r - R 包无法用 gcc 编译

Question

我下载了 bioconductor 并尝试安装一个成功安装的软件包（“limma”），但是当我尝试更新 bioconductor 时，我不断收到与无效编译器选项有关的错误。它似乎特定于 gcc，gfortran 包安装没有问题。

这是输出：

[xxx]$ su -c 'R'
Password: 

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> biocLite("BiocUpgrade")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Old packages: 'Biobase', 'foreign', 'IRanges', 'lattice', 'MASS', 'Matrix',
  'mvtnorm', 'nlme', 'rpart', 'survival', 'waveslim', 'wavethresh'
Update all/some/none? [a/s/n]: a
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Biobase_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1913386 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/foreign_0.8-52.tar.gz'
Content type 'application/x-gzip' length 318387 bytes (310 Kb)
opened URL
==================================================
downloaded 310 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/IRanges_1.16.5.tar.gz'
Content type 'application/x-gzip' length 699291 bytes (682 Kb)
opened URL
==================================================
downloaded 682 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/lattice_0.20-13.tar.gz'
Content type 'application/x-gzip' length 367715 bytes (359 Kb)
opened URL
==================================================
downloaded 359 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/MASS_7.3-23.tar.gz'
Content type 'application/x-gzip' length 472005 bytes (460 Kb)
opened URL
==================================================
downloaded 460 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/Matrix_1.0-11.tar.gz'
Content type 'application/x-gzip' length 1676392 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/mvtnorm_0.9-9994.tar.gz'
Content type 'application/x-gzip' length 322279 bytes (314 Kb)
opened URL
==================================================
downloaded 314 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/nlme_3.1-108.tar.gz'
Content type 'application/x-gzip' length 694594 bytes (678 Kb)
opened URL
==================================================
downloaded 678 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/rpart_4.1-0.tar.gz'
Content type 'application/x-gzip' length 808365 bytes (789 Kb)
opened URL
==================================================
downloaded 789 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.37-2.tar.gz'
Content type 'application/x-gzip' length 1714302 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/waveslim_1.7.1.tar.gz'
Content type 'application/x-gzip' length 703759 bytes (687 Kb)
opened URL
==================================================
downloaded 687 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/wavethresh_4.6.1.tar.gz'
Content type 'application/x-gzip' length 525390 bytes (513 Kb)
opened URL
==================================================
downloaded 513 Kb

* installing *source* package ‘Biobase’ ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c Rinit.c -o Rinit.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
Rinit.c:1: error: bad value (generic) for -mtune= switch
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package ‘Biobase’
* removing ‘/usr/lib64/R/library/Biobase’
* restoring previous ‘/usr/lib64/R/library/Biobase’
* installing *source* package ‘foreign’ ...
** package ‘foreign’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c R_systat.c -o R_systat.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
R_systat.c:1: error: bad value (generic) for -mtune= switch
make: *** [R_systat.o] Error 1
ERROR: compilation failed for package ‘foreign’
* removing ‘/usr/lib64/R/library/foreign’
* restoring previous ‘/usr/lib64/R/library/foreign’
* installing *source* package ‘IRanges’ ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c AEbufs.c -o AEbufs.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
AEbufs.c:1: error: bad value (generic) for -mtune= switch
make: *** [AEbufs.o] Error 1
ERROR: compilation failed for package ‘IRanges’
* removing ‘/usr/lib64/R/library/IRanges’
* restoring previous ‘/usr/lib64/R/library/IRanges’
* installing *source* package ‘lattice’ ...
** package ‘lattice’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c init.c -o init.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
init.c:1: error: bad value (generic) for -mtune= switch
make: *** [init.o] Error 1
ERROR: compilation failed for package ‘lattice’
* removing ‘/usr/lib64/R/library/lattice’
* restoring previous ‘/usr/lib64/R/library/lattice’
* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c MASS.c -o MASS.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
MASS.c:1: error: bad value (generic) for -mtune= switch
make: *** [MASS.o] Error 1
ERROR: compilation failed for package ‘MASS’
* removing ‘/usr/lib64/R/library/MASS’
* restoring previous ‘/usr/lib64/R/library/MASS’
* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c miwa.c -o miwa.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
miwa.c:1: error: bad value (generic) for -mtune= switch
make: *** [miwa.o] Error 1
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘/usr/lib64/R/library/mvtnorm’
* restoring previous ‘/usr/lib64/R/library/mvtnorm’
* installing *source* package ‘rpart’ ...
** package ‘rpart’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c anova.c -o anova.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
anova.c:1: error: bad value (generic) for -mtune= switch
make: *** [anova.o] Error 1
ERROR: compilation failed for package ‘rpart’
* removing ‘/usr/lib64/R/library/rpart’
* restoring previous ‘/usr/lib64/R/library/rpart’
* installing *source* package ‘survival’ ...
** package ‘survival’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c agexact.c -o agexact.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
agexact.c:1: error: bad value (generic) for -mtune= switch
make: *** [agexact.o] Error 1
ERROR: compilation failed for package ‘survival’
* removing ‘/usr/lib64/R/library/survival’
* restoring previous ‘/usr/lib64/R/library/survival’
* installing *source* package ‘waveslim’ ...
** package ‘waveslim’ successfully unpacked and MD5 sums checked
** libs
gfortran -m64   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-    protector --param=ssp-buffer-size=4  -m64 -mtune=generic -I/usr/lib64/gfortran/modules  -c     bell-p-w.f -o bell-p-w.o
bell-p-w.f:131.15:

         MAXIT=(K+3)*ROOTN                                              
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
bell-p-w.f:344.18:

      INTEGER N, I, L, K, IFAULT                                        
                  1
Warning: Unused variable 'i' declared at (1)
bell-p-w.f:345.36:

      DOUBLE PRECISION V(N), RN, STD, DSUM, DWSUM, ZERO, ONE,           
                                    1
Warning: Unused variable 'std' declared at (1)
bell-p-w.f:346.18:

     * TWO, ZFLOAT                                                      
                  1
Warning: Unused variable 'zfloat' declared at (1)
bell-p-w.f: In function ‘dpss’:
bell-p-w.f:203:0: warning: ‘sum’ may be used uninitialized in this function [-Wmaybe-    uninitialized]
bell-p-w.f:207:0: warning: ‘ssnorm’ may be used uninitialized in this function [-Wmaybe-    uninitialized]
bell-p-w.f:203:0: warning: ‘diff’ may be used uninitialized in this function     [-Wmaybe-    uninitialized]
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c dwt.c -o dwt.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
dwt.c:1: error: bad value (generic) for -mtune= switch
make: *** [dwt.o] Error 1
ERROR: compilation failed for package ‘waveslim’
* removing ‘/usr/lib64/R/library/waveslim’
* restoring previous ‘/usr/lib64/R/library/waveslim’
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-    protector --param=ssp-buffer-size=4  -m64 -mtune=generic  -c CHMfactor.c -o CHMfactor.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
CHMfactor.c:1: error: bad value (generic) for -mtune= switch
make: *** [CHMfactor.o] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/usr/lib64/R/library/Matrix’
* restoring previous ‘/usr/lib64/R/library/Matrix’
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector     --param=ssp-buffer-size=4  -m64 -mtune=generic  -c corStruct.c -o corStruct.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
corStruct.c:1: error: bad value (generic) for -mtune= switch
make: *** [corStruct.o] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/usr/lib64/R/library/nlme’
* restoring previous ‘/usr/lib64/R/library/nlme’
* installing *source* package ‘wavethresh’ ...
** package ‘wavethresh’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -O2 -g -pipe     -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4      -m64 -mtune=generic  -c WAVDE.c -o WAVDE.o
cc1: error: unrecognized command line option "-fstack-protector"
cc1: error: invalid parameter `ssp-buffer-size'
WAVDE.c:1: error: bad value (generic) for -mtune= switch
make: *** [WAVDE.o] Error 1
ERROR: compilation failed for package ‘wavethresh’
* removing ‘/usr/lib64/R/library/wavethresh’
* restoring previous ‘/usr/lib64/R/library/wavethresh’

The downloaded source packages are in
        ‘/tmp/RtmpKXUsRY/downloaded_packages’
Updating HTML index of packages in '.Library'

Making packages.html  ... done
There were 13 warnings (use warnings() to see them)

我正在运行：Linux fedora 3.6.8-2.fc17.x86_64 gcc-4.7.2-2.fc17.x86_64 R 2.15.2 但是我在 /usr/bin 中看到的只是 gcc34，所以我不确定。我必须用 sudo 启动 R，因为除了包 data.tables 之外，它无权安装在目录中。

Answer 1

我在 Ubuntu 上尝试在 R 中安装 mvtnorm 时遇到了类似的问题。我收到了错误：

gcc: error: unrecognized command line option "-fstack-protector-strong"

我查看了默认使用哪个版本的 gcc

which gcc
/home/ralien/anaconda3/bin/gcc

事实证明，出于某种原因，Anaconda 使用了一个非常旧的 gcc、g++ 和 gfortran 编译器：版本 4.8.5。此版本似乎不支持 -fstack-protector-strong 参数。

我检查了 /usr/bin 中的 gcc、g++ 和 gfortran 版本，发现我的系统编译器要新得多，大约为 5.4。诀窍是通过创建来强制 R 使用新的编译器

~/.R/Makevars

并将所有编译器的路径更改为系统版本。因此 Makevars 文件将包含以下条目：

CC=/usr/bin/gcc
CXX=/usr/bin/g++
FC=/usr/bin/gfortran
F77=/usr/bin/gfortran

然后，您可以使用 R CMD INSTALL 使用新版本的 gcc、g++ 和 gfortran 编译包。

或者至少这对我有用。

Answer 2

修改您的 PATH 以确保找到比 gcc 3.2 更新的 gcc 编译器。

如有必要，创建一个指向最近的链接（假设您仍想保留 gcc 3.2）：

mkdir $HOME/bin
ln -s /usr/bin/gcc-VERSION $HOME/bin/gcc
export PATH=$HOME/bin:$PATH
# proceed to your normal installation

VERSION 表示您系统中通常使用的编译器的 gcc 版本