title: Error in installing package: fatal error: stdlib.h: no such file or directory
body: <p>I have just set up my linux mint system and now I want to install an R package. I did:</p>
  
  <pre><code>sudo apt-get install r-base
  
  sudo R
  </code></pre>
  
  <p>In R I entered (just like indicated on the bioconductor homepage):</p>
  
  <pre><code>source("http://bioconductor.org/biocLite.R")
  
  biocLite("GEOquery")
  </code></pre>
  
  <p>This is the result:</p>
  
  <pre><code>&gt; source("http://bioconductor.org/biocLite.R")
  Installing package into ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0’
  (as ‘lib’ is unspecified)
  trying URL 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/BiocInstaller_1.12.1.tar.gz'
  Content type 'application/x-gzip' length 13520 bytes (13 Kb)
  opened URL
  ==================================================
  downloaded 13 Kb
  
  * installing *source* package ‘BiocInstaller’ ...
  ** R
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
  A newer version of Bioconductor is available after installing a new version of
    R, ?BiocUpgrade for help
  * DONE (BiocInstaller)
  
  The downloaded source packages are in
      ‘/tmp/RtmpDSnlDj/downloaded_packages’
  Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
  A newer version of Bioconductor is available after installing a new version of
    R, ?BiocUpgrade for help
  &gt; biocLite("GEOquery")
  BioC_mirror: http://bioconductor.org
  Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
  Installing package(s) 'GEOquery'
  also installing the dependencies ‘BiocGenerics’, ‘bitops’, ‘Biobase’, ‘XML’, ‘RCurl’
  
  trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz'
  Content type 'application/x-gzip' length 30969 bytes (30 Kb)
  opened URL
  ==================================================
  downloaded 30 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz'
  Content type 'application/x-gzip' length 8734 bytes
  opened URL
  ==================================================
  downloaded 8734 bytes
  
  trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Biobase_2.22.0.tar.gz'
  Content type 'application/x-gzip' length 1848944 bytes (1.8 Mb)
  opened URL
  ==================================================
  downloaded 1.8 Mb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz'
  Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb)
  opened URL
  ==================================================
  downloaded 1.5 Mb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.3.tar.gz'
  Content type 'application/x-gzip' length 879143 bytes (858 Kb)
  opened URL
  ==================================================
  downloaded 858 Kb
  
  trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GEOquery_2.28.0.tar.gz'
  Content type 'application/x-gzip' length 13630252 bytes (13.0 Mb)
  opened URL
  ==================================================
  downloaded 13.0 Mb
  
  * installing *source* package ‘BiocGenerics’ ...
  ** R
  ** inst
  ** preparing package for lazy loading
  Creating a new generic function for ‘append’ in package ‘BiocGenerics’
  Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
  Creating a new generic function for ‘as.vector’ in package ‘BiocGenerics’
  Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
  Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
  Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
  Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
  Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
  Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
  Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
  Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
  Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
  Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
  Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
  Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
  Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
  Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
  Creating a new generic function for ‘get’ in package ‘BiocGenerics’
  Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
  Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
  Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘match’ in package ‘BiocGenerics’
  Creating a new generic function for ‘order’ in package ‘BiocGenerics’
  Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
  Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
  Creating a new generic function for ‘rep.int’ in package ‘BiocGenerics’
  Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
  Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
  Creating a new generic function for ‘union’ in package ‘BiocGenerics’
  Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
  Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
  Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
  Creating a new generic function for ‘table’ in package ‘BiocGenerics’
  Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
  Creating a new generic function for ‘unlist’ in package ‘BiocGenerics’
  Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
  Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
  Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
  Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
  Warning in getPackageName(environment(fdef)) :
    Created a package name, ‘2014-08-07 15:23:56’, when none found
  Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
  Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
  Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  * DONE (BiocGenerics)
  * installing *source* package ‘bitops’ ...
  ** package ‘bitops’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c bit-ops.c -o bit-ops.o
  In file included from bit-ops.c:1:0:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [bit-ops.o] Error 1
  ERROR: compilation failed for package ‘bitops’
  * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/bitops’
  * installing *source* package ‘XML’ ...
  ** package ‘XML’ successfully unpacked and MD5 sums checked
  checking for gcc... gcc
  checking for C compiler default output file name... rm: cannot remove 'a.out.dSYM': Is a directory
  
  configure: error: C compiler cannot create executables
  See `config.log' for more details.
  ERROR: configuration failed for package ‘XML’
  * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/XML’
  * installing *source* package ‘Biobase’ ...
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c Rinit.c -o Rinit.o
  In file included from Rinit.c:1:0:
  /usr/share/R/include/Rinternals.h:32:20: fatal error: stdio.h: No such file or directory
   # include &lt;stdio.h&gt;
                      ^
  compilation terminated.
  make: *** [Rinit.o] Error 1
  ERROR: compilation failed for package ‘Biobase’
  * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/Biobase’
  ERROR: dependency ‘bitops’ is not available for package ‘RCurl’
  * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/RCurl’
  ERROR: dependencies ‘Biobase’, ‘XML’, ‘RCurl’ are not available for package ‘GEOquery’
  * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/GEOquery’
  
  The downloaded source packages are in
      ‘/tmp/RtmpDSnlDj/downloaded_packages’
  Old packages: 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice',
    'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial'
  Update all/some/none? [a/s/n]: a
  trying URL 'http://cran.fhcrc.org/src/contrib/boot_1.3-11.tar.gz'
  Content type 'application/x-gzip' length 230713 bytes (225 Kb)
  opened URL
  ==================================================
  downloaded 225 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/class_7.3-11.tar.gz'
  Content type 'application/x-gzip' length 19592 bytes (19 Kb)
  opened URL
  ==================================================
  downloaded 19 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/cluster_1.15.2.tar.gz'
  Content type 'application/x-gzip' length 271734 bytes (265 Kb)
  opened URL
  ==================================================
  downloaded 265 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/foreign_0.8-61.tar.gz'
  Content type 'application/x-gzip' length 333301 bytes (325 Kb)
  opened URL
  ==================================================
  downloaded 325 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/KernSmooth_2.23-12.tar.gz'
  Content type 'application/x-gzip' length 33518 bytes (32 Kb)
  opened URL
  ==================================================
  downloaded 32 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/lattice_0.20-29.tar.gz'
  Content type 'application/x-gzip' length 347091 bytes (338 Kb)
  opened URL
  ==================================================
  downloaded 338 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/MASS_7.3-33.tar.gz'
  Content type 'application/x-gzip' length 486785 bytes (475 Kb)
  opened URL
  ==================================================
  downloaded 475 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/Matrix_1.1-4.tar.gz'
  Content type 'application/x-gzip' length 1670503 bytes (1.6 Mb)
  opened URL
  ==================================================
  downloaded 1.6 Mb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/mgcv_1.8-2.tar.gz'
  Content type 'application/x-gzip' length 663555 bytes (648 Kb)
  opened URL
  ==================================================
  downloaded 648 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/nlme_3.1-117.tar.gz'
  Content type 'application/x-gzip' length 759268 bytes (741 Kb)
  opened URL
  ==================================================
  downloaded 741 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/nnet_7.3-8.tar.gz'
  Content type 'application/x-gzip' length 28424 bytes (27 Kb)
  opened URL
  ==================================================
  downloaded 27 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/rpart_4.1-8.tar.gz'
  Content type 'application/x-gzip' length 818733 bytes (799 Kb)
  opened URL
  ==================================================
  downloaded 799 Kb
  
  trying URL 'http://cran.fhcrc.org/src/contrib/spatial_7.3-8.tar.gz'
  Content type 'application/x-gzip' length 43593 bytes (42 Kb)
  opened URL
  ==================================================
  downloaded 42 Kb
  
  * installing *source* package ‘boot’ ...
  ** package ‘boot’ successfully unpacked and MD5 sums checked
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  * DONE (boot)
  * installing *source* package ‘cluster’ ...
  ** package ‘cluster’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c clara.c -o clara.o
  clara.c:12:18: fatal error: math.h: No such file or directory
   #include &lt;math.h&gt;
                    ^
  compilation terminated.
  make: *** [clara.o] Error 1
  ERROR: compilation failed for package ‘cluster’
  * removing ‘/usr/lib/R/library/cluster’
  * restoring previous ‘/usr/lib/R/library/cluster’
  * installing *source* package ‘foreign’ ...
  ** package ‘foreign’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c R_systat.c -o R_systat.o
  R_systat.c:20:19: fatal error: stdio.h: No such file or directory
   #include &lt;stdio.h&gt;
                     ^
  compilation terminated.
  make: *** [R_systat.o] Error 1
  ERROR: compilation failed for package ‘foreign’
  * removing ‘/usr/lib/R/library/foreign’
  * restoring previous ‘/usr/lib/R/library/foreign’
  * installing *source* package ‘KernSmooth’ ...
  ** package ‘KernSmooth’ successfully unpacked and MD5 sums checked
  ** libs
  gfortran   -fpic  -O3 -pipe  -g  -c blkest.f -o blkest.o
  /bin/bash: gfortran: command not found
  make: *** [blkest.o] Error 127
  ERROR: compilation failed for package ‘KernSmooth’
  * removing ‘/usr/lib/R/library/KernSmooth’
  * restoring previous ‘/usr/lib/R/library/KernSmooth’
  * installing *source* package ‘lattice’ ...
  ** package ‘lattice’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
  In file included from init.c:2:0:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [init.o] Error 1
  ERROR: compilation failed for package ‘lattice’
  * removing ‘/usr/lib/R/library/lattice’
  * restoring previous ‘/usr/lib/R/library/lattice’
  * installing *source* package ‘MASS’ ...
  ** package ‘MASS’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c MASS.c -o MASS.o
  In file included from MASS.c:18:0:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [MASS.o] Error 1
  ERROR: compilation failed for package ‘MASS’
  * removing ‘/usr/lib/R/library/MASS’
  * restoring previous ‘/usr/lib/R/library/MASS’
  * installing *source* package ‘nnet’ ...
  ** package ‘nnet’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c nnet.c -o nnet.o
  In file included from nnet.c:25:0:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [nnet.o] Error 1
  ERROR: compilation failed for package ‘nnet’
  * removing ‘/usr/lib/R/library/nnet’
  * restoring previous ‘/usr/lib/R/library/nnet’
  * installing *source* package ‘rpart’ ...
  ** package ‘rpart’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c anova.c -o anova.o
  In file included from rpart.h:6:0,
                   from anova.c:4:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [anova.o] Error 1
  ERROR: compilation failed for package ‘rpart’
  * removing ‘/usr/lib/R/library/rpart’
  * restoring previous ‘/usr/lib/R/library/rpart’
  * installing *source* package ‘spatial’ ...
  ** package ‘spatial’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
  In file included from init.c:18:0:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [init.o] Error 1
  ERROR: compilation failed for package ‘spatial’
  * removing ‘/usr/lib/R/library/spatial’
  * restoring previous ‘/usr/lib/R/library/spatial’
  * installing *source* package ‘class’ ...
  ** package ‘class’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c class.c -o class.o
  In file included from class.c:19:0:
  /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [class.o] Error 1
  ERROR: compilation failed for package ‘class’
  * removing ‘/usr/lib/R/library/class’
  * restoring previous ‘/usr/lib/R/library/class’
  * installing *source* package ‘Matrix’ ...
  ** package ‘Matrix’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config     -fpic  -O3 -pipe  -g  -c CHMfactor.c -o CHMfactor.o
  In file included from Mutils.h:10:0,
                   from CHMfactor.h:4,
                   from CHMfactor.c:2:
  /usr/lib/gcc/x86_64-linux-gnu/4.8/include/stdint.h:9:26: fatal error: stdint.h: No such file or directory
   # include_next &lt;stdint.h&gt;
                            ^
  compilation terminated.
  make: *** [CHMfactor.o] Error 1
  ERROR: compilation failed for package ‘Matrix’
  * removing ‘/usr/lib/R/library/Matrix’
  * restoring previous ‘/usr/lib/R/library/Matrix’
  * installing *source* package ‘nlme’ ...
  ** package ‘nlme’ successfully unpacked and MD5 sums checked
  ** libs
  gfortran   -fpic  -O3 -pipe  -g  -c chol.f -o chol.o
  /bin/bash: gfortran: command not found
  make: *** [chol.o] Error 127
  ERROR: compilation failed for package ‘nlme’
  * removing ‘/usr/lib/R/library/nlme’
  * restoring previous ‘/usr/lib/R/library/nlme’
  * installing *source* package ‘mgcv’ ...
  ** package ‘mgcv’ successfully unpacked and MD5 sums checked
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -O3 -pipe  -g  -c coxph.c -o coxph.o
  coxph.c:13:20: fatal error: stdlib.h: No such file or directory
   #include &lt;stdlib.h&gt;
                      ^
  compilation terminated.
  make: *** [coxph.o] Error 1
  ERROR: compilation failed for package ‘mgcv’
  * removing ‘/usr/lib/R/library/mgcv’
  * restoring previous ‘/usr/lib/R/library/mgcv’
  
  The downloaded source packages are in
      ‘/tmp/RtmpDSnlDj/downloaded_packages’
  Updating HTML index of packages in '.Library'
  Making 'packages.html' ... done
  There were 17 warnings (use warnings() to see them)
  </code></pre>
  
  <p>Why does it fail? I haven't done anything special, I just want to install a package =(</p>
  
  <p>The first error that I see says that he cannot find stdlib.h - why should he be unable to find this library?</p>