Installing via conda

[olgabot]

Hi Paolo,
I'm trying to use your package on Mac OS X by manually installing the dependencies via conda. I realize this isn't exactly following your instructions but I wanted to try anyway :) If this works, then we can make a portable package that anyone on any OS can use, not just Ubuntu, since conda will handle the C/C++ dependencies for us.

I was able to install boost and Python and Graphviz. Here is the full log of my installation. The punchline is that when I try to make all, I get an error that seems to have to do with locating boost libraries:

(ExpressionMatrix2) ➜  Release git:(master) make all
Building file: ../src/CellSets.cpp
Invoking: GCC C++ Compiler
g++ -std=c++0x -I/usr/include/python3.5m -O3 -msse4.2 -Wall -Wconversion -c -fmessage-length=0 -fPIC -MMD -MP -MF"src/CellSets.d" -MT"src/CellSets.d" -o "src/CellSets.o" "../src/CellSets.cpp"
In file included from ../src/CellSets.cpp:1:
In file included from ../src/CellSets.hpp:5:
In file included from ../src/MemoryMappedVector.hpp:7:
../src/CZI_ASSERT.hpp:8:10: fatal error: 'boost/lexical_cast.hpp' file not found
#include <boost/lexical_cast.hpp>
         ^
1 error generated.
make: *** [src/CellSets.o] Error 1

Do you have any suggestions?
Thanks!
Olga

[olgabot]

Forgot to say: conda is an open source, cross-platform package manager that can be used for any language: Python, R, Ruby, Lua, Scala, Java, Javascript, C/ C++, FORTRAN

[paoloczi]

You need to install the boost libraries. The standard version for ubuntu is 1.58, but the code should not be too dependent on the precise version. Perhaps conda lets you do that easily? Otherwise there is some discussion on that here: https://stackoverflow.com/questions/104322/how-do-you-install-boost-on-macos However I suspect even after solving this you will bump into other portability issues. I know nothing about software development on Mac, but I will still try to help as much as I can. Another thought: the makefiles are created automatically by Eclipse, not ny me, and are specific to Linux and the gcc compiler. The top directory has Eclipse project files .project and .cproject. You could open them in Eclipse, and there should be a way to tell Eclipse to configure the project for your system. Paolo

…

On Fri, Jun 23, 2017 at 10:48 AM, Olga Botvinnik ***@***.***> wrote: Hi Paolo, I'm trying to use your package on Mac OS X by manually installing the dependencies via conda. I realize this isn't exactly following your instructions but I wanted to try anyway :) If this works, then we can make a portable package that anyone on any OS can use, not just Ubuntu, since conda will handle the C/C++ dependencies for us. I was able to install boost and Python and Graphviz. Here <https://gist.github.com/olgabot/f1a4d1b6966027bb646a6bb222658d31> is the full log of my installation. The punchline is that when I try to make all, I get an error that seems to have to do with locating boost libraries: (ExpressionMatrix2) ➜ Release git:(master) make all Building file: ../src/CellSets.cpp Invoking: GCC C++ Compiler g++ -std=c++0x -I/usr/include/python3.5m -O3 -msse4.2 -Wall -Wconversion -c -fmessage-length=0 -fPIC -MMD -MP -MF"src/CellSets.d" -MT"src/CellSets.d" -o "src/CellSets.o" "../src/CellSets.cpp" In file included from ../src/CellSets.cpp:1: In file included from ../src/CellSets.hpp:5: In file included from ../src/MemoryMappedVector.hpp:7: ../src/CZI_ASSERT.hpp:8:10: fatal error: 'boost/lexical_cast.hpp' file not found #include <boost/lexical_cast.hpp> ^ 1 error generated. make: *** [src/CellSets.o] Error 1 Do you have any suggestions? Thanks! Olga — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYNxTSXNypeot1aNjZSih64aJRmLvuNdks5sG_pZgaJpZM4OD28n> .

[paoloczi]

P. S. In other words, Eclipse should have capability similar to what you describe for conda, and my code is already setup with Eclipse. On Fri, Jun 23, 2017 at 10:57 AM, Paolo Carnevali <paolo@chanzuckerberg.com> wrote:

…

You need to install the boost libraries. The standard version for ubuntu is 1.58, but the code should not be too dependent on the precise version. Perhaps conda lets you do that easily? Otherwise there is some discussion on that here: https://stackoverflow.com/questions/104322/how-do-you- install-boost-on-macos However I suspect even after solving this you will bump into other portability issues. I know nothing about software development on Mac, but I will still try to help as much as I can. Another thought: the makefiles are created automatically by Eclipse, not ny me, and are specific to Linux and the gcc compiler. The top directory has Eclipse project files .project and .cproject. You could open them in Eclipse, and there should be a way to tell Eclipse to configure the project for your system. Paolo On Fri, Jun 23, 2017 at 10:48 AM, Olga Botvinnik ***@***.*** > wrote: > Hi Paolo, > I'm trying to use your package on Mac OS X by manually installing the > dependencies via conda. I realize this isn't exactly following your > instructions but I wanted to try anyway :) If this works, then we can make > a portable package that anyone on any OS can use, not just Ubuntu, since > conda will handle the C/C++ dependencies for us. > > I was able to install boost and Python and Graphviz. Here > <https://gist.github.com/olgabot/f1a4d1b6966027bb646a6bb222658d31> is > the full log of my installation. The punchline is that when I try to make > all, I get an error that seems to have to do with locating boost > libraries: > > (ExpressionMatrix2) ➜ Release git:(master) make all > Building file: ../src/CellSets.cpp > Invoking: GCC C++ Compiler > g++ -std=c++0x -I/usr/include/python3.5m -O3 -msse4.2 -Wall -Wconversion -c -fmessage-length=0 -fPIC -MMD -MP -MF"src/CellSets.d" -MT"src/CellSets.d" -o "src/CellSets.o" "../src/CellSets.cpp" > In file included from ../src/CellSets.cpp:1: > In file included from ../src/CellSets.hpp:5: > In file included from ../src/MemoryMappedVector.hpp:7: > ../src/CZI_ASSERT.hpp:8:10: fatal error: 'boost/lexical_cast.hpp' file not found > #include <boost/lexical_cast.hpp> > ^ > 1 error generated. > make: *** [src/CellSets.o] Error 1 > > Do you have any suggestions? > Thanks! > Olga > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#1>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AYNxTSXNypeot1aNjZSih64aJRmLvuNdks5sG_pZgaJpZM4OD28n> > . >

[paoloczi]

Perhaps conda can work with the Eclipse project files? On Fri, Jun 23, 2017 at 10:58 AM, Paolo Carnevali <paolo@chanzuckerberg.com> wrote:

…

P. S. In other words, Eclipse should have capability similar to what you describe for conda, and my code is already setup with Eclipse. On Fri, Jun 23, 2017 at 10:57 AM, Paolo Carnevali < ***@***.***> wrote: > You need to install the boost libraries. The standard version for ubuntu > is 1.58, but the code should not be too dependent on the precise version. > Perhaps conda lets you do that easily? Otherwise there is some discussion > on that here: > > https://stackoverflow.com/questions/104322/how-do-you-instal > l-boost-on-macos > > However I suspect even after solving this you will bump into other > portability issues. I know nothing about software development on Mac, but I > will still try to help as much as I can. > > Another thought: the makefiles are created automatically by Eclipse, not > ny me, and are specific to Linux and the gcc compiler. The top directory > has Eclipse project files .project and .cproject. You could open them in > Eclipse, and there should be a way to tell Eclipse to configure the project > for your system. > > Paolo > > On Fri, Jun 23, 2017 at 10:48 AM, Olga Botvinnik < > ***@***.***> wrote: > >> Hi Paolo, >> I'm trying to use your package on Mac OS X by manually installing the >> dependencies via conda. I realize this isn't exactly following your >> instructions but I wanted to try anyway :) If this works, then we can make >> a portable package that anyone on any OS can use, not just Ubuntu, since >> conda will handle the C/C++ dependencies for us. >> >> I was able to install boost and Python and Graphviz. Here >> <https://gist.github.com/olgabot/f1a4d1b6966027bb646a6bb222658d31> is >> the full log of my installation. The punchline is that when I try to make >> all, I get an error that seems to have to do with locating boost >> libraries: >> >> (ExpressionMatrix2) ➜ Release git:(master) make all >> Building file: ../src/CellSets.cpp >> Invoking: GCC C++ Compiler >> g++ -std=c++0x -I/usr/include/python3.5m -O3 -msse4.2 -Wall -Wconversion -c -fmessage-length=0 -fPIC -MMD -MP -MF"src/CellSets.d" -MT"src/CellSets.d" -o "src/CellSets.o" "../src/CellSets.cpp" >> In file included from ../src/CellSets.cpp:1: >> In file included from ../src/CellSets.hpp:5: >> In file included from ../src/MemoryMappedVector.hpp:7: >> ../src/CZI_ASSERT.hpp:8:10: fatal error: 'boost/lexical_cast.hpp' file not found >> #include <boost/lexical_cast.hpp> >> ^ >> 1 error generated. >> make: *** [src/CellSets.o] Error 1 >> >> Do you have any suggestions? >> Thanks! >> Olga >> >> — >> You are receiving this because you are subscribed to this thread. >> Reply to this email directly, view it on GitHub >> <#1>, or mute >> the thread >> <https://github.com/notifications/unsubscribe-auth/AYNxTSXNypeot1aNjZSih64aJRmLvuNdks5sG_pZgaJpZM4OD28n> >> . >> > >

[paoloczi]

We are not going to provide installation via conda, at least for now. A practical way to run under MacOS is using Docker.