R 安装包时出错：致命错误：stdlib.h:没有这样的文件或目录

我刚刚安装了LinuxMint系统，现在我想安装一个R包。我做到了：

sudo apt-get install r-base

sudo R

在R中，我输入（如bioconductor主页所示）：

结果是：

> 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
> 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 <stdlib.h>
                    ^
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 <stdio.h>
                    ^
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 <math.h>
                  ^
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 <stdio.h>
                   ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdint.h>
                          ^
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 <stdlib.h>
                    ^
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)

>源代码（“http://bioconductor.org/biocLite.R")
将软件包安装到“/home/robert/R/x86_64-pc-linux-gnu-library/3.0”中
（由于“lib”未指定）
正在尝试URL'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/BiocInstaller_1.12.1.tar.gz'
内容类型“应用程序/x-gzip”长度13520字节（13 Kb）
打开的URL
==================================================
下载13 Kb
*正在安装*source*包“BiocInstaller”。。。
**R
**仪表
**为延迟加载准备包
**帮助
***安装帮助索引
**建立一揽子指数
**测试是否可以加载已安装的软件包
Bioconductor版本2.13（BiocInstaller 1.12.1），？biocLite寻求帮助
安装新版本的Bioconductor后，可获得新版本的Bioconductor
R、 ？需要帮助吗
*完成（安装程序）
下载的源程序包位于中
“/tmp/RtmpDSnlDj/download_packages”
Bioconductor版本2.13（BiocInstaller 1.12.1），？biocLite寻求帮助
安装新版本的Bioconductor后，可获得新版本的Bioconductor
R、 ？需要帮助吗
>生物晶石（“地质查询”）
生物镜：http://bioconductor.org
使用Bioconductor版本2.13（BioInstaller 1.12.1），R版本3.0.2。
安装程序包“GEOquery”
同时安装依赖项“BioGenerics”、“bitops”、“Biobase”、“XML”、“RCurl”
正在尝试URL'http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz'
内容类型“应用程序/x-gzip”长度30969字节（30 Kb）
打开的URL
==================================================
下载30 Kb
正在尝试URL'http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz'
内容类型“应用程序/x-gzip”长度为8734字节
打开的URL
==================================================
下载8734字节
正在尝试URL'http://bioconductor.org/packages/2.13/bioc/src/contrib/Biobase_2.22.0.tar.gz'
内容类型“应用程序/x-gzip”长度1848944字节（1.8 Mb）
打开的URL
==================================================
下载1.8MB
正在尝试URL'http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz'
内容类型“应用程序/x-gzip”长度158216字节（1.5 Mb）
打开的URL
==================================================
下载1.5 Mb
正在尝试URL'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.3.tar.gz'
内容类型“应用程序/x-gzip”长度879143字节（858 Kb）
打开的URL
==================================================
下载858KB
正在尝试URL'http://bioconductor.org/packages/2.13/bioc/src/contrib/GEOquery_2.28.0.tar.gz'
内容类型“应用程序/x-gzip”长度13630252字节（13.0 Mb）
打开的URL
==================================================
下载13.0 Mb
*正在安装*source*包“BioGenerics”。。。
**R
**仪表
**为延迟加载准备包
为“BioGenerics”包中的“append”创建新的泛型函数
为“BioGenerics”包中的“as.data.frame”创建新的通用函数
为“BioGenerics”包中的“as.vector”创建新的泛型函数
在“BioGenerics”包中为“cbind”创建新的通用函数
在“BioGenerics”包中为“rbind”创建新的通用函数
为“BioGenerics”包中的“duplicated”创建新的通用函数
为“BioGenerics”包中的“anyDuplicated”创建新的通用函数
在“BioGenerics”包中为“eval”创建新的通用函数
在“BioGenerics”包中为“pmax”创建新的通用函数
在“BioGenerics”包中为“pmin”创建新的通用函数
为“BioGenerics”包中的“pmax.int”创建新的通用函数
为“BioGenerics”包中的“pmin.int”创建新的通用函数
在“BioGenerics”包中为“Reduce”创建新的通用函数
为“BioGenerics”包中的“Filter”创建新的通用函数
为“BioGenerics”包中的“Find”创建新的通用函数
为“BioGenerics”包中的“Map”创建新的通用函数
为“BioGenerics”包中的“Position”创建新的通用函数
在“BioGenerics”包中为“get”创建新的通用函数
在“BioGenerics”包中为“mget”创建新的通用函数
正在为“BioGenerics”包中的“is.unsorted”创建新的泛型函数
在“BioGenerics”包中为“Lappy”创建新的通用函数
在“BioGenerics”包中为“Sappy”创建新的通用函数
在“BioGenerics”包中为“mapply”创建新的通用函数
为“BioGenerics”包中的“match”创建新的通用函数
为“BioGenerics”包中的“order”创建新的通用函数
为“BioGenerics”包中的“粘贴”创建新的通用函数
为“BioGenerics”包中的“rank”创建新的通用函数
为“BioGenerics”包中的“rep.int”创建新的通用函数
为包“BioGenerics”中的“rownames”创建新的泛型函数
为“BioGenerics”包中的“colnames”创建新的泛型函数
在“BioGenerics”包中为“union”创建新的通用函数
为“BioGenerics”包中的“intersect”创建新的通用函数
在“BioGenerics”包中为“setdiff”创建新的通用函数
为“BioGenerics”包中的“sort”创建新的通用函数
为“BioGenerics”包中的“table”创建新的通用函数
在“BioGenerics”包中为“tapply”创建新的通用函数
为“BioGenerics”包中的“unique”创建新的通用函数
创建一个
> 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
> 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 <stdlib.h>
                    ^
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 <stdio.h>
                    ^
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 <math.h>
                  ^
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 <stdio.h>
                   ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdlib.h>
                    ^
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 <stdint.h>
                          ^
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 <stdlib.h>
                    ^
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)