Install Rstudio-server in CentOS release 6.10 (Final)

Install Rstudio-server in CentOS release 6.10 (Final)

1. down load rstudio-server-rhel-1.2.5042-x86_64.rpm

2.sudo yum install rstudio-server-rhel-1.2.5042-x86_64.rpm

Resolving Dependencies
--> Running transaction check
---> Package rstudio-server.x86_64 0:1.2.5042-1 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

===============================================
 Package                                         Arch                                    Version                                       Repository                                                             Size
===============================================
Installing:
 rstudio-server                                  x86_64                                  1.2.5042-1                                    /rstudio-server-rhel-1.2.5042-x86_64                                  341 M

Transaction Summary
===============================================
Install       1 Package(s)

Total size: 341 M
Installed size: 341 M
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : rstudio-server-1.2.5042-1.x86_64                                                                                                                                                                1/1 
groupadd: group 'rstudio-server' already exists
rstudio-server start/running, process 91848
  Verifying  : rstudio-server-1.2.5042-1.x86_64                                                                                                                                                                1/1 

Installed:
  rstudio-server.x86_64 0:1.2.5042-1                                                                                                                                                                               

Complete!

3.   edit /etc/rstudio/rserver.conf

rsession-which-r=/usr/local/bin/R
www-port=8787

4. 然后悲剧地发现R之前编译时没加--enable-R-shlib

$sudo rstudio-server verify-installation
25 Dec 2020 11:35:07 [rserver] ERROR Unable to find libR.so in expected locations within R Home directory /usr/local/lib64/R; LOGGED FROM: bool rstudio::core::r_util::{anonymous}::detectRLocationsUsingR(const string&, rstudio::core::FilePath*, rstudio::core::FilePath*, rstudio::core::config_utils::Variables*, std::string*, const string&) /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/core/r_util/REnvironmentPosix.cpp:552
25 Dec 2020 11:35:08 [rserver] ERROR R shared library (/usr/local/lib64/R/lib/libR.so) not found. If this is a custom build of R, was it built with the --enable-R-shlib option?; LOGGED FROM: bool rstudio::core::r_util::{anonymous}::validateREnvironment(const EnvironmentVars&, const rstudio::core::FilePath&, std::string*) /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/core/r_util/REnvironmentPosix.cpp:368
R shared library (/usr/local/lib64/R/lib/libR.so) not found. If this is a custom build of R, was it built with the --enable-R-shlib option?

5.之前的R装的包太多,不想破坏,于是安装同版本R到别的路径

./configure --enable-R-shlib --prefix=/xxx/xxx/tools/R/R-3.2.2
...
R is now configured for x86_64-pc-linux-gnu

  Source directory:          .
  Installation directory:    /xxx/xxx/tools/R/R-3.2.2

  C compiler:                gcc -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  C++ 11 compiler:           g++  -std=c++0x -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:	      

  Interfaces supported:      X11, tcltk
  External libraries:        readline
  Additional capabilities:   NLS
  Options enabled:           shared R library, shared BLAS, R profiling

  Capabilities skipped:      PNG, JPEG, TIFF, cairo, ICU
  Options not enabled:       memory profiling

  Recommended packages:      yes

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages

6.以为这样再make&make install就结束了? 太天真了. 意想不到的意外正在后面等着.

$make
...

installing 'sysdata.rda'
make[4]: Leaving directory `/xxx/xxx/install_log/R/R-3.2.2/src/library/tools'
Error in parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) : 
  invalid multibyte character in parser at line 35075
Error: unable to load R code in package 'tools'
Execution halted

这里的invalid multibyte character in parser at line 35075 来自于之前的一个软件的骚操作使用了GBK字符集, 所以正好由$export LANG="zh_CN.GBK"  触发了错误

后面换'干净'的terminal才正常:

conftest.c: In function 鈥榤ain鈥�:
conftest.c:4: warning: implicit declaration of function 鈥楯NI_CreateJavaVM鈥�
make[2]: *** [conftest.o] Error 1
make[2]: Leaving directory `/tmp/Rjavareconf.tGqgEM'
Unable to compile a JNI program


JAVA_HOME        : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.221.x86_64/jre
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /xxx/xxx/install_log/R/R-3.2.2
Done.

验证:

$ls tools/R/R-3.2.2
bin  lib64  share


$ tools/R/R-3.2.2/bin/R
R version 3.2.2 (2015-08-14) -- "Fire Safety"
...
> .libPaths()
[1] "/xxx/xxx/tools/R/R-3.2.2/lib64/R/library"
> q('no')

遗留问题: 因为之前R是装在/usr/local/bin/R, 这导致无法通过$export PATH=$PATH:/xxx/xxx/R/R-3.2.2/bin 使用新安装的

--

ok,到这里为止, R重新装好了.

重新配置rstudio-server后, rstudio-server test-config , rstudio-server verify-installation 都没问题.

然后sudo rstudio-server start 就rstudio-server start/running, process 132020, 和sudo rstudio-server status输出的一样.

--

然后配置防火墙

sudo /etc/init.d/iptables status
Table: nat
Chain PREROUTING (policy ACCEPT)
num  target     prot opt source               destination         
1    DOCKER     all  --  0.0.0.0/0            0.0.0.0/0           ADDRTYPE match dst-type LOCAL 

Chain POSTROUTING (policy ACCEPT)
num  target     prot opt source               destination         
1    MASQUERADE  all  --  172.17.0.0/16        0.0.0.0/0           

Chain OUTPUT (policy ACCEPT)
num  target     prot opt source               destination         
1    DOCKER     all  --  0.0.0.0/0           !127.0.0.0/8         ADDRTYPE match dst-type LOCAL 

Chain DOCKER (2 references)
num  target     prot opt source               destination         

Table: filter
Chain INPUT (policy ACCEPT)
num  target     prot opt source               destination         
1    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           state RELATED,ESTABLISHED 
2    ACCEPT     icmp --  0.0.0.0/0            0.0.0.0/0           
3    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
4    ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0           state NEW tcp dpt:22 
5    REJECT     all  --  0.0.0.0/0            0.0.0.0/0           reject-with icmp-host-prohibited 

Chain FORWARD (policy ACCEPT)
num  target     prot opt source               destination         
1    DOCKER     all  --  0.0.0.0/0            0.0.0.0/0           
2    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           ctstate RELATED,ESTABLISHED 
3    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
4    REJECT     all  --  0.0.0.0/0            0.0.0.0/0           reject-with icmp-host-prohibited 
5    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           

Chain OUTPUT (policy ACCEPT)
num  target     prot opt source               destination         

Chain DOCKER (1 references)
num  target     prot opt source               destination   

可以看到分nat和filter 两部分.

$sudo iptables -I INPUT -p tcp --dport 8787 -j ACCEPT

$sudo service iptables restart
iptables: Setting chains to policy ACCEPT: filter          [  OK  ]
iptables: Flushing firewall rules:                         [  OK  ]
iptables: Unloading modules:                               [  OK  ]
iptables: Applying firewall rules:                         [  OK  ]

--
sudo /etc/init.d/iptables status
Table: filter
Chain INPUT (policy ACCEPT)
num  target     prot opt source               destination         
1    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           state RELATED,ESTABLISHED 
2    ACCEPT     icmp --  0.0.0.0/0            0.0.0.0/0           
3    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
4    ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0           state NEW tcp dpt:22 
5    REJECT     all  --  0.0.0.0/0            0.0.0.0/0           reject-with icmp-host-prohibited 

Chain FORWARD (policy ACCEPT)
num  target     prot opt source               destination         
1    REJECT     all  --  0.0.0.0/0            0.0.0.0/0           reject-with icmp-host-prohibited 

Chain OUTPUT (policy ACCEPT)
num  target     prot opt source               destination  
--
$sudo iptables -I INPUT -p tcp --dport 8787 -j ACCEPT
--
$sudo /etc/init.d/iptables status
Table: filter
Chain INPUT (policy ACCEPT)
num  target     prot opt source               destination         
1    ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0           tcp dpt:8787 
2    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           state RELATED,ESTABLISHED 
3    ACCEPT     icmp --  0.0.0.0/0            0.0.0.0/0           
4    ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
5    ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0           state NEW tcp dpt:22 
6    REJECT     all  --  0.0.0.0/0