在Linux中安装BioConductor_R_Rstudio_Bioconductor

在Linux中安装BioConductor

在Linux中安装BioConductor,r,rstudio,bioconductor,R,Rstudio,Bioconductor,我知道这已经被问了很多次了，但我无法从StackOverflow或BioConductor安装页面上的答案中找到答案。我已将R安装并更新至最新的3.1.3版本，该版本在安装页面上明确说明与BioConductor 3.0配合使用然后，我安装了BioConductor，并使用以下命令确保所有内容都是最新的： source("http://bioconductor.org/biocLite.R") biocLite(ask=FALSE) biocLite("BiocUpgrade") 到目前为止

我知道这已经被问了很多次了，但我无法从StackOverflow或BioConductor安装页面上的答案中找到答案。我已将R安装并更新至最新的3.1.3版本，该版本在安装页面上明确说明与BioConductor 3.0配合使用

然后，我安装了BioConductor，并使用以下命令确保所有内容都是最新的：

source("http://bioconductor.org/biocLite.R")
biocLite(ask=FALSE)
biocLite("BiocUpgrade")

到目前为止，一切正常，但当我使用以下工具安装任何BioConductor软件包时：

biocLite(c("flowCore"))

install.packages("robustbase", dependencies=TRUE)

我将得到如下几个错误：

1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘robustbase’ had non-zero exit status

我的理解是，这个错误表明R和软件包之间的版本不匹配，但听起来BioConductor的所有内容都应该与R版本3.1.3配合使用

当我尝试手动安装错误中列出的软件包时，请使用，例如：

biocLite(c("flowCore"))

install.packages("robustbase", dependencies=TRUE)

在非零退出状态下，我将得到与上面相同类型的错误

有人知道最好的办法吗？我假设我不需要降级到以前版本的R或任何东西，但我真的不知道在这一点上该怎么做。谢谢

根据以下注释的要求，使用以下代码安装包flowCore的完整输出如下：

biocLite(c("flowCore"))

输出：

    BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'flowCore'
also installing the dependencies ‘robustbase’, ‘mvtnorm’, ‘cluster’, ‘pcaPP’, ‘rrcov’

trying URL 'http://cran.rstudio.com/src/contrib/robustbase_0.92-3.tar.gz'
Content type 'application/x-gzip' length 3144393 bytes (3.0 MB)
opened URL
==================================================
downloaded 3.0 MB

trying URL 'http://cran.rstudio.com/src/contrib/mvtnorm_1.0-2.tar.gz'
Content type 'application/x-gzip' length 155092 bytes (151 KB)
opened URL
==================================================
downloaded 151 KB

trying URL 'http://cran.rstudio.com/src/contrib/cluster_2.0.1.tar.gz'
Content type 'application/x-gzip' length 280102 bytes (273 KB)
opened URL
==================================================
downloaded 273 KB

trying URL 'http://cran.rstudio.com/src/contrib/pcaPP_1.9-60.tar.gz'
Content type 'application/x-gzip' length 191565 bytes (187 KB)
opened URL
==================================================
downloaded 187 KB

trying URL 'http://cran.rstudio.com/src/contrib/rrcov_1.3-8.tar.gz'
Content type 'application/x-gzip' length 992215 bytes (968 KB)
opened URL
==================================================
downloaded 968 KB

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/flowCore_1.32.2.tar.gz'
Content type 'application/x-gzip' length 8962871 bytes (8.5 MB)
opened URL
==================================================
downloaded 8.5 MB

* installing *source* package ‘robustbase’ ...
** package ‘robustbase’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c R-rng4ftn.c -o R-rng4ftn.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c eigen.f -o eigen.o
/bin/bash: gfortran: command not found
make: *** [eigen.o] Error 127
ERROR: compilation failed for package ‘robustbase’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/robustbase’
* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c miwa.c -o miwa.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c mvt.f -o mvt.o
/bin/bash: gfortran: command not found
make: *** [mvt.o] Error 127
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/mvtnorm’
* installing *source* package ‘cluster’ ...
** package ‘cluster’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c clara.c -o clara.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c daisy.f -o daisy.o
/bin/bash: gfortran: command not found
make: *** [daisy.o] Error 127
ERROR: compilation failed for package ‘cluster’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/cluster’
ERROR: dependency ‘mvtnorm’ is not available for package ‘pcaPP’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/pcaPP’
ERROR: dependencies ‘robustbase’, ‘mvtnorm’, ‘cluster’, ‘pcaPP’ are not available for package ‘rrcov’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/rrcov’
ERROR: dependency ‘rrcov’ is not available for package ‘flowCore’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/flowCore’

The downloaded source packages are in
    ‘/tmp/RtmpB8elmi/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘robustbase’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘mvtnorm’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘cluster’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘pcaPP’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘rrcov’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘flowCore’ had non-zero exit status

因此，我安装了gfortran，但仍然出现类似错误，尽管它看起来有点进一步，看起来像是llapack和lblas的问题，但我不确定它们是什么，我没有在apt缓存搜索中找到它们：

> biocLite(c("flowCore"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'flowCore'
also installing the dependencies ‘robustbase’, ‘mvtnorm’, ‘cluster’, ‘pcaPP’, ‘rrcov’

trying URL 'http://cran.rstudio.com/src/contrib/robustbase_0.92-3.tar.gz'
Content type 'application/x-gzip' length 3144393 bytes (3.0 MB)
opened URL
==================================================
downloaded 3.0 MB

trying URL 'http://cran.rstudio.com/src/contrib/mvtnorm_1.0-2.tar.gz'
Content type 'application/x-gzip' length 155092 bytes (151 KB)
opened URL
==================================================
downloaded 151 KB

trying URL 'http://cran.rstudio.com/src/contrib/cluster_2.0.1.tar.gz'
Content type 'application/x-gzip' length 280102 bytes (273 KB)
opened URL
==================================================
downloaded 273 KB

trying URL 'http://cran.rstudio.com/src/contrib/pcaPP_1.9-60.tar.gz'
Content type 'application/x-gzip' length 191565 bytes (187 KB)
opened URL
==================================================
downloaded 187 KB

trying URL 'http://cran.rstudio.com/src/contrib/rrcov_1.3-8.tar.gz'
Content type 'application/x-gzip' length 992215 bytes (968 KB)
opened URL
==================================================
downloaded 968 KB

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/flowCore_1.32.2.tar.gz'
Content type 'application/x-gzip' length 8962871 bytes (8.5 MB)
opened URL
==================================================
downloaded 8.5 MB

* installing *source* package ‘robustbase’ ...
** package ‘robustbase’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c R-rng4ftn.c -o R-rng4ftn.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c eigen.f -o eigen.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c lmrob.c -o lmrob.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mc.c -o mc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c monitor.c -o monitor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c qn_sn.c -o qn_sn.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c rf-common.f -o rf-common.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c rffastmcd.f -o rffastmcd.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c rfltsreg.f -o rfltsreg.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c rllarsbi.f -o rllarsbi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c rob-utils.c -o rob-utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c wgt_himed.c -o wgt_himed.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o robustbase.so R-rng4ftn.o eigen.o init.o lmrob.o mc.o monitor.o qn_sn.o rf-common.o rffastmcd.o rfltsreg.o rllarsbi.o rob-utils.o rowMedians.o wgt_himed.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [robustbase.so] Error 1
ERROR: compilation failed for package ‘robustbase’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/robustbase’
* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c miwa.c -o miwa.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c mvt.f -o mvt.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c mvtnorm-init.c -o mvtnorm-init.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c tvpack.f -o tvpack.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/alex/R/x86_64-pc-linux-gnu-library/3.1/mvtnorm/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mvtnorm)
* installing *source* package ‘cluster’ ...
** package ‘cluster’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c clara.c -o clara.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c daisy.f -o daisy.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c dysta.f -o dysta.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c fanny.c -o fanny.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4  -c mona.f -o mona.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c pam.c -o pam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c sildist.c -o sildist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c spannel.c -o spannel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c twins.c -o twins.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/alex/R/x86_64-pc-linux-gnu-library/3.1/cluster/libs
** 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 (cluster)
* installing *source* package ‘pcaPP’ ...
** package ‘pcaPP’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -DR_PACKAGE_FILE     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c L1Median_HoCr.cpp -o L1Median_HoCr.o
/bin/bash: g++: command not found
make: *** [L1Median_HoCr.o] Error 127
ERROR: compilation failed for package ‘pcaPP’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/pcaPP’
ERROR: dependencies ‘robustbase’, ‘pcaPP’ are not available for package ‘rrcov’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/rrcov’
ERROR: dependency ‘rrcov’ is not available for package ‘flowCore’
* removing ‘/home/alex/R/x86_64-pc-linux-gnu-library/3.1/flowCore’

The downloaded source packages are in
    ‘/tmp/RtmpB8elmi/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘robustbase’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘pcaPP’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘rrcov’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘flowCore’ had non-zero exit status

根据你没有说你正在使用哪种Linux风格，但是因为你提到了apt缓存，我假设这是相关的，尽管答案是几年前的，安装LAPACK和BLAS所需的软件包是

libblas3gf
libblas-doc
libblas-dev

liblapack3gf
liblapack-doc
liblapack-dev

然而，我的印象是R附带了这些库的自己版本，所以可能只是正确设置LD_库路径的问题

还要注意的是，您似乎也缺少g++。

robustbase不是Bioc软件包。是否在更新R后首先执行更新。PackagesCheckBuild=TRUE。TRUE它不是Bioc包。是的，我也更新了所有软件包。尝试查找每个cran软件包的依赖项，下载源代码.tar.gz文件，并使用install.packagespkg-name、repos=NULL、type=source逐个安装。执行此操作时，请在R脚本中记录这些步骤，并将这些源代码保存到某些地方，以便将来使用。您可以通过下载源代码并单独安装来对bioconductor软件包执行相同的操作。您只需确保依赖项的顺序正确，因此不会弹出安装错误。可以从每个bioconductor软件包web存储库获取bioconductor软件包源代码