在R中安装bsts包的错误 [英] install error of bsts package in R

问题描述

在CentOS 6.3上安装R软件包 bsts 失败与下面的（截断）错误。我已经尝试将这里更新为GCC版本4.8.2 。还有其他建议吗？

• 安装 b $ b **程序包Boom已成功解压缩并检查MD5总数
  ** libs
  g ++ -m64 -std = c ++ 0x -I / usr / include / R -DNDEBUG -I。 -I ../ inst / include -IBmath -Imath / cephes -Icblas -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE -I / usr / local / include -I/ usr / lib64 / R / library / BH / include-fpic -O2 -g -pipe -Wall -Wp，-D_FORTIFY_SOURCE = 2 -fexceptions -fstack-protector --param = ssp-buffer-size = 4 -m64 -mtune = generic -c Models / Bart / Bart.cpp -o Models /Bart/Bart.o
  Models / Bart / Bart.cpp：在成员函数'void BOOM :: Bart :: VariableSummary :: finalize（int，
  BOOM :: Bart :: ContinuousCutpointStrategy）'：
  Models / Bart / Bart.cpp：110：65：warning：有符号和无符号整数表达式之间的比较[-Wsign-compare]
  if（number_of_unique_values< obser_values_.size（））{
  ^
  Models / Bart / Bart.cpp：117：65：warning：有符号和无符号整数表达式之间的比较[-Wsign-compare]
  if（number_of_unique_values< obser_values_.size（））{
  ^
  Models / Bart / Bart.cpp：129：61：warning：有符号和无符号整数表达式之间的比较[-Wsign-compare]
  if（number_of_unique_values< observe_values_.size（））{
  ^

>

  Models / Bart / Bart.cpp：1393：50：warning：有符号和无符号整数表达式之间的比较[-Wsign-compare] 
 if（number_of_trees_to_remove> = trees_.size（））{
 ^ 
 {标准输入}：汇编消息：
 {标准输入}：71：错误： 
 {标准输入}：664：错误：在`rep'之后需要字符串指令
 {标准输入}：617： ：727：错误：在`rep'之后遇到字符串指令
 {标准输入}：790：错误：在`rep'之后需要字符串指令
 {标准输入}：1171： 
 {标准输入}：1231：错误：在`rep'之后需要字符串指令
 {标准输入}：1180：错误： ：2704：错误：在`rep'之后遇到字符串指令
 {标准输入}：2796：错误：在`rep'之后遇到字符串指令
 {标准输入}：7412： 
 {标准输入}：19481：错误：在`rep'之后需要字符串指令
 {标准输入} ：23959：错误：在`rep'之后遇到字符串指令
 make：*** [Models / Bart / Bart.o]错误1 
错误：程序包Boom的编译失败
 *删除'/ usr / lib64 / R / library / Boom'
错误：dependency'Boom'不适用于包'BoomSpikeSlab'
 *删除'/ usr / lib64 / R / library / BoomSpikeSlab'
错误：dependencies'BoomSpikeSlab'，'Boom'不可用于包'bsts'
 *删除'/ usr / lib64 / R / library / bsts'
 
下载的源软件包在
'/ tmp / Rtmpf9YQJJ / downloaded_pa​​ckages'
更新'.Library'中的软件包的HTML索引
 make'packages.html'... done 
'/ usr / lib64 / R / bin / R'--vanilla CMD INSTALL \ 
'/ tmp / Rtmpf9YQJJ / devtoolsa12a5ce5a465 / google-CausalImpact-9c9286f'\ 
 --library ='/ usr / lib64 / R / library'--install-tests 
 
错误：依赖'bsts'不可用于包'CausalImpact'
 *删除'/ usr / lib64 / R / library / CausalImpact'
错误：命令失败（1）
此外：警告消息：
 1：在utils :: install.packages（deps，dependencies = NA，Ncpus = threads）：
安装的包'Boom'有非零退出状态
 2：在utils :: install.packages（deps，dependencies = NA，Ncpus = threads）：
安装的包'BoomSpikeSlab'有非零退出状态
 3：在utils :: install.packages（deps，dependencies = NA，Ncpus = threads）：
安装程序包'bsts'有非零退出状态
  
 
 
解决方案
在我的例子中，安装C ++和Fortran编译器的新版本a href =http://stackoverflow.com/questions/36034316/r-package-boom-fails-to-install-on-ubuntu-linux/36034866#36034866> R软件包Boom无法在Ubuntu linux上安装，帽子提示Dirk Eddelbuettel）。我之前版本4.8，他们没有工作。
 
 
 
我不知道如何在CentOS上，但我确定可以升级编译器单向或其他。 Ubuntu（14.04）的步骤是：
 
 
添加 ubuntu-toolchain-r  PPA与 add-apt-repository 。我另外使用固定（ https://help.ubuntu.com/community/PinningHowto ），以便 c> gfortran-4.9    / code>。
 
 
设置环境变量 CXX = g ++  -  4.9 和 CXX1X = g ++ -4.9 在〜/ .R / Makevars 或您的 / etc / R / Makeconf 。
 
 
安装Boom。
 
 
 
Installation of the R package bsts on CentOS 6.3 fails with (truncated) error below. I already tried updating GCC to version 4.8.2 as suggested here. Any other suggestions?

  

  
installing source package ‘Boom’ ...
  ** package ‘Boom’ successfully unpacked and MD5 sums checked
  ** libs
  g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I. -I../inst/include -IBmath -Imath/cephes -Icblas -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE -I/usr/local/include -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
  Models/Bart/Bart.cpp: In member function ‘void BOOM::Bart::VariableSummary::finalize(int,
  BOOM::Bart::ContinuousCutpointStrategy)’:
  Models/Bart/Bart.cpp:110:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               if (number_of_unique_values < observed_values_.size()) {
                                                                   ^
  Models/Bart/Bart.cpp:117:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               if (number_of_unique_values < observed_values_.size()) {
                                                                   ^
  Models/Bart/Bart.cpp:129:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (number_of_unique_values < observed_values_.size()) {
                                                               ^
  
Lots of this:
 Models/Bart/Bart.cpp:1393:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (number_of_trees_to_remove >= trees_.size()) {
                                                   ^
 {standard input}: Assembler messages:
 {standard input}:71: Error: expecting string instruction after `rep'
 {standard input}:617: Error: expecting string instruction after `rep'
 {standard input}:664: Error: expecting string instruction after `rep'
 {standard input}:727: Error: expecting string instruction after `rep'
 {standard input}:790: Error: expecting string instruction after `rep'
 {standard input}:1171: Error: expecting string instruction after `rep'
 {standard input}:1180: Error: expecting string instruction after `rep'
 {standard input}:1231: Error: expecting string instruction after `rep'
 {standard input}:2704: Error: expecting string instruction after `rep'
 {standard input}:2796: Error: expecting string instruction after `rep'
 {standard input}:7412: Error: expecting string instruction after `rep'
 {standard input}:7504: Error: expecting string instruction after `rep'
 {standard input}:19481: Error: expecting string instruction after `rep'
 {standard input}:23959: Error: expecting string instruction after `rep'
 make: *** [Models/Bart/Bart.o] Error 1
 ERROR: compilation failed for package ‘Boom’
 * removing ‘/usr/lib64/R/library/Boom’
 ERROR: dependency ‘Boom’ is not available for package ‘BoomSpikeSlab’
 * removing ‘/usr/lib64/R/library/BoomSpikeSlab’
 ERROR: dependencies ‘BoomSpikeSlab’, ‘Boom’ are not available for package ‘bsts’
 * removing ‘/usr/lib64/R/library/bsts’

 The downloaded source packages are in
    ‘/tmp/Rtmpf9YQJJ/downloaded_packages’
 Updating HTML index of packages in '.Library'
 Making 'packages.html' ... done
 '/usr/lib64/R/bin/R' --vanilla CMD INSTALL  \
   '/tmp/Rtmpf9YQJJ/devtoolsa12a5ce5a465/google-CausalImpact-9c9286f'  \
   --library='/usr/lib64/R/library' --install-tests 

 ERROR: dependency ‘bsts’ is not available for package ‘CausalImpact’
 * removing ‘/usr/lib64/R/library/CausalImpact’
 Error: Command failed (1)
 In addition: Warning messages:
 1: In utils::install.packages(deps, dependencies = NA, Ncpus = threads) :
   installation of package ‘Boom’ had non-zero exit status
 2: In utils::install.packages(deps, dependencies = NA, Ncpus = threads) :
   installation of package ‘BoomSpikeSlab’ had non-zero exit status
 3: In utils::install.packages(deps, dependencies = NA, Ncpus = threads) :
   installation of package ‘bsts’ had non-zero exit status

解决方案
In my case installing new versions (4.9) of C++ and Fortran compilers helped (see R package 'Boom' fails to install on Ubuntu linux, hat tip to Dirk Eddelbuettel). I had versions 4.8 earlier and they did not work.

I am not sure how to do that on CentOS, but I am sure it is possible to upgrade the compilers one way or another. The steps for Ubuntu (14.04) are:

Add ubuntu-toolchain-r PPA with add-apt-repository. I additionally used pinning (https://help.ubuntu.com/community/PinningHowto) so that other packages are not automatically updated from that PPA.
Install packages g++-4.9 and gfortran-4.9.
Set the environment variables CXX=g++-4.9 and CXX1X=g++-4.9 in either ~/.R/Makevars or your /etc/R/Makeconf.
Install 'Boom'.


                        
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