Commit 218dd1a7 authored by Kelvin Rodriguez's avatar Kelvin Rodriguez
Browse files

updated env and removed findlibc line

parent 8ee7386e

environment.yml

+116 −117
Original line number Diff line number Diff line 
name: isis

channels:

  - krodriguez

  - usgs-astrogeology

  - conda-forge

  - probcomp

  - anaconda

  - usgs-astrogeology

  - jlaura

  - krodriguez

  - conda-forge

  - defaults

dependencies:

  - ca-certificates=2017.08.26=h1d4fec5_0

  - dbus=1.10.20=0

  - future=0.16.0=py27_1

  - ca-certificates==2017.08.26=h1d4fec5_0

  - dbus==1.10.20=0

  - future==0.16.0=y27_1

  - gst-plugins-base=1.8.0=0

  - gstreamer=1.8.0=0

  - jsoncpp=1.8.3=h3a67955_0

  - libgcc=4.8.5=1

  - libgcc-ng=7.2.0=h7cc24e2_2

  - libgfortran=3.0=0

  - libstdcxx-ng=7.2.0=h7a57d05_2

  - libxcb=1.12=1

  - mysql=5.7.20=h55eaa98_0

  - ncurses=5.9=10

  - ninja=1.7.2=0

  - patchelf=0.9=hf79760b_2

  - pip=9.0.1=py27_1

  - gstreamer==1.8.0=0

  - jsoncpp==1.8.3=h3a67955_0

  - libgcc==4.8.5=1

  - libgcc-ng==7.2.0=h7cc24e2_2

  - libgfortran==3.0=0

  - libstdcxx-ng==7.2.0=h7a57d05_2

  - libxcb==1.12=1

  - mysql==5.7.20=h55eaa98_0

  - ncurses==5.9=10

  - ninja==1.7.2=0

  - patchelf==0.9=hf79760b_2

  - pip==9.0.1=py27_1

  - setuptools=38.5.1=py27_0

  - wheel=0.30.0=py27h2bc6bb2_1

  - xerces-c=3.1.4=0

  - xz=5.2.3=0

  - zlib=1.2.11=0

  - blas=1.1=openblas

  - boost=1.65.1=py27_0

  - boost-cpp=1.65.1=1

  - bzip2=1.0.6=1

  - cairo=1.14.6=4

  - certifi=2018.1.18=py27_0

  - cmake=3.9.1=0

  - cspice=66=0

  - curl=7.55.1=0

  - doxygen=1.8.14=0

  - eigen=3.3.3=0

  - embree=2.14.0=0

  - expat=2.2.5=0

  - ffmpeg=3.2.4=3

  - flann=1.8.4=0

  - fontconfig=2.12.1=4

  - freeglut=3.0.0=4

  - freetype=2.7=1

  - geos=3.5.1=1

  - geotiff=1.4.2=1

  - gettext=0.19.8.1=0

  - giflib=5.1.4=0

  - glib=2.51.4=0

  - gmp=6.1.2=0

  - gsl=2.2.1=blas_openblas_3

  - harfbuzz=1.3.4=2

  - hdf5=1.8.18=2

  - icu=58.2=0

  - jasper=1.900.1=1

  - jbig=2.1=0

  - jpeg=9b=2

  - krb5=1.14.2=0

  - lapack=3.6.1=1

  - libffi=3.2.1=3

  - libiconv=1.15=0

  - libpng=1.6.28=2

  - libssh2=1.8.0=2

  - libtiff=4.0.9=0

  - libuv=1.11.0=0

  - libwebp=0.5.2=7

  - libxml2=2.9.7=0

  - llvm-meta=5.0.0=0

  - llvmdev=5.0.0=default_1

  - m4=1.4.17=1

  - mesalib=17.2.0=0

  - metis=5.1.0=3

  - mpc=1.0.3=4

  - mpfr=3.1.5=0

  - mysql-connector-c=6.1.6=0

  - nanoflann=1.2.2=0

  - nn=1.86.0=2

  - numpy=1.13.3=py27_blas_openblas_200

  - openblas=0.2.19=2

  - opencv=3.2.0=np113py27_blas_openblas_203

  - openssl=1.0.2n=0

  - pcre=8.39=0

  - pixman=0.34.0=1

  - proj4=4.9.3=5

  - pthread-stubs=0.3=1

  - python=2.7.14=2

  - readline=6.2=0

  - rhash=1.3.4=0

  - six=1.11.0=py27_1

  - sqlite=3.13.0=1

  - suitesparse=4.5.4=blas_openblas_200

  - superlu=5.2.1=blas_openblas_201

  - tbb=4.4_20160526=1

  - tk=8.5.19=2

  - vtk=8.1.0=py27_mesalib_0

  - x264=20131217=3

  - xorg-kbproto=1.0.7=1

  - xorg-libx11=1.6.4=6

  - xorg-libxau=1.0.8=3

  - xorg-libxdmcp=1.1.2=3

  - xorg-libxrender=0.9.10=0

  - xorg-renderproto=0.11.1=1

  - xorg-xproto=7.0.31=6

  - bz2file=0.98=py27_0

  - cloog=0.18.0=0

  - gcc=4.8.5=7

  - isl=0.12.2=0

  - protobuf=2.6.1=py27_1

  - system=5.8=2

  - libprotobuf=2.6.1=0

  - bullet=2.86.1=0

  - ds9=7.5=0

  - gmm=5.0=0

  - jama=125=0

  - pcl=1.8.1=0

  - qhull=7.2.0=0

  - qt=5.7.1=0

  - qwt=6.1.3=0

  - tnt=126=0

  - xalan-c=1.11=0

  - wheel==0.30.0=py27h2bc6bb2_1

  - xerces-c==3.1.4=0

  - xz==5.2.3=0

  - zlib==1.2.11=0

  - blas==1.1=openblas

  - boost==1.65.1=py27_0

  - boost-cpp==1.65.1=1

  - bzip2==1.0.6=1

  - cairo==1.14.6=4

  - certifi==2018.1.18=py27_0

  - cmake==3.9.1=0

  - cspice==66=0

  - curl==7.55.1=0

  - doxygen==1.8.14=0

  - eigen==3.3.3=0

  - embree==2.14.0=0

  - expat==2.2.5=0

  - ffmpeg==3.2.4=3

  - flann==1.8.4=0

  - fontconfig==2.12.1=4

  - freeglut==3.0.0=4

  - freetype==2.7=1

  - geos==3.5.1=1

  - geotiff==1.4.2=1

  - gettext==0.19.8.1=0

  - giflib==5.1.4=0

  - glib==2.51.4=0

  - gmp==6.1.2=0

  - gsl==2.2.1=blas_openblas_3

  - harfbuzz==1.3.4=2

  - hdf5==1.8.18=2

  - icu==58.2=0

  - jasper==1.900.1=1

  - jbig==2.1=0

  - jpeg==9b=2

  - krb5==1.14.2=0

  - lapack==3.6.1=1

  - libffi==3.2.1=3

  - libiconv==1.15=0

  - libpng==1.6.28=2

  - libssh2==1.8.0=2

  - libtiff==4.0.9=0

  - libuv==1.11.0=0

  - libwebp==0.5.2=7

  - libxml2==2.9.7=0

  - llvm-meta==5.0.0=0

  - llvmdev==5.0.0=default_1

  - m4==1.4.17=1

  - mesalib==17.2.0=0

  - metis==5.1.0=3

  - mpc==1.0.3=4

  - mpfr==3.1.5=0

  - mysql-connector-c==6.1.6=0

  - nanoflann==1.2.2=0

  - nn==1.86.0=2

  - numpy==1.13.3=py27_blas_openblas_200

  - openblas==0.2.19=2

  - opencv==3.2.0=np113py27_blas_openblas_203

  - openssl==1.0.2n=0

  - pcre==8.39=0

  - pixman==0.34.0=1

  - proj4==4.9.3=5

  - pthread-stubs==0.3=1

  - python==2.7.14=2

  - readline==6.2=0

  - rhash==1.3.4=0

  - six==1.11.0=py27_1

  - sqlite==3.13.0=1

  - suitesparse==4.5.4=blas_openblas_200

  - superlu==5.2.1=blas_openblas_201

  - tbb==4.4_20160526=1

  - tk==8.5.19=2

  - vtk==8.1.0=py27_mesalib_0

  - x264==20131217=3

  - xorg-kbproto==1.0.7=1

  - xorg-libx11==1.6.4=6

  - xorg-libxau==1.0.8=3

  - xorg-libxdmcp==1.1.2=3

  - xorg-libxrender==0.9.10=0

  - xorg-renderproto==0.11.1=1

  - xorg-xproto==7.0.31=6

  - bz2file==0.98=py27_0

  - cloog==0.18.0=0

  - gcc==4.8.5=7

  - isl==0.12.2=0

  - protobuf==2.6.1=py27_1

  - system==5.8=2

  - libprotobuf==2.6.1=0

  - bullet==2.86.1=0

  - ds9==7.5=0

  - gmm==5.0=0

  - jama==125=0

  - pcl==1.8.1=0

  - qhull==7.2.0=0

  - qt==5.7.1=0

  - qwt==6.1.3=0

  - tnt==126=0

  - xalan-c==1.11=0

prefix: /scratch/anaconda3/envs/isis

isis/CMakeLists.txt

+0 −1
Original line number Diff line number Diff line
@@ -62,7 +62,6 @@ set(BUILD_SHARED_LIBS ON) 
# sometimes third parties do not set their rpaths correctly

set(thirdPartyCppFlags -Wall -std=c++11 -DISIS_LITTLE_ENDIAN=1 -fPIC -Wno-unused-parameter -Wno-overloaded-virtual  -Wl,-rpath,$ENV{CONDA_PREFIX}/lib)





# Specify user options that can be passed in with the initial CMake command.

option(isis3Data       "Directory containing Isis3Data"                 OFF )

option(isis3TestData   "Directory containing Isis3TestData"             OFF )

isis/cmake/FindAllDependencies.cmake

+11 −11
Original line number Diff line number Diff line
@@ -52,26 +52,26 @@ find_package(Qt5 COMPONENTS 
# For these, we pass in a version number, and use it in the path suffix

# This only applies to v007, and outside of the building, we should only expect standard installs

# The v007-specific installs are listed beside their find_package calls below:

find_package(Boost     1.59.0  REQUIRED) # "boost/boost${Boost_FIND_VERSION}/boost/"

find_package(Boost     1.59.0  REQUIRED)

find_package(Bullet    2.86    REQUIRED)

find_package(Cholmod   4.4.5   REQUIRED) # "SuiteSparse/SuiteSparse${Cholmod_FIND_VERSION}/SuiteSparse/"

find_package(Cholmod   4.4.5   REQUIRED)

find_package(CSPICE    65      REQUIRED)

find_package(Eigen             REQUIRED)

find_package(Embree    2.15.0  REQUIRED)

find_package(GeoTIFF   2       REQUIRED)

find_package(GMM       5.0     REQUIRED) # "/gmm/gmm-${GMM_FIND_VERSION}/gmm/"

find_package(GMM       5.0     REQUIRED)

find_package(GSL       19      REQUIRED)

find_package(HDF5      1.8.15  REQUIRED)

find_package(Jama      125     REQUIRED) # Jama version is 1.2.5, but v007 directory is "jama/jama125/"

find_package(Jama      125     REQUIRED)

find_package(NN                REQUIRED)

find_package(OpenCV    3.1.0   REQUIRED)

find_package(PCL       1.8     REQUIRED) # "pcl-${PCL_FIND_VERSION}"

find_package(Protobuf  2.6.1   REQUIRED) # "google-protobuf/protobuf${Protobuf_FIND_VERSION}/"

find_package(Qwt       6       REQUIRED) # "qwt${Qwt_FIND_VERSION}"

find_package(SuperLU   4.3     REQUIRED) # "superlu/superlu${SuperLU_FIND_VERSION}/superlu/"

find_package(TIFF      4.0.5   REQUIRED) # "tiff/tiff-${TIFF_FIND_VERSION}"

find_package(TNT       126     REQUIRED) # TNT version is 1.2.6, but v007 directory is "tnt/tnt126/"

find_package(XercesC   3.1.2   REQUIRED) # "xercesc/xercesc-${XercesC_FIND_VERSION}/"

find_package(PCL       1.8     REQUIRED)

find_package(Protobuf  2.6.1   REQUIRED)

find_package(Qwt       6       REQUIRED)

find_package(SuperLU   4.3     REQUIRED)

find_package(TIFF      4.0.5   REQUIRED)

find_package(TNT       126     REQUIRED)

find_package(XercesC   3.1.2   REQUIRED) 

find_package(X11       6       REQUIRED)

find_package(nanoflann         REQUIRED)

find_package(PNG               REQUIRED)

isis/cmake/FindBoost.cmake

+0 −8
Original line number Diff line number Diff line
@@ -136,11 +136,3 @@ find_library(BOOST_RANDOM_MT_LIBRARY 
find_library(BOOST_WSERIALIZATION_MT_LIBRARY

  NAMES boost_wserialization-mt boost_wserialization

)
 


find_library(PYTHON_LIBRARY

  NAMES python2 python2.7 python3

)



find_library(C_LIBRARY

  NAMES c

)

isis/cmake/RunMakeFileTest.cmake

+2 −2
Original line number Diff line number Diff line
@@ -49,8 +49,8 @@ function(run_app_makefile_test makefile inputFolder outputFolder truthFolder bin 
#   set(code "")

#   execute_process(COMMAND rm -rf ${outputFolder})

#   execute_process(COMMAND rm -f ${logFile})



  execute_process(COMMAND make test MODE=LOUD WORKING_DIRECTORY ${sourceFolder} OUTPUT_VARIABLE result)

  message("SOURCE FOLDER ${sourceFolder}")

  execute_process(COMMAND make test WORKING_DIRECTORY ${sourceFolder} OUTPUT_VARIABLE result)

  message("result: ${result}")

  if (result MATCHES "OK")

      set(failed "OFF")