Question

主要目标是使用DiffBind（R包）来分析我的ChIPseq数据。

（我发现another post可能与我的问题有关，并试图从中提取解决方案，但我想内容太高了＃34;高级＆＃34;对我来说......）< / p>

遵循我might need to update my DiffBind的建议我试着安装它的新版本。

通过检查dependency of DiffBind我猜以前的安装会自动安装旧版本的DiffBind，因为我的R不符合当前版本的DiffBind的要求。

但我在根目录下使用R，对此我无能为力。所以我决定在我自己的目录下安装一个更新版本的R.我managed to do that.

然后我尝试安装当前版本的DiffBind，我收到了错误

ERROR: compilation failed for package ‘RcppArmadillo’

结果是依赖性lib＆＃34; RcppArmadillo＆＃34;需要一个更新的编译器，再次，我在根目录下使用gcc编译器，所以我在我自己的目录下安装了新版本的gcc。

    $ gcc --version

    gcc (GCC) 6.1.0

    Copyright (C) 2016 Free Software Foundation, Inc.

    This is free software; see the source for copying conditions.  There is NO

    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

    $ which gcc

/$HOME/Programme/gcc-6.1.0/bin//gcc

之后我尝试再次安装DiffBind（RcppArmadillo），但遇到了另一个错误：

* installing *source* package ‘RcppArmadillo’ ...
**   package 'RcppArmadillo' successfully unpacked and MD5 sums checked 
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking whether g++ version is sufficient... (6.1.0) yes
checking LAPACK_LIBS... fallback LAPACK from R 3.3.0 or later used
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloLapack.h
** libs
g++ -I/$HOME/Programme/R-3.3.1/lib64/R/include -DNDEBUG  -I//$HOME/Programme/zlib-1.2.11/include -I//$HOME/Programme/bzip2-1.0.6/include -I//$HOME/Programme/xz-5.2.3/include -I//$HOME/Programme/pcre-8.40/include -I//$HOME/Programme/curl-7.52.1/include -I"/$HOME/Programme/R-3.3.1/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -I/$HOME/Programme/R-3.3.1/lib64/R/include -DNDEBUG  -I//$HOME/Programme/zlib-1.2.11/include -I//$HOME/Programme/bzip2-1.0.6/include -I//$HOME/Programme/xz-5.2.3/include -I//$HOME/Programme/pcre-8.40/include -I//$HOME/Programme/curl-7.52.1/include -I"/$HOME/Programme/R-3.3.1/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/$HOME/Programme/R-3.3.1/lib64/R/include -DNDEBUG  -I//$HOME/Programme/zlib-1.2.11/include -I//$HOME/Programme/bzip2-1.0.6/include -I//$HOME/Programme/xz-5.2.3/include -I//$HOME/Programme/pcre-8.40/include -I//$HOME/Programme/curl-7.52.1/include -I"/$HOME/Programme/R-3.3.1/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c fastLm.cpp -o fastLm.o
g++ -shared -L/$HOME/Programme/R-3.3.1/lib64/R/lib -L//$HOME/Programme/zlib-1.2.11/lib -L//$HOME/Programme/bzip2-1.0.6/lib -L//$HOME/Programme/xz-5.2.3/lib -L//$HOME/Programme/pcre-8.40/lib -L//$HOME/Programme/curl-7.52.1/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/$HOME/Programme/R-3.3.1/lib64/R/lib -lRlapack -L/$HOME/Programme/R-3.3.1/lib64/R/lib -lRblas -lgfortran -lm -L/$HOME/Programme/R-3.3.1/lib64/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status**

结果发现无法找到gfortran。但当我检查存在gfortran时，它存在：

$ which gfortran

/usr/bin/gfortran

$ gfortran --version 

GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)

Copyright (C) 2010 Free Software Foundation, Inc.



GNU Fortran comes with NO WARRANTY, to the extent permitted by law.

You may redistribute copies of GNU Fortran

under the terms of the GNU General Public License.

For more information about these matters, see the file named COPYING

所以我假设gcc找不到gfortran，它位于根目录下。我怎么能解决这个问题？或者gcc和gfortran之间的不匹配是否有可能成为问题？如果是这样的话，可以做些什么来规避呢？

我的R版本：

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

locale:
 [1] LC_CTYPE=ja_JP.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=ja_JP.UTF-8    
 [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=ja_JP.UTF-8   
 [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Answer 1

我认为这里提到的问题已经解决了。正如VladimirF在评论中提到的，当我安装新版本的gcc时，我没有启用Fortran，这不是默认设置，因此我以前的尝试中没有安装gfortran。

我删除了之前的Gcc，并按如下方式重新编译：

tar -xvf gcc-6.1.0.tar.gz
cd gcc-6.1.0
./contrib/download_prerequisites 
mkdir build
cd build
../configure --prefix=$HOME/Programme/gcc-6.1.0 --enable-languages=c,c++,fortran --disable-multilib
make -j 8
make install

设置新gcc和lib的路径

有效！

/ usr / bin / ld：在安装＆＃39; RcppArmadillo＆＃39;时找不到-lgfortran。在R

1 个答案: