在MacOS X上从源代码安装Kernlab时出错（延迟加载失败）

Question

我一直在尝试从源代码安装R包，Kernlab，但我一直在遇到问题。起初，我不得不gfortran相关的一些错误，所以我从网上下载http://r.research.att.com/tools/

的GNU C++编译器然后当我键入以下命令，R CMD INSTALL kernlab_0.9-12.tar.gz

我得到出现以下错误：

installing to /Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab/libs/x86_64 
** R 
** data 
** inst 
** preparing package for lazy loading 
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) : 
    the "superClass" list for class "list", includes an undefined class "input" 
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) : 
    the "superClass" list for class "numeric", includes an undefined class "output" 
Error : evaluation nested too deeply: infinite recursion/options(expressions=)? 
Error in setClassUnion("listI", c("list", "numeric", "vector", "integer", : 
    unable to create union class: could not set members "list", "numeric" 
Error : unable to load R code in package 'kernlab' 
ERROR: lazy loading failed for package ‘kernlab’ 
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’ 
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’ 

有没有人知道如何解决这个错误？ PS。对于我下载的GNU fortran编译器来说，它表示Xcode版本高达3.2.5;我有Xcode版本3.2.6。这是我的错误的来源，还是我看错了方向？

Answer 1

它必须与您的系统有关。在我的Linux系统中，kernlab_0.9-12精细安装：

edd@max:/tmp$ R CMD INSTALL kernlab_0.9-12.tar.gz 
* installing to library ‘/usr/local/lib/R/site-library’ 
* installing *source* package ‘kernlab’ ... 
** libs 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c brweight.cpp -o brweight.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c ctable.cpp -o ctable.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c cweight.cpp -o cweight.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dbreakpt.c -o dbreakpt.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dcauchy.c -o dcauchy.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpnrm.c -o dgpnrm.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpstep.c -o dgpstep.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprecond.c -o dprecond.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprsrch.c -o dprsrch.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dspcg.c -o dspcg.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtron.c -o dtron.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrpcg.c -o dtrpcg.o 
dtrpcg.c: In function ‘dtrpcg’: 
dtrpcg.c:157: warning: value computed is not used 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrqsol.c -o dtrqsol.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c esa.cpp -o esa.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c expdecayweight.cpp -o expdecayweight.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c inductionsort.cpp -o inductionsort.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c kspectrumweight.cpp -o kspectrumweight.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c lcp.cpp -o lcp.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c misc.c -o misc.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c msufsort.cpp -o msufsort.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c solvebqp.c -o solvebqp.o 
gcc-4.4 -I/usr/share/R/include  -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c stringk.c -o stringk.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c stringkernel.cpp -o stringkernel.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c svm.cpp -o svm.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c wkasailcp.cpp -o wkasailcp.o 
g++-4.4 -I/usr/share/R/include  -fpic -O3 -pipe -c wmsufsort.cpp -o wmsufsort.o 
g++ -shared -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR 
installing to /usr/local/lib/R/site-library/kernlab/libs 
** R 
** data 
** inst 
** preparing package for lazy loading 
Creating a new generic function for "terms" in "kernlab" 
Creating a new generic function for "fitted" in "kernlab" 
Creating a new generic function for "coef" in "kernlab" 
Creating a new generic function for "predict" in "kernlab" 
Creating a new generic function for "plot" in "kernlab" 
** help 
*** installing help indices 
** building package indices ... 
** testing if installed package can be loaded 

* DONE (kernlab) 
edd@max:/tmp$ 

而且，它还具有无关gfortran的包似乎只包含C和C++文件。

Answer 2

我怀疑Xcode中的一个小版本转换是问题的根源（Fortran的未声明版本和R的未声明版本），但为什么不安装Mac二进制文件？

http://cran.r-project.org/bin/macosx/leopard/contrib/r-release/kernlab_0.9-12.tgz