R软件包无法编译gcc [英] R Packages Fail to Compile with gcc
本文介绍了R软件包无法编译gcc的处理方法，对大家解决问题具有一定的参考价值，需要的朋友们下面随着小编来一起学习吧！
问题描述
我下载了bioconductor并试图安装成功安装的软件包（limma），但是当我尝试更新bioconductor时，我总是收到与无效编译器选项有关的错误。这似乎是特定于gcc，gfortran软件包安装没有问题。
以下是输出：
<$ p $ t
$对待
Copyright（C）2012 R统计计算基金会
ISBN 3-900051-07-0
平台：x86_64-redhat-linux-gnu（64位）
R是免费软件，并附带绝对保证。
欢迎在特定条件下重新分配。
输入'license（）'或'license（）'以获取分配细节。
自然语言支持，但在英语语言环境中运行
R是与许多贡献者合作的项目。
如何在出版物中引用R或R包，请键入'contributors（）'以获取更多信息，并输入
'citation（）'。
为某些演示键入'demo（）'，为在线帮助键入'help（）'，或者为HTML浏览器界面键入
'help.start（）'以提供帮助。
输入'q（）'退出R.
>来源（http://bioconductor.org/biocLite.R）
Bioconductor版本2.11（BiocInstaller 1.8.3），？biocLite for help
> biocLite（BiocUpgrade）
BioC_mirror：http://bioconductor.org
使用Bioconductor 2.11版（BiocInstaller 1.8.3），R 2.15版。
旧套餐：'Biobase'，'foreign'，'IRanges'，'lattice'，'MASS'，'Matrix'，
'mvtnorm'，'nlme'，'rpart'，'survival' ，'wavelim'，'wavethresh'
更新全部/部分/无？ [a / s / n]：a
尝试网址'http://bioconductor.org/packages/2.11/bioc/src/contrib/Biobase_2.18.0.tar.gz'
内容类型'申请/ x-gzip'长度1913386字节（1.8 Mb）
已打开URL
============================ ======================
已下载1.8 Mb
尝试网址'http://cran.fhcrc.org/ src / contrib / foreign_0.8-52.tar.gz'
内容类型'application / x-gzip'长度318387字节（310 Kb）
打开URL
====== ============================================
已下载310 Kb
尝试网址'http://bioconductor.org/packages/2.11/bioc/src/contrib/IRanges_1.16.5.tar.gz'
内容类型'application / x-gzip '长度699291字节（682 Kb）
打开URL
================================ ==================
已下载682 Kb
尝试网址'http://cran.fhcrc.org/src/contrib/ lattice_0.20-13.tar.gz'
内容类型'application / x-gzip'长度367715字节（359 Kb）
打开URL
========== =========== =============================
已下载359 Kb
尝试URL'http：/ /cran.fhcrc.org/src/contrib/MASS_7.3-23.tar.gz'
内容类型'application / x-gzip'长度472005字节（460 Kb）
打开的URL
================================================= =
已下载460 Kb
尝试网址'http://cran.fhcrc.org/src/contrib/Matrix_1.0-11.tar.gz'
内容类型' application / x-gzip'length 1676392 bytes（1.6 Mb）
打开URL
=========================== =======================
已下载1.6 Mb
尝试网址'http://cran.fhcrc.org /src/contrib/mvtnorm_0.9-9994.tar.gz'
内容类型'application / x-gzip'长度322279字节（314 Kb）
打开URL
===== =============================================
已下载314 Kb
尝试网址'http://cran.fhcrc.org/src/contrib/nlme_3.1-108.tar.gz'
内容类型'application / x-gzip'长度694594字节（678 Kb）
打开URL
==================== ==============================
已下载678 Kb
尝试URL'http： //cran.fhcrc.org/src/contrib/rpart_4.1-0.tar.gz'
内容类型'application / x-gzip'长度808365字节（789 Kb）
打开URL
================================================ ==
已下载789 Kb
尝试网址'http://cran.fhcrc.org/src/contrib/survival_2.37-2.tar.gz'
内容类型'application / x-gzip'长度1714302字节（1.6 Mb）
打开URL
========================== ========================
已下载1.6 Mb
尝试URL'http：//cran.fhcrc。 org / src / contrib / waveslimlim_1.7.1.tar.gz'
内容类型'application / x-gzip'长度703759字节（687 Kb）
打开URL
====== ============================================
已下载687 Kb
尝试网址'http://cran.fhcrc.org/src/contrib/wavethresh_4.6.1.tar.gz'
内容类型'application / x-gzip'长度525390字节（513 Kb）
打开URL
=============== ===================================
已下载513 Kb
*安装*源*包'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 =通用-c Rinit.c -o Rinit.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数ssp-buffer-size'
Rinit.c：1：错误：错误值for -mtune = switch
make：*** [Rinit.o]错误1
错误：程序包'Biobase'的编译失败
*去除'/ usr / lib64 / R / library / Biobase'
*恢复以前的'/ usr / lib64 / R / library / Biobase'
*安装*源*包'foreign'...
**包'foreign'成功解包并且检查MD5总和
** 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 =通用-c R_systat.c -o R_systat.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
R_systat.c：1：错误：-mtune = switch $ b $错误（通用） b make：*** [R_systat.o]错误1
错误：程序包'foreign'的编译失败
*删除'/ usr / lib64 / R / library / foreign'
*恢复以前的'/ usr / lib64 / R / library / foreign'
*安装*源*包'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 =通用-c AEbufs.c -o AEbufs.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
AEbufs.c：1：错误：错误值（通用）for -mtune = switch
make：*** [AEbufs.o]错误1
错误：编译包'IRanges'
*删除'/ usr / lib64 / R /库失败/ IRanges'
*恢复以前的'/ usr / lib64 / R / library / IRanges'
*安装*源*包'lattice'...
**包'lattice'成功解包并检查MD5总和
** 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 =通用-c init.c -o init.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
init.c：1：错误：-mtune = switch $ b $错误值b make：*** [init.o]错误1
错误：程序包'lattice'的编译失败
*删除'/ usr / lib64 / R / library / lattice'
*恢复前面的'/ usr / lib64 / R / library / lattice'
*安装* source * package'MASS'...
** package'MASS'已成功解压并检查MD5总和
** libs
gcc -m64 -std = gnu99 -I / usr / include / R -DNDEBUG -I / usr / local / include -fpic -O2 -g -pipe -Wall -Wp，-D_FORTIFY_SOURCE = 2 -fexceptions -fstack-protector -param = ssp-buffer-size = 4 -m64 -mtune =通用-c MASS.c -o MASS.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
MASS.c：1：错误：错误值（通用）for -mtune =开关$ b $ make：*** [MASS.o]错误1
错误：程序包'MASS'的编译失败
*删除'/ usr / lib64 / R / library / MASS'
*恢复以前的'/ usr / lib64 / R / library / MASS'
*安装*源*包'mvtnorm'.. 。
** package'mvtnorm'已成功解压并检查了MD5总和
** libs
gcc -m64 -std = gnu99 -I / usr / include / R -DNDEBUG -I / usr / local / include -fpic -O2 -g -pipe -Wall -Wp，-D_FORTIFY_SOURCE = 2 -fex ceptions -fstack-protector -param = ssp-buffer-size = 4 -m64 -mtune = generic -c miwa.c -o miwa.o
cc1：error：无法识别的命令行选项-fstack-protector
cc1：error：无效参数`ssp-buffer-size'
miwa.c：1：错误：错误值（generic）for -mtune =开关$ b $ make：*** [miwa .o]错误1
错误：程序包'mvtnorm'的编译失败
*删除'/ usr / lib64 / R / library / mvtnorm'
*恢复以前的'/ usr / lib64 / R / library / mvtnorm'
* installed * source * package'rpart'...
** package'rpart'已成功解压并检查MD5总和
** 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 =通用-c anova.c -o anova.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数'ssp-buffer-size'
anova.c：1：err或者：对于-mtune = switch
make：*** [anova.o]错误值（通用）错误1
错误：程序包'rpart'编译失败
*去除'/ usr / lib64 / R / library / rpart'
*恢复以前的'/ usr / lib64 / R / library / rpart'
*安装*源*包'生存'...
** package'survival'解压成功并且MD5总和被检查
** 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：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数ssp-buffer-size'
agexact.c：1：error：bad value（generic）for - mtune = switch
make：*** [agexact.o]错误1
错误：程序包'生存'编译失败
*删除'/ usr / lib64 / R / library / survival'
*恢复以前的'/ usr / lib64 / R / libra ry / survival'
*安装* source *包'waveslim''...
**包'waveslim'成功解包并检查MD5总和
** 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-pw.f -o bell-pw.o
bell-pw.f：131.15：
MAXIT =（K + 3）* ROOTN
1
警告：在（1）转换为REAL（8）至INTEGER（4）时可能发生的变化
bell-pw.f：344.18：
INTEGER N，I，L ，K，IFAULT
1
警告：在（1）
处宣布未使用的变量'i'bell-pw.f：345.36：
双精度V（N ），RN，STD，DSUM，DWSUM，ZERO，ONE，
1
警告：在（1）
声明未使用的变量'std'bell-pw.f：3 46.18：
* TWO，ZFLOAT
1
警告：在（1）
声明未使用的变量'zfloat'bell-pw.f：在函数'dpss' ：
bell-pw.f：203：0：warning：'sum'可以在这个函数中初始化使用[-Wmaybe- uninitialized]
bell-pw.f：207：0：warning：' ssnorm'可以在这个函数中初始化使用[-Wmaybe- uninitialized]
bell-pw.f：203：0：warning：'diff'可以在这个函数中初始化使用[-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 =通用-c dwt.c -o dwt.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
dwt.c：1：错误：错误值（通用）for -mtune =开关
make：*** [dwt.o ]错误1
错误：程序包'waves''编译失败
*删除'/ usr / lib64 / R / library / waves /临时'
*恢复以前的'/ usr / lib64 / R / library / waves'lim'
*安装*源*包'Matrix'...
**包'Matrix'成功解包并检查MD5总和
** 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-保护程序--param = ssp-buffer-size = 4 -m64 -mtune =通用-c CHMfactor.c -o CHMfactor.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
CHMfactor.c：1：错误：错误值（通用）for -mtune =开关
make：*** [CHMfactor.o]错误1
错误：程序包'Matrix'编译失败
*删除'/ usr / lib64 / R / library / Matrix'
*恢复以前的'/ usr / lib64 / R / library / Matrix '
*安装* source * package'nlme'...
** package'nlme'已成功解压并检查MD5总和
** 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 =通用-c corStruct.c -o corStruct.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数ssp-buffer-size '
corStruct.c：1：错误：不正确的值（通用）for -mtune =开关
make：*** [corStruct.o]错误1
错误： nlme'
*删除'/ usr / lib64 / R / library / nlme'
*恢复以前的'/ usr / lib64 / R / library / nlme'
* wavethresh'...
** package'wavethresh'已成功解压并检查了MD5总和
** libs
gcc -m64 -std = gnu99 -I / usr / include / R -DNDEBUG - 我/ usr / local / include -fpic -O2 -g -pi pe -Wall -Wp，-D_FORTIFY_SOURCE = 2 -fexceptions -fstack-protector -param = ssp-buffer-size = 4 -m64 -mtune = generic -c WAVDE.c -o WAVDE.o
cc1：错误：无法识别的命令行选项-fstack-protector
cc1：错误：无效参数`ssp-buffer-size'
WAVDE.c：1：错误：-mtune = switch
make：*** [WAVDE.o]错误1
错误：程序包'wavethresh'的编译失败
*删除'/ usr / lib64 / R / library / wavethresh'
*恢复以前的'/ usr / lib64 / R / library / wavethresh'
下载的源码包在
'/ tmp / RtmpKXUsRY / downloaded_packages'
更新HTML索引'.Library'中的包
制作packages.html ...完成
有13个警告（使用警告（）来查看它们）
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中看到的所有内容都是gcc34，所以我没有完全确定。我必须用sudo启动R，因为除了包data.tables以外，它都无法安装在目录中。
解决方案
修改PATH以确保找到比gcc 3.2更新的gcc编译器。
如果需要的话，创建一个到最近的链接（假设你仍然保留gcc 3.2）：
mkdir $ HOME / bin
ln -s / usr / bin / gcc -VERSION $ HOME / bin / gcc
export PATH = $ HOME / bin：$ PATH
＃继续到您的正常安装
VERSION表示系统中通常使用的编译器的gcc版本
I downloaded bioconductor and attempted to install a package ("limma") which installed successfully, however when I tried to update bioconductor I keep getting errors relating to invalid compiler options. It seems to be specific to gcc, the gfortran packages install without issue.
Here is the output:
[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)
I am running: Linux fedora 3.6.8-2.fc17.x86_64 gcc-4.7.2-2.fc17.x86_64 R 2.15.2 However all I see in /usr/bin is gcc34, so I'm not exactly sure. I have to start R with sudo because for all but the package data.tables, it doesn't have access to install in the directories.
解决方案
Modify your PATH to make sure that a gcc compiler more recent than gcc 3.2 is found.
If necessary, create a link to the recent one (assuming you want to still keep gcc 3.2 around):
mkdir $HOME/bin
ln -s /usr/bin/gcc-VERSION $HOME/bin/gcc
export PATH=$HOME/bin:$PATH
# proceed to your normal installation
VERSION indicates the gcc version of the compiler normally used in your system
这篇关于R软件包无法编译gcc的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
查看全文
