfortran.so.4.0.0 (from the libgfortran-ng-7.2.0-h9f7466a_2 package) shows one of its needed shared libraries is libquadmath.so.0. However, none of the packages I can find in the "defaults" channel provides this dynamic library.

When building a simple "hello world" FORTRAN application, I get the following error:

$ $CONDA_PREFIX/bin/x86_64-conda_cos6-linux-gnu-gfortran hello-world.f90 -o hello-world
$CONDA_PREFIX/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lquadmath

The contents of hello-world.f90:

program HelloWorld
print*,"Hello world"
end program

Missing recipe for libxcb-devel

pycairo-feedstock already depend on it, so I suppose the recipe is just not yet commit to the repo, and not filing a pull request.

FYI: Buidling pygobject with libffi.

Currently libffi installs the header to $CONDA_PREFIX/include. The cross compilation tools cannot find these headers. libffi shall perhaps be converted to cdt .

I ran into this issue while building pygobject with the cdt packages and pip install -- had to create a symlink to the header files in $CONDA_PREFIX/x86_64-conda_cos6-linux-gnu/sysroot/usr/include to proceed.

The pip install compiled pygobject package worked with the host platform's gtk-3 after setting

GIR_PATH=/usr/share/gir-1.0/
GI_TYPELIB_PATH=/usr/lib64/girepository-1.0/

This could be a way to get around the low gtk version currently provided by anaconda. xdot requires gtk3.

Set CPATH, LIBRARY_PATH pointing to PREFIX in [unix] compiler environments

Compiler environments set CPPFLAGS and LDFLAGS with the include and library directory keys pointing to conda environment directories. However, some simple and non-standard makefiles and build scripts might not take these variables into account, which breaks virtualization of the compiler environment. However, there is another way to supply conda environment locations to the compiler - thorugh CPATH and LIBRARY_PATH environment variables which will be respected by the compilers directly, without any mediating script.

I have already started implementing this idea for [win] since it was not aligned with [unix] compilers in their ability to "virtualize" build environment for a compiler: #86

pytorch 0.4.1 does not place a bound on nccl but fails for nccl >=2

As the recipe exists now, pytorch is built against nccl 1.3.5, and so at runtime, tries to load libnccl.so.1:

> curl -L -O https://repo.continuum.io/pkgs/main/linux-64/pytorch-0.4.1-py37ha74772b_0.tar.bz2
> tar -xvjf pytorch-0.4.1-py37ha74772b_0.tar.bz2
> ldd lib/python3.7/site-packages/torch/_C.cpython-37m-x86_64-linux-gnu.so 
/home/adamson/github/pytorchhh/lib/python3.7/site-packages/torch/lib/libcaffe2_gpu.so)
	linux-vdso.so.1 =>  (0x00007ffdeb39b000)
	libshm.so => /home/adamson/github/pytorchhh/lib/python3.7/site-packages/torch/lib/libshm.so (0x00007f549462b000)
	libcudart.so.9.0 => not found
	libnvToolsExt.so.1 => not found
	libcaffe2.so => /home/adamson/github/pytorchhh/lib/python3.7/site-packages/torch/lib/libcaffe2.so (0x00007f549328e000)
	libcaffe2_gpu.so => /home/adamson/github/pytorchhh/lib/python3.7/site-packages/torch/lib/libcaffe2_gpu.so (0x00007f547d8b3000)
	libnccl.so.1 => not found
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f547d69d000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f547d480000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f547d0f3000)
	/lib64/ld-linux-x86-64.so.2 (0x00005616c661e000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f547ceea000)
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f547cbe3000)
	libmkl_intel_lp64.so => not found
	libmkl_gnu_thread.so => not found
	libmkl_core.so => not found
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f547c960000)
	libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f547c751000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f547c54d000)
	libcusparse.so.9.0 => not found
	libmkl_intel_lp64.so => not found
	libmkl_gnu_thread.so => not found
	libmkl_core.so => not found
	libcudnn.so.7 => not found
	libcufft.so.9.0 => not found
	libcublas.so.9.0 => not found

However, the meta.yaml does not pin nccl to 1., so you get a dlopen failure if you have nccl 2 around. This is not an issue in public conda since nccl 2 isn't currently distributed on any of the Continuum-maintained repositories. However, if you do have nccl 2 available on a default channel, you will run into this issue. Would you be open to pinning the runtime version of nccl to 1. for pytorch? I'd be happy to make a PR for it.

Unable to launch applications from environemnt with spaces

macOS 10.13.1
Navigator 1.8.2

Steps to reproduce:
-create an environment with a space in the name from terminal

from within navigator launch an application from the environment

screen shot 2018-03-27 at 8 41 10 pm

Actual Result:
The application does not launch

see an example error for jupyter notebook:

/Users/sarmadriaz/anaconda2/envs/sar\ mad/bin/jupyter_mac.command ; exit;
Sarmads-MacBook-Pro:~ sarmadriaz$ /Users/sarmadriaz/anaconda2/envs/sar\ mad/bin/jupyter_mac.command ; exit;
usage: dirname path
/Users/sarmadriaz/anaconda2/envs/sar mad/bin/jupyter_mac.command: line 3: /jupyter-notebook: No such file or directory
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
Deleting expired sessions...4405 completed.

[Process completed]

Tricky to use fiona from defaults

I can't seem to import fiona from defaults (unless I constrain the version of poppler), whereas I can from conda-forge (as long as I make sure gdal is also from conda-forge).

defaults

$ conda create -n popplertest python=3.6
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/popplertest

  added / updated specs: 
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2018.4.16          |           py36_0         142 KB

The following NEW packages will be INSTALLED:

    ca-certificates: 2018.03.07-0           
    certifi:         2018.4.16-py36_0       
    libedit:         3.1.20170329-h6b74fdf_2
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       7.2.0-hdf63c60_3       
    libstdcxx-ng:    7.2.0-hdf63c60_3       
    ncurses:         6.1-hf484d3e_0         
    openssl:         1.0.2o-h20670df_0      
    pip:             10.0.1-py36_0          
    python:          3.6.5-hc3d631a_2       
    readline:        7.0-ha6073c6_4         
    setuptools:      39.1.0-py36_0          
    sqlite:          3.23.1-he433501_0      
    tk:              8.6.7-hc745277_3       
    wheel:           0.31.1-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-ha838bed_2      

Proceed ([y]/n)? y


Downloading and Extracting Packages
certifi-2018.4.16    |  142 KB | : 100% 1.0/1 [00:00<00:00,  8.16it/s]               
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate popplertest
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate popplertest
(popplertest)$ conda install poppler fiona
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/popplertest

  added / updated specs: 
    - fiona
    - poppler


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    poppler-data-0.4.9         |                0         3.5 MB
    click-plugins-1.0.3        |           py36_0           9 KB
    cligj-0.4.0                |           py36_0          14 KB
    ------------------------------------------------------------
                                           Total:         3.6 MB

The following NEW packages will be INSTALLED:

    blas:           1.0-mkl              
    bzip2:          1.0.6-h14c3975_5     
    cairo:          1.14.12-h8948797_3   
    click:          6.7-py36h5253387_0   
    click-plugins:  1.0.3-py36_0         
    cligj:          0.4.0-py36_0         
    curl:           7.60.0-h84994c4_0    
    expat:          2.2.5-he0dffb1_0     
    fiona:          1.7.10-py36h48a52f0_0
    fontconfig:     2.13.0-h9420a91_0    
    freetype:       2.9.1-h8a8886c_0     
    freexl:         1.0.5-h14c3975_0     
    gdal:           2.2.2-py36hc209d97_1 
    geos:           3.6.2-heeff764_2     
    giflib:         5.1.4-h26a3ec6_1     
    glib:           2.56.1-h000015b_0    
    hdf4:           4.2.13-h3ca952b_2    
    hdf5:           1.10.1-h9caa474_1    
    icu:            58.2-h9c2bf20_1      
    intel-openmp:   2018.0.0-8           
    jpeg:           9b-h024ee3a_2        
    json-c:         0.12.1-ha6a3662_2    
    kealib:         1.4.7-h79811e5_5     
    krb5:           1.16-h3f6afd0_6      
    libboost:       1.65.1-habcd387_4    
    libcurl:        7.60.0-h1ad7b7a_0    
    libdap4:        3.19.0-h5bd89bb_2    
    libgdal:        2.2.2-h804cdde_1     
    libgfortran-ng: 7.2.0-hdf63c60_3     
    libkml:         1.3.0-h9d32c78_3     
    libnetcdf:      4.4.1.1-h816af47_8   
    libpng:         1.6.34-hb9fc6fc_0    
    libpq:          10.3-h1ad7b7a_0      
    libspatialite:  4.3.0a-h72746d6_18   
    libssh2:        1.8.0-h9cfc8f7_4     
    libtiff:        4.0.9-he85c1e1_1     
    libuuid:        1.0.3-h1bed415_2     
    libxcb:         1.13-h1bed415_1      
    libxml2:        2.9.8-h26e45fe_1     
    mkl:            2018.0.2-1           
    mkl_fft:        1.0.1-py36h3010b51_0 
    mkl_random:     1.0.1-py36h629b387_0 
    munch:          2.3.2-py36_0         
    numpy:          1.14.3-py36hcd700cb_1
    numpy-base:     1.14.3-py36h9be14a7_1
    openjpeg:       2.3.0-h05c96fa_1     
    pcre:           8.42-h439df22_0      
    pixman:         0.34.0-hceecf20_3    
    poppler:        0.65.0-h581218d_1    
    poppler-data:   0.4.9-0              
    proj4:          4.9.3-hc8507d1_7     
    shapely:        1.6.4-py36h0c48222_0 
    six:            1.11.0-py36h372c433_1
    xerces-c:       3.2.1-hac72e42_0     

Proceed ([y]/n)? y


Downloading and Extracting Packages
poppler-data-0.4.9   |  3.5 MB | : 100% 1.0/1 [00:00<00:00,  1.06it/s]               
click-plugins-1.0.3  |    9 KB | : 100% 1.0/1 [00:00<00:00, 31.51it/s]
cligj-0.4.0          |   14 KB | : 100% 1.0/1 [00:00<00:00, 26.03it/s]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(popplertest)$ python -c "import fiona"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/cio/mc3/envs/popplertest/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/cio/mc3/envs/popplertest/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: libpoppler.so.71: cannot open shared object file: No such file or directory
(popplertest)$ ls -l /cio/mc3/envs/popplertest/lib/*poppler*
lrwxrwxrwx 1 ceball ceball      23 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-cpp.so -> libpoppler-cpp.so.0.5.0
lrwxrwxrwx 1 ceball ceball      23 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-cpp.so.0 -> libpoppler-cpp.so.0.5.0
-rwxrwxr-x 2 ceball ceball  123312 May 25 16:17 /cio/mc3/envs/popplertest/lib/libpoppler-cpp.so.0.5.0
lrwxrwxrwx 1 ceball ceball      24 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-glib.so -> libpoppler-glib.so.8.9.0
lrwxrwxrwx 1 ceball ceball      24 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-glib.so.8 -> libpoppler-glib.so.8.9.0
-rwxrwxr-x 2 ceball ceball  488400 May 25 16:17 /cio/mc3/envs/popplertest/lib/libpoppler-glib.so.8.9.0
lrwxrwxrwx 1 ceball ceball      20 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler.so -> libpoppler.so.76.0.0
lrwxrwxrwx 1 ceball ceball      20 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler.so.76 -> libpoppler.so.76.0.0
-rwxrwxr-x 1 ceball ceball 3056976 May 28 15:38 /cio/mc3/envs/popplertest/lib/libpoppler.so.76.0.0
(popplertest)$ conda deactivate

If I install an older version of poppler, things seem to be ok:

(popplertest)$ conda install "poppler<=0.60.1"
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/popplertest

  added / updated specs:
    - poppler[version='<=0.60.1']


The following packages will be DOWNGRADED:

    cairo:      1.14.12-h8948797_3 --> 1.14.12-h77bcde2_0
    fontconfig: 2.13.0-h9420a91_0  --> 2.12.6-h49f89f6_0
    freetype:   2.9.1-h8a8886c_0   --> 2.8-hab7d2ae_1
    glib:       2.56.1-h000015b_0  --> 2.53.6-h5d9569c_2
    poppler:    0.65.0-h581218d_1  --> 0.60.1-hc909a00_0

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(popplertest)$ python -c "import fiona"
(popplertest)$

conda-forge

$ conda create -c conda-forge -n cfpopplertest python=3.6
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest

  added / updated specs: 
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2018.4.16          |           py36_0         142 KB  conda-forge

The following NEW packages will be INSTALLED:

    ca-certificates: 2018.4.16-0       conda-forge
    certifi:         2018.4.16-py36_0  conda-forge
    libgcc-ng:       7.2.0-hdf63c60_3             
    ncurses:         5.9-10            conda-forge
    openssl:         1.0.2o-0          conda-forge
    pip:             9.0.3-py36_0      conda-forge
    python:          3.6.5-1           conda-forge
    readline:        7.0-0             conda-forge
    setuptools:      39.2.0-py36_0     conda-forge
    sqlite:          3.20.1-2          conda-forge
    tk:              8.6.7-0           conda-forge
    wheel:           0.31.0-py36_0     conda-forge
    xz:              5.2.3-0           conda-forge
    zlib:            1.2.11-h470a237_2 conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
certifi-2018.4.16    |  142 KB | : 100% 1.0/1 [00:01<00:00,  1.25s/it]               
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate cfpopplertest
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate cfpopplertest
(cfpopplertest)$ conda install -c conda-forge poppler fiona gdal
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest

  added / updated specs: 
    - fiona
    - gdal
    - poppler


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cligj-0.4.0                |           py36_0          12 KB  conda-forge
    poppler-data-0.4.9         |                0         3.5 MB  conda-forge
    click-plugins-1.0.3        |           py36_0           7 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.6 MB

The following NEW packages will be INSTALLED:

    boost:          1.66.0-py36_1         conda-forge
    boost-cpp:      1.66.0-1              conda-forge
    bzip2:          1.0.6-1               conda-forge
    cairo:          1.14.10-0             conda-forge
    click:          6.7-py_1              conda-forge
    click-plugins:  1.0.3-py36_0          conda-forge
    cligj:          0.4.0-py36_0          conda-forge
    curl:           7.60.0-0              conda-forge
    expat:          2.2.5-0               conda-forge
    fiona:          1.7.11-py36_3         conda-forge
    fontconfig:     2.12.6-0              conda-forge
    freetype:       2.8.1-0               conda-forge
    freexl:         1.0.5-0               conda-forge
    gdal:           2.2.4-py36_0          conda-forge
    geos:           3.6.2-1               conda-forge
    geotiff:        1.4.2-1               conda-forge
    gettext:        0.19.8.1-0            conda-forge
    giflib:         5.1.4-0               conda-forge
    glib:           2.55.0-0              conda-forge
    hdf4:           4.2.13-0              conda-forge
    hdf5:           1.10.1-2              conda-forge
    icu:            58.2-0                conda-forge
    jpeg:           9b-2                  conda-forge
    json-c:         0.12.1-0              conda-forge
    kealib:         1.4.7-4               conda-forge
    krb5:           1.14.6-0              conda-forge
    libdap4:        3.18.3-2              conda-forge
    libffi:         3.2.1-3               conda-forge
    libgdal:        2.2.4-2               conda-forge
    libgfortran:    3.0.0-1                          
    libgfortran-ng: 7.2.0-hdf63c60_3                 
    libiconv:       1.15-0                conda-forge
    libkml:         1.3.0-6               conda-forge
    libnetcdf:      4.6.1-2               conda-forge
    libopenblas:    0.2.20-h9ac9557_4                
    libpng:         1.6.34-0              conda-forge
    libpq:          9.6.3-0               conda-forge
    libspatialite:  4.3.0a-19             conda-forge
    libssh2:        1.8.0-2               conda-forge
    libtiff:        4.0.9-0               conda-forge
    libxml2:        2.9.8-0               conda-forge
    munch:          2.3.2-py_0            conda-forge
    numpy:          1.14.3-py36h28100ab_1            
    numpy-base:     1.14.3-py36h0ea5e3f_1            
    openjpeg:       2.3.0-2               conda-forge
    pcre:           8.41-1                conda-forge
    pixman:         0.34.0-2              conda-forge
    poppler:        0.61.1-3              conda-forge
    poppler-data:   0.4.9-0               conda-forge
    proj4:          4.9.3-5               conda-forge
    shapely:        1.6.4-py36_0          conda-forge
    six:            1.11.0-py36_1         conda-forge
    util-linux:     2.21-0                           
    xerces-c:       3.2.0-0               conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
cligj-0.4.0          |   12 KB | : 100% 1.0/1 [00:00<00:00,  1.14it/s] 
poppler-data-0.4.9   |  3.5 MB | : 100% 1.0/1 [00:02<00:00,  2.38s/it]               
click-plugins-1.0.3  |    7 KB | : 100% 1.0/1 [00:00<00:00,  1.81it/s] 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(cfpopplertest)$ python -c "import fiona"
(cfpopplertest)$

If I don't specify gdal, it ends up coming from defaults, so same problem:

$ conda create -c conda-forge -n cfpopplertest2 python=3.6
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest2

  added / updated specs: 
    - python=3.6


The following NEW packages will be INSTALLED:

    ca-certificates: 2018.4.16-0       conda-forge
    certifi:         2018.4.16-py36_0  conda-forge
    libgcc-ng:       7.2.0-hdf63c60_3             
    ncurses:         5.9-10            conda-forge
    openssl:         1.0.2o-0          conda-forge
    pip:             9.0.3-py36_0      conda-forge
    python:          3.6.5-1           conda-forge
    readline:        7.0-0             conda-forge
    setuptools:      39.2.0-py36_0     conda-forge
    sqlite:          3.20.1-2          conda-forge
    tk:              8.6.7-0           conda-forge
    wheel:           0.31.0-py36_0     conda-forge
    xz:              5.2.3-0           conda-forge
    zlib:            1.2.11-h470a237_2 conda-forge

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate cfpopplertest2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate cfpopplertest2
(cfpopplertest2)$ conda install -c conda-forge poppler fiona
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest2

  added / updated specs: 
    - fiona
    - poppler


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    xerces-c-3.2.1             |                0         3.9 MB  conda-forge

The following NEW packages will be INSTALLED:

    boost:          1.66.0-py36_1         conda-forge
    boost-cpp:      1.66.0-1              conda-forge
    bzip2:          1.0.6-1               conda-forge
    cairo:          1.14.10-0             conda-forge
    click:          6.7-py_1              conda-forge
    click-plugins:  1.0.3-py36_0          conda-forge
    cligj:          0.4.0-py36_0          conda-forge
    curl:           7.60.0-0              conda-forge
    expat:          2.2.5-0               conda-forge
    fiona:          1.7.11-py36_3         conda-forge
    fontconfig:     2.12.6-0              conda-forge
    freetype:       2.8.1-0               conda-forge
    freexl:         1.0.5-0               conda-forge
    gdal:           2.2.2-py36hc209d97_1             
    geos:           3.6.2-1               conda-forge
    gettext:        0.19.8.1-0            conda-forge
    giflib:         5.1.4-0               conda-forge
    glib:           2.55.0-0              conda-forge
    hdf4:           4.2.13-0              conda-forge
    hdf5:           1.10.1-2              conda-forge
    icu:            58.2-0                conda-forge
    jpeg:           9b-2                  conda-forge
    json-c:         0.12.1-0              conda-forge
    kealib:         1.4.7-4               conda-forge
    krb5:           1.14.6-0              conda-forge
    libdap4:        3.19.2-1              conda-forge
    libffi:         3.2.1-3               conda-forge
    libgdal:        2.2.2-h804cdde_1                 
    libgfortran:    3.0.0-1                          
    libgfortran-ng: 7.2.0-hdf63c60_3                 
    libiconv:       1.15-0                conda-forge
    libkml:         1.3.0-6               conda-forge
    libnetcdf:      4.4.1.1-10            conda-forge
    libopenblas:    0.2.20-h9ac9557_4                
    libpng:         1.6.34-0              conda-forge
    libpq:          9.6.6-h4e02ad2_0                 
    libspatialite:  4.3.0a-19             conda-forge
    libssh2:        1.8.0-2               conda-forge
    libstdcxx-ng:   7.2.0-hdf63c60_3                 
    libtiff:        4.0.9-0               conda-forge
    libxml2:        2.9.8-0               conda-forge
    munch:          2.3.2-py_0            conda-forge
    numpy:          1.14.3-py36h28100ab_1            
    numpy-base:     1.14.3-py36h0ea5e3f_1            
    openjpeg:       2.3.0-2               conda-forge
    pcre:           8.41-1                conda-forge
    pixman:         0.34.0-2              conda-forge
    poppler:        0.64.0-0              conda-forge
    poppler-data:   0.4.9-0               conda-forge
    proj4:          4.9.3-5               conda-forge
    shapely:        1.6.4-py36_0          conda-forge
    six:            1.11.0-py36_1         conda-forge
    util-linux:     2.21-0                           
    xerces-c:       3.2.1-0               conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
xerces-c-3.2.1       |  3.9 MB | : 100% 1.0/1 [00:26<00:00, 26.17s/it]              
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(cfpopplertest2)$ python -c "import fiona"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/cio/mc3/envs/cfpopplertest2/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/cio/mc3/envs/cfpopplertest2/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: libpoppler.so.71: cannot open shared object file: No such file or directory

conda info:


     active environment : popplertest
    active env location : /cio/mc3/envs/popplertest
            shell level : 1
       user config file : /home/ceball/.condarc
 populated config files :
          conda version : 4.5.4
    conda-build version : 3.10.1
         python version : 3.6.4.final.0
       base environment : /cio/mc3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /cio/mc3/pkgs
                          /home/ceball/.conda/pkgs
       envs directories : /cio/mc3/envs
                          /home/ceball/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.4 Linux/3.16.0-4-amd64 debian/8 glibc/2.19
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

building llvm compilers on mac

I'm attempting to build the clang toolchain in an effort to add omp.h (at @msarahan's advice). A couple issues so far:

  1. I had to change the hash for the main llvm download as below. There's some support for the new hash at here, but I'm worried that I'm building from different source than the recipe is expecting
-{% set clang_llvm_bin_sha256 = '5ef4f1f72d0fe4cf03d8eaefb972b4d24219da67124a869ae75e3a6aeb1578f6' %}
+#{% set clang_llvm_bin_sha256 = '5ef4f1f72d0fe4cf03d8eaefb972b4d24219da67124a869ae75e3a6aeb1578f6' %}
+{% set clang_llvm_bin_sha256 = '5f697801a46239c04251730b7ccccd3ebbacb9043ad381a061ae6812409e9eae' %}
  1. (the blocking problem) In a link line I get some unresolved symbols. Full cmake error log (~/toolchainconda/conda-bld/llvm-suite_1507343700837/work/llvm_tapi_build/CMakeFiles/CMakeError.log) is here. I'm not requesting any grand investigation, just wondering if this error rings any bells or even if my conda-build command (further below) is wrong. Thanks for any help!
/usr/bin/clang++ --sysroot /Users/loriab/linux/toolchainconda/conda-bld/llvm-suite_1507395752745/work/bootstrap/MacOSX10.9.sdk -std=c++11 -o ld src/ld/ld.o src/ld/Options.o src/ld/InputFiles.o src/ld/Snapshot.o src/ld/SymbolTable.o src/ld/Resolver.o src/ld/OutputFile.o src/ld/passes/branch_island.o src/ld/passes/branch_shim.o src/ld/passes/code_dedup.o src/ld/passes/compact_unwind.o src/ld/passes/dtrace_dof.o src/ld/passes/dylibs.o src/ld/passes/got.o src/ld/passes/huge.o src/ld/passes/objc.o src/ld/passes/order.o src/ld/passes/bitcode_bundle.o src/ld/passes/stubs/stubs.o src/ld/passes/tlvp.o src/ld/parsers/archive_file.o src/ld/parsers/lto_file.o src/ld/parsers/macho_dylib_file.o src/ld/parsers/macho_relocatable_file.o src/ld/parsers/opaque_section_file.o src/ld/parsers/textstub_dylib_file.o src/ld/debugline.o -L/Users/loriab/linux/toolchainconda/conda-bld/llvm-suite_1507395752745/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/Users/loriab/linux/toolchainconda/conda-bld/llvm-suite_1507395752745/work/prefix/lib -multiply_defined suppress -Wl,-rpath,@loader_path/../lib/ -L../libstuff -lstuff   -lpthread -lLTO -ltapi -lxar /usr/lib/libcrypto.dylib
Undefined symbols for architecture x86_64:
  "_UCNV_FROM_U_CALLBACK_STOP_58", referenced from:
      _openIcuConverter in libxar.a(encoding.o)
  "_UCNV_TO_U_CALLBACK_STOP_58", referenced from:
      _openIcuConverter in libxar.a(encoding.o)
  "_ucnv_close_58", referenced from:
      _xmlFindCharEncodingHandler in libxar.a(encoding.o)
      _openIcuConverter in libxar.a(encoding.o)
      _xmlCharEncCloseFunc in libxar.a(encoding.o)
  "_ucnv_convertEx_58", referenced from:
      _xmlCharEncFirstLineInt in libxar.a(encoding.o)
      _xmlCharEncFirstLineInput in libxar.a(encoding.o)
      _xmlCharEncInput in libxar.a(encoding.o)
      _xmlCharEncInFunc in libxar.a(encoding.o)
      _xmlCharEncOutput in libxar.a(encoding.o)
      _xmlCharEncOutFunc in libxar.a(encoding.o)
      _xmlByteConsumed in libxar.a(encoding.o)
      ...
  "_ucnv_open_58", referenced from:
      _openIcuConverter in libxar.a(encoding.o)
  "_ucnv_setFromUCallBack_58", referenced from:
      _openIcuConverter in libxar.a(encoding.o)
  "_ucnv_setToUCallBack_58", referenced from:
      _openIcuConverter in libxar.a(encoding.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [ld] Error 1

General conditions:

  • aggregate repo is at 3ee1782
  • OSX is 10.10 or 10.11 (tried on two computers)
  • conda vers
>>> conda list
...
conda                     4.3.27           py36hb556a21_0    defaults
conda-build               3.0.25           py36h1d84e97_0    defaults
conda-env                 2.6.0                         0    defaults
conda-verify              2.0.0            py36he837df3_0    defaults
  • build command:
(aggregate) >>> conda build llvm-compilers-feedstock -m llvm-compilers-feedstock/recipe/conda_build_config.macOS_10.9.yaml

include gcov in linux-64 toolchain

My thanks to the conda-build devs for the fantastic upgrade of compiler packages in particular and cb3 in general.

The only thing I've noticed to be missing is the gcov executable, though it looks (below) like the library and headers are present. If this wasn't deliberate, I'd petition for its eventual inclusion, as it'd be very handy for producing coverage reports from conda-builds.

(base) psilocaluser@bash:psinet:/home/psilocaluser/gits/aggregate: (master) find /home/psilocaluser/toolchainconda/pkgs/ -name "*gcov*"
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/include/gcov.h
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/plugin/include/gcov-counter.def
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/plugin/include/gcov-io.h
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/libgcov.a
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/share/man/man1/x86_64-conda_cos6-linux-gnu-gcov-dump.1
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/share/man/man1/x86_64-conda_cos6-linux-gnu-gcov-tool.1
/home/psilocaluser/toolchainconda/pkgs/gcc_impl_linux-64-7.2.0-habb00fd_3/share/man/man1/x86_64-conda_cos6-linux-gnu-gcov.1
/home/psilocaluser/toolchainconda/pkgs/qt-5.9.5-h7e424d6_0/mkspecs/features/gcov.prf
(base) psilocaluser@bash:psinet:/home/psilocaluser/gits/aggregate: (master) find /home/psilocaluser/toolchainconda/pkgs/ -name "*gprof*"
/home/psilocaluser/toolchainconda/pkgs/binutils_impl_linux-64-2.28.1-had2808c_3/share/info/gprof.info
/home/psilocaluser/toolchainconda/pkgs/binutils_impl_linux-64-2.28.1-had2808c_3/share/man/man1/x86_64-conda_cos6-linux-gnu-gprof.1
/home/psilocaluser/toolchainconda/pkgs/binutils_impl_linux-64-2.28.1-had2808c_3/bin/x86_64-conda_cos6-linux-gnu-gprof

Shipping `openmp` with `clang`

It appears that openmp does not ship with clang from defaults (particularly on macOS). In contrast, it does ship with gcc from defaults (particularly on Linux). It would be nice to have OpenMP enabled compilers ship by default on all OSes and have the OpenMP run time libraries automatically included as well (when using {{ compiler(...) }}).

libatomic.a static lib missing from ctng-compilers

$ find dev/ | grep libatomic
dev/x86_64-conda_cos6-linux-gnu/sysroot/lib/libatomic.so.1.2.0
dev/x86_64-conda_cos6-linux-gnu/sysroot/lib/libatomic.so
dev/x86_64-conda_cos6-linux-gnu/sysroot/lib/libatomic.so.1
dev/lib/libatomic.so.1.2.0
dev/lib/libatomic.so
dev/lib/libatomic.so.1

mkl_fft and mkl_random do not require cython once installed

The setup.py files for mkl_fft and mkl_random have cython in install_requires. This leads to cython being in the requires.txt file in the .egg-info directory for the installed package. For something following conda create -n test numpy && conda activate test, any operation using pip 10 warns when cython is not installed.

(py3) $ pip install --no-binary :all: django-twilio
Collecting django-twilio
  Downloading

... <TRUNCATED> ...

Skipping bdist_wheel for urllib3, due to binaries being disabled for it.
mkl-random 1.0.1 requires cython, which is not installed.
mkl-fft 1.0.0 requires cython, which is not installed.

The lines about mkl-random and mkl-fft are also printed to the terminal in red.

The easiest solution is to remove cython from install_requires in the setup.py file used to build the conda packages.

reference: https://github.com/IntelPython/mkl_fft/blob/v1.0.2/setup.py#L90
reference: https://github.com/IntelPython/mkl_random/blob/v1.0.1/setup.py#L80

Update dask and distributed libraries

These have been updated on conda-forge. It would be nice to have them in defaults as well (this is now blocking some docker work if I want to continue using the defaults channel).

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