我刚刚设置好了我的Linux Mint系统，现在我想安装一个R包。我做了以下操作:
sudo apt-get install r-base
sudo R
在R中，我输入了（就像生物信息学主页上所指示的那样）：
source("http://bioconductor.org/biocLite.R")
biocLite("GEOquery")
这是结果：
> 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)
为什么会失败？我没有做任何特殊的事情，只是想安装一个软件包 =(
我看到的第一个错误是说找不到stdlib.h - 为什么他找不到这个库呢？