【发布时间】：2017-09-28 14:19:33
【问题描述】：
我的系统配置
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8
[5] LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
[1] stats graphics grDevices utils datasets methods base
我的生物导体版本
Bioconductor 3.0 版（BiocInstaller 1.16.1）
我的问题
我想安装我认为有 75 个依赖项的 RforProteomics！根据作者的指示，我做了这个 biocLite("RforProteomics",dependecies =T) 这显示错误消息并且无法完成安装。据我了解，很少有依赖项无法安装，因此发生了错误。
错误信息
rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
#include <netcdf.h>
^
compilation terminated.
make: *** [rnetCDF.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/usr/lib64/R/library/mzR’
ERROR: dependency ‘mzR’ is not available for package ‘MSnbase’
* removing ‘/usr/lib64/R/library/MSnbase’
ERROR: dependency ‘mzR’ is not available for package ‘xcms’
* removing ‘/usr/lib64/R/library/xcms’
ERROR: dependency ‘mzR’ is not available for package ‘MSGFgui’
* removing ‘/usr/lib64/R/library/MSGFgui’
ERROR: dependency ‘MSnbase’ is not available for package ‘synapter’
* removing ‘/usr/lib64/R/library/synapter’
ERROR: dependency ‘MSnbase’ is not available for package ‘pRoloc’
* removing ‘/usr/lib64/R/library/pRoloc’
ERROR: dependency ‘MSnbase’ is not available for package ‘pRolocdata’
* removing ‘/usr/lib64/R/library/pRolocdata’
ERROR: dependencies ‘MSnbase’, ‘mzR’ are not available for package ‘MSnID’
* removing ‘/usr/lib64/R/library/MSnID’
ERROR: dependency ‘MSnbase’ is not available for package ‘RforProteomics’
* removing ‘/usr/lib64/R/library/RforProteomics’
Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
The downloaded source packages are in
‘/tmp/Rtmpnro4j4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
之后我做了什么
我发现 rnetCDF 是主要组件之一，它没有安装或我的系统中没有，我确实 install.packages("RNetCDF") 显示另一组错误
RNetCDF 安装错误
==================================================
downloaded 74 Kb
* installing *source* package ‘RNetCDF’ ...
** package ‘RNetCDF’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -m64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking for nc_open in -lnetcdf... no
checking for nc_create in -lnetcdf... no
configure: error: netcdf library not found
ERROR: configuration failed for package ‘RNetCDF’
* removing ‘/usr/lib64/R/library/RNetCDF’
The downloaded source packages are in
‘/tmp/Rtmpnro4j4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("RNetCDF") :
installation of package ‘RNetCDF’ had non-zero exit status
我再次安装了.pacakges("ncdf")。但这也不是安装。
接下来我该怎么做？
请帮帮我
【问题讨论】：
-
page 4 of
Using R and Bioconductor for Proteomics Data Analysis说需要先安装外部依赖项，mzR是特别提到的软件包之一。你试过了吗？ -
是的，我试过了。请参阅上面我在安装 RnetCDF 时出错，然后我尝试了 ncdf，即使它也没有安装。
-
是的，我试过了。请参阅上面我提到了安装 RnetCDF 的错误，然后我尝试了 ncdf，即使它也没有安装。作者提到了我不知道如何安装的 libcdf。请给我建议。我不是计算机专家；请详细说明您的建议。谢谢
-
我认为您需要使系统库 libnetcdf 的“开发”版本可用，可能类似于
sudo apt-get install libnetcdf-dev。这可能是部分误导性建议；你需要这个库，我只是不确定 libnetcdf 是否是正确的选择。 -
既然你是红帽，请关注these instructions（安装系统库）部分。
标签： r bioconductor