title: R Packages Fail to Compile with gcc
body: <p>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.</p>
  
  <p>Here is the output:</p>
  
  <pre><code>[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.
  
  &gt; source("http://bioconductor.org/biocLite.R")
  Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
  &gt; 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)
  </code></pre>
  
  <p>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. </p>