Open mmokrejs opened 8 years ago
Hi,
ILOG/IBM CPLEX is required - it's used internally to solve Quadratic and Linear Programming problem. It's a difficult dependency, which requires installing obtaining a license from IBM (free from academic usage).
It should be possible to port the code to use some open source solver, but I don't have time for this.
Also, if you decide to install CPLEX and continue compiling, you might want to change the custom include path to match your directories:
-I/usr/include/bamtools -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include -I/data/bio/alexeygritsenk/apps/ILOG/concert/include -I/usr/include/ncbi-tools++
Alexey
I learned by the hard way already. ;-)
https://www.mail-archive.com/gentoo-commits@lists.gentoo.org/msg184287.html
I wonder whether you would better include standard paths into the Makefile.config , everybody except you has to edit the file. ;-)
Also, would be nice if you provided the manual.tex converted into .pdf or .txt.
If you can provided an edited Makefile, I will merge it.
2016-02-11 22:18 GMT+01:00 mmokrejs notifications@github.com:
I learned by the hard way already. ;-)
https://www.mail-archive.com/gentoo-commits@lists.gentoo.org/msg184287.html
I wonder whether you would better include standard paths into the Makefile.config , everybody except you has to edit the file. ;-)
Also, would be nice if you provided the manual.tex converted into .pdf or .txt.
— Reply to this email directly or view it on GitHub https://github.com/AlexeyG/GRASS/issues/6#issuecomment-183063229.
Here it is, but while we are at it I think that:
CFLAGS = $(CFLAGS) -std=gnu++0x
CXX ?= g++
# C++ compiler
CCC = g++
# Compiler flags (you probably don't need to change anything here)
CCCFLAGS = -O2 -m64 -std=gnu++0x -Wall
# include directory
CCCINC = -I../Common/ -I/usr/include/bamtools
# library directory and libraries
CCCLIB = -lbamtools
# Extra flags. Used for compiling scaffoldOptimizer (it uses the NCBI C++ Toolkit and CPLEX API)
CCEFLAGS = -fPIC -fexceptions -fopenmp -DNDEBUG -DIL_STD
CCEINC = -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include -I/data/bio/alexeygritsenk/apps/ILOG/concert/include -I/usr/include/ncbi-tools++
CCELIB = -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert -lm -pthread
# Do not change anything below unless (you think) you know what you're doing.
MAKE = make
MD = mkdir
CDIR = ../Common
ODIR = obj
BDIR = ../bin
I updated the makefile with the changes you propose.
It does not seem so. Here is what I meant.
fix_Makefile_variablenames.patch.txt
Oh yes, I still need to install the CPLEX library anyway.
I was facing similar problem while integrating CPLEX with R, and installing the cplexAPI package, see https://cran.r-project.org/web/packages/cplexAPI/ there were few mistakes that I was doing, first of all, the problem arises because R does not know where IBM CPLEX is installed, so you have to manually change the file Makevars.win in the cplexAPI_1.3.3.tar.gz PKG_CPPFLAGS=-g -DR=1 -DUSE_R=1 -I"${CPLEX_STUDIO_DIR}\cplex\include" PKG_LIBS=-L"${CPLEX_STUDIO_LIB}" -lm -lcplex1261
two thing that you need to check is -L"${CPLEX_STUDIO_LIB}" is replaced by in my case, -L"C:/Program Files/IBM/ILOG/CPLEX_Studio1271/cplex/bin/x64_win64" (see bin/x64_win64) , replace $ too
second inside the folder x64_win64, look for cplex12**.dll file, this the file where -lcplex1261 is pointing to, here manually change -lcplex1261 to whatever your file name is (in my case it was cplex1271.dll, so I changed -lcplex1261 to -lcplex1271,
similarly ${CPLEX_STUDIO_DIR} must be replaced by C:/Program Files/IBM/ILOG/CPLEX_Studio1271 (in my case).
After this, follow the instruction given in https://www.r-bloggers.com/using-cplex-in-r-installing-cplexapi-in-windows-10/, essentially use the following command (from command lines) to repackage and install cplexAPI_1.3.3.tar.gz (make sure you have Rtools installed, and make sure environment variables have PATH pointing to installation files of R, essentially taking to R.exe and Rcmd.exe for the commands to run)
R CMD build --no-build-vignettes --no-manual --md5 C:\Users{computer name here}\Desktop\cplexAPI R CMD INSTALL --build --no-multiarch .\cplexAPI_1.3.3.tar.gz
Hi, I am trying to prepare a package for Gentoo Linux. The following error seems that you maybe use some IBM development CPLEX library? Any details whether it is required or not?