Install problem #1
Comments
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Hi, I have not tested it on CentOS. I am wondering if you were able to compile Thanks, On Wed, Apr 6, 2016 at 8:47 PM, wqshi [email protected] wrote:
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Yes, you are right. I can't compile. Which gcc version is requied? Our machine is And the compile error: |
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I would recommend using a newer version of GCC (preferably GCC4.7 or newer) Thanks, On Thu, Apr 7, 2016 at 12:03 PM, wqshi [email protected] wrote:
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Thanks. Mahmoud. Wenqiang |
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Hi Mahmoud, We updated the gcc version. Now I sucessfully compiled the gkmsvm-1.3.tar.gz. But when I try to install the R package, it still gives me the similar error. One thing I notice is that the package seems to go to a wrong path to find the library. For instance, the first line of the error is: I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CalcWmML.cpp -o CalcWmML.o I don't know why all the paths are prefixed by 'I'. I guess this is the issue. The /homed/home/shi/packages/R-3.1.3/include actually exists. Thanks for your help. Wenqiang |
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Could you check if you can also compile the C++ code for the gkmSVM ver2.0 Thanks, On Thu, Apr 7, 2016 at 5:44 PM, wqshi [email protected] wrote:
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Yes. I can compile it. |
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Try installing using devtools. Then, use the install_github command to install gkmSVM directly from devtools::install_github("mghandi/gkmSVM") I hope this works. Otherwise, your other option would be to use the C++ Best, On Thu, Apr 7, 2016 at 6:12 PM, wqshi [email protected] wrote:
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Still the same error. I will use the C++ version. Thanks for the help. |
Dear Authors,
I'm trying to use gkmSVM package following the tutorial at http://www.beerlab.org/gkmsvm/gkmsvm-tutorial.htm. But I get some compile error when I try to do R CMD INSTALL gkmSVM.
Also I tried to use install.package command in R to install it, and get same error.
I'm working on CentOS 5.5. Does gkmSVM support it?
The following is the error information:
loire@deltaSVM~R CMD INSTALL gkmSVM
** libs
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CalcWmML.cpp -o CalcWmML.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CalcWmML.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CbinMMtable.cpp -o CbinMMtable.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CbinMMtable.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CbinMMtree.cpp -o CbinMMtree.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CbinMMtree.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CiDLPasses.cpp -o CiDLPasses.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CiDLPasses.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c Converter.cpp -o Converter.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [Converter.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CountKLmers.cpp -o CountKLmers.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CountKLmers.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CountKLmersGeneral.cpp -o CountKLmersGeneral.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CountKLmersGeneral.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c CountKLmersH.cpp -o CountKLmersH.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [CountKLmersH.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c EstimLogRatio.cpp -o EstimLogRatio.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [EstimLogRatio.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c GTree.cpp -o GTree.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [GTree.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c GTree2.cpp -o GTree2.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [GTree2.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c GTreeLeafData.cpp -o GTreeLeafData.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [GTreeLeafData.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c GTreeLeafData2.cpp -o GTreeLeafData2.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [GTreeLeafData2.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c KLmer.cpp -o KLmer.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [KLmer.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c LKTree.cpp -o LKTree.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [LKTree.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c LList.cpp -o LList.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [LList.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c LTree.cpp -o LTree.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [LTree.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c LTreeS.cpp -o LTreeS.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [LTreeS.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c LTreef.cpp -o LTreef.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [LTreef.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c MLEstimKLmers.cpp -o MLEstimKLmers.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [MLEstimKLmers.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c MLEstimKLmersLog.cpp -o MLEstimKLmersLog.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [MLEstimKLmersLog.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c RcppExports.cpp -o RcppExports.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [RcppExports.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c SVMtrain.cpp -o SVMtrain.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [SVMtrain.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c Sequence.cpp -o Sequence.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [Sequence.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c SequenceData.cpp -o SequenceData.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [SequenceData.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c SequenceNames.cpp -o SequenceNames.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [SequenceNames.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c gkmCommonLib.cpp -o gkmCommonLib.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [gkmCommonLib.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c gkmsvm_classify.cpp -o gkmsvm_classify.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [gkmsvm_classify.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c gkmsvm_kernel.cpp -o gkmsvm_kernel.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [gkmsvm_kernel.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c global.cpp -o global.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [global.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c mainGkmKernel.cpp -o mainGkmKernel.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [mainGkmKernel.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c mainSVMclassify.cpp -o mainSVMclassify.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [mainSVMclassify.o] Error 127 (ignored)
I/homed/home/shi/packages/R-3.1.3/include -DNDEBUG -I/usr/local/include -I"/shared2/RAW/shi/data/pakage/R-3.1.3/library/Rcpp/include" -c mainSVMtrain.cpp -o mainSVMtrain.o
/bin/sh: I/homed/home/shi/packages/R-3.1.3/include: No such file or directory
make: [mainSVMtrain.o] Error 127 (ignored)
-shared -L/usr/local/lib64 -o gkmSVM.so CalcWmML.o CbinMMtable.o CbinMMtree.o CiDLPasses.o Converter.o CountKLmers.o CountKLmersGeneral.o CountKLmersH.o EstimLogRatio.o GTree.o GTree2.o GTreeLeafData.o GTreeLeafData2.o KLmer.o LKTree.o LList.o LTree.o LTreeS.o LTreef.o MLEstimKLmers.o MLEstimKLmersLog.o RcppExports.o SVMtrain.o Sequence.o SequenceData.o SequenceNames.o gkmCommonLib.o gkmsvm_classify.o gkmsvm_kernel.o global.o mainGkmKernel.o mainSVMclassify.o mainSVMtrain.o
/bin/sh: line 2: -shared: command not found
make: *** [gkmSVM.so] Error 127
ERROR: compilation failed for package ?.kmSVM?
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