本文详细记录了在CentOS 6.10上安装Rstudio-server的过程，包括下载安装包、解决R编译问题、处理字符集错误、配置R环境以及解决依赖问题等步骤，最后成功启动并访问Rstudio-server。
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=87874. 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 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 /etc/init.d/iptables save
iptables: Saving firewall rules to /etc/sysconfig/iptables:[ OK ]
--
$sudo service 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 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 至此, 方可通过浏览器正常访问.
20210203, 补充configure enable关于png, jpg等部分:
#之前没在configure时配置png,jpeg等:
> capabilities()
jpeg png tiff tcltk X11 aqua
FALSE FALSE FALSE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE TRUE TRUE
NLS profmem cairo ICU long.double libcurl
TRUE FALSE FALSE FALSE TRUE FALSE
#按照编译png必须的包:
yum -y install gcc gcc-c++ autoconf libjpeg libjpeg-devel libpng libpng-devel freetype freetype-devel libxml2 libxml2-devel zlib zlib-devel glibc glibc-devel glib2 glib2-devel bzip2 bzip2-devel ncurses ncurses-devel curl curl-devel e2fsprogs e2fsprogs-devel krb5 krb5-devel libidn libidn-devel openssl openssl-devel openldap openldap-devel nss_ldap openldap-clients openldap-servers gd gd2 gd-devel gd2-devel perl-CPAN pcre-devel
否则会在make时报错:
gcc -fPIC -shared -fopenmp -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a ../extra/tre/libtre.a ../extra/xz/liblzma.a -L../../lib -lRblas -lgfortran -lm -lreadline -lrt -ldl -lm
/usr/bin/ld: CommandLineArgs.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
CommandLineArgs.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1
===================================================================================================================================================================================================================
Package Arch Version Repository Size
===================================================================================================================================================================================================================
Installing:
e2fsprogs-devel x86_64 1.41.12-24.el6 base 161 k
gd x86_64 2.0.35-11.el6 base 142 k
gd-devel x86_64 2.0.35-11.el6 base 78 k
glib2-devel x86_64 2.28.8-10.el6 base 300 k
libcurl-devel x86_64 7.19.7-54.el6_10 updates 247 k
libidn-devel x86_64 1.18-2.el6 base 137 k
libxml2-devel x86_64 2.7.6-21.el6_8.1 base 1.1 M
openldap-clients x86_64 2.4.40-16.el6 base 166 k
openldap-devel x86_64 2.4.40-16.el6 base 1.1 M
openldap-servers x86_64 2.4.40-16.el6 base 2.0 M
pcre-devel x86_64 7.8-7.el6 base 320 k
Updating:
curl x86_64 7.19.7-54.el6_10 updates 198 k
freetype x86_64 2.3.11-19.el6_10 updates 361 k
freetype-devel x86_64 2.3.11-19.el6_10 updates 366 k
openssl x86_64 1.0.1e-58.el6_10 updates 1.5 M
openssl-devel x86_64 1.0.1e-58.el6_10 updates 1.2 M
Installing for dependencies:
cyrus-sasl-devel x86_64 2.1.23-15.el6_6.2 base 303 k
libXpm x86_64 3.5.10-2.el6 base 51 k
libXpm-devel x86_64 3.5.10-2.el6 base 33 k
libtool-ltdl x86_64 2.2.6-15.5.el6 base 44 k
Updating for dependencies:
libcurl x86_64 7.19.7-54.el6_10 updates 170 k
Transaction Summary
===================================================================================================================================================================================================================
Install 15 Package(s)
Upgrade 6 Package(s)
Total download size: 9.9 M
Downloading Packages:
(1/21): curl-7.19.7-54.el6_10.x86_64.rpm | 198 kB 00:00
(2/21): cyrus-sasl-devel-2.1.23-15.el6_6.2.x86_64.rpm | 303 kB 00:00
(3/21): e2fsprogs-devel-1.41.12-24.el6.x86_64.rpm | 161 kB 00:00
(4/21): freetype-2.3.11-19.el6_10.x86_64.rpm | 361 kB 00:00
(5/21): freetype-devel-2.3.11-19.el6_10.x86_64.rpm | 366 kB 00:00
(6/21): gd-2.0.35-11.el6.x86_64.rpm | 142 kB 00:00
(7/21): gd-devel-2.0.35-11.el6.x86_64.rpm | 78 kB 00:00
(8/21): glib2-devel-2.28.8-10.el6.x86_64.rpm | 300 kB 00:00
(9/21): libXpm-3.5.10-2.el6.x86_64.rpm | 51 kB 00:00
(10/21): libXpm-devel-3.5.10-2.el6.x86_64.rpm | 33 kB 00:00
(11/21): libcurl-7.19.7-54.el6_10.x86_64.rpm | 170 kB 00:00
(12/21): libcurl-devel-7.19.7-54.el6_10.x86_64.rpm | 247 kB 00:00
(13/21): libidn-devel-1.18-2.el6.x86_64.rpm | 137 kB 00:00
(14/21): libtool-ltdl-2.2.6-15.5.el6.x86_64.rpm | 44 kB 00:00
(15/21): libxml2-devel-2.7.6-21.el6_8.1.x86_64.rpm | 1.1 MB 00:00
(16/21): openldap-clients-2.4.40-16.el6.x86_64.rpm | 166 kB 00:00
(17/21): openldap-devel-2.4.40-16.el6.x86_64.rpm | 1.1 MB 00:00
(18/21): openldap-servers-2.4.40-16.el6.x86_64.rpm | 2.0 MB 00:00
(19/21): openssl-1.0.1e-58.el6_10.x86_64.rpm | 1.5 MB 00:00
(20/21): openssl-devel-1.0.1e-58.el6_10.x86_64.rpm | 1.2 MB 00:00
(21/21): pcre-devel-7.8-7.el6.x86_64.rpm | 320 kB 00:00
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
./configure --enable-R-shlib --with-libpng --with-jpeglib --with-libtiff --with-x --prefix=/home/xxx/tools/R/R-3.2.2
make clean
make
make install
然后就能在rstudio-server里看到:
> capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets libxml fifo cledit
TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE
iconv NLS profmem cairo ICU long.double libcurl
TRUE TRUE FALSE TRUE FALSE TRUE FALSE
20210204 20:11更新, 因为ggplot2, BiocManager等原因, 安装R 3.6.0, 在安装的过程中发现编译R需要升级gcc, 于是又下载gcc编译...
新技能rpm
$rpm -qa | grep zlib
zlib-1.2.3-29.el6.x86_64
zlib-devel-1.2.3-29.el6.x86_64
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are required
$gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
$wget http://www.zlib.net/fossils/zlib-1.2.6.tar.gz
$./configure --prefix=/xxx/yyy/lib/zlib-1.2.6
$make
$make install
$./configure --enable-R-shlib --with-libpng --with-jpeglib --with-libtiff --with-x --prefix=/xxx/yyy/R/R-3.6.0 LDFLAGS="-L/xxx/yyy/lib/zlib-1.2.6/lib" CPPFLAGS="-I/xxx/yyy/lib/zlib-1.2.6/include"checking if bzip2 version >= 1.0.6... no
这个bzip2有点难下,$wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz 下不动:
2021-02-03 17:45:59 (169 B/s) - “bzip2-1.0.6.tar.gz.1” saved [16207]
$yum search bzip2
Loaded plugins: fastestmirror, security
Determining fastest mirrors
epel/metalink | 4.3 kB 00:00
* epel: d2lzkl7pfhq30w.cloudfront.net
base | 3.7 kB 00:00
extras | 3.4 kB 00:00
home_tange | 1.3 kB 00:00
home_tange 2/2
updates | 3.4 kB 00:00
=================================================================== N/S Matched: bzip2 ===================================================================
bzip2-devel.i686 : Header files developing apps which will use bzip2
bzip2-devel.x86_64 : Header files developing apps which will use bzip2
bzip2-libs.i686 : Libraries for applications using bzip2
bzip2-libs.x86_64 : Libraries for applications using bzip2
lbzip2.x86_64 : Fast, multi-threaded bzip2 utility
lbzip2-utils.x86_64 : Utilities for working with bzip2 compressed files
pbzip2.x86_64 : Parallel implementation of bzip2
perl-Compress-Raw-Bzip2.x86_64 : Low-Level Interface to bzip2 compression library
perl-IO-Compress-Bzip2.x86_64 : Perl interface to allow reading and writing of bzip2 data
bzip2.x86_64 : A file compression utility
python2-bz2file.noarch : Read and write bzip2-compressed files
Name and summary matches only, use "search all" for everything.
但后面还是下原码,因为要修改 bzip2-1.0.6 的 Makefile 文件:
$cd bzip2-1.0.6
#修改 bzip2-1.0.6 的 Makefile 文件
CC=gcc -fPIC
AR=ar
RANLIB=ranlib
LDFLAGS=
BIGFILES=-D_FILE_OFFSET_BITS=64
$make -f Makefile-libbz2_so
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c
gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6
rm -f libbz2.so.1.0
ln -s libbz2.so.1.0.6 libbz2.so.1.0
$make clean
rm -f *.o libbz2.a bzip2 bzip2recover \
sample1.rb2 sample2.rb2 sample3.rb2 \
sample1.tst sample2.tst sample3.tst
$make
If compilation produces errors, or a large number of warnings,
please read README.COMPILATION.PROBLEMS -- you might be able to
adjust the flags in this Makefile to improve matters.
Also in README.COMPILATION.PROBLEMS are some hints that may help
if your build produces an executable which is unable to correctly
handle so-called 'large files' -- files of size 2GB or more.
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
ranlib libbz2.a
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2 bzip2.o -L. -lbz2
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2recover.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2recover bzip2recover.o
Doing 6 tests (3 compress, 3 uncompress) ...
If there's a problem, things might stop at this point.
./bzip2 -1 < sample1.ref > sample1.rb2
./bzip2 -2 < sample2.ref > sample2.rb2
./bzip2 -3 < sample3.ref > sample3.rb2
./bzip2 -d < sample1.bz2 > sample1.tst
./bzip2 -d < sample2.bz2 > sample2.tst
./bzip2 -ds < sample3.bz2 > sample3.tst
cmp sample1.bz2 sample1.rb2
cmp sample2.bz2 sample2.rb2
cmp sample3.bz2 sample3.rb2
cmp sample1.tst sample1.ref
cmp sample2.tst sample2.ref
cmp sample3.tst sample3.ref
If you got this far and the 'cmp's didn't complain, it looks
like you're in business.
To install in /usr/local/bin, /usr/local/lib, /usr/local/man and
/usr/local/include, type
make install
To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type
make install PREFIX=/xxx/yyy
If you are (justifiably) paranoid and want to see what 'make install'
is going to do, you can first do
make -n install or
make -n install PREFIX=/xxx/yyy respectively.
The -n instructs make to show the commands it would execute, but
not actually execute them.
Instructions for use are in the preformatted manual page, in the file
bzip2.txt. For more detailed documentation, read the full manual.
It is available in Postscript form (manual.ps), PDF form (manual.pdf),
and HTML form (manual.html).
You can also do "bzip2 --help" to see some helpful information.
"bzip2 -L" displays the software license.
$make -n install PREFIX=/xxx/yyy/lib/bzip2-1.0.6
$make install PREFIX=/xxx/yyy/lib/bzip2-1.0.6
...
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking for lzma_version_number in -llzma... no
configure: error: "liblzma library and headers are required"
$wget https://nchc.dl.sourceforge.net/project/lzmautils/xz-5.2.3.tar.gz
$./configure --prefix=/xxx/yyy/lib/xz-5.2.3
make
make install
$./configure --enable-R-shlib --with-libpng --with-jpeglib --with-libtiff --with-x --prefix=/xxx/yyy/R/R-3.6.0 LDFLAGS="-L/xxx/yyy/lib/zlib-1.2.6/lib -L/xxx/yyy/lib/bzip2-1.0.6/lib -L/xxx/yyy/lib/xz-5.2.3/lib " CPPFLAGS="-I/xxx/yyy/lib/zlib-1.2.6/include -I/xxx/yyy//lib/bzip2-1.0.6/include -I/xxx/yyy/lib/xz-5.2.3/include "
...
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... no
checking whether PCRE support suffices... configure: error: pcre >= 8.20 library and headers are required
$wget https://ftp.pcre.org/pub/pcre/pcre-8.40.tar.gz --no-check-certificate
$./configure --prefix=/xxx/yyy/lib/pcre-8.40
C preprocessor .................. : gcc -E
C compiler ...................... : gcc
C++ preprocessor ................ : g++ -E
C++ compiler .................... : g++
Linker .......................... : /usr/bin/ld -m elf_x86_64
C preprocessor flags ............ :
C compiler flags ................ : -g -O2 -fvisibility=hidden
C++ compiler flags .............. : -O2 -fvisibility=hidden -fvisibility-inlines-hidden
Linker flags .................... :
Extra libraries ................. :
Build 8 bit pcre library ........ : yes
Build 16 bit pcre library ....... : no
Build 32 bit pcre library ....... : no
Build C++ library ............... : yes
Enable JIT compiling support .... : no
Enable UTF-8/16/32 support ...... : no
Unicode properties .............. : no
Newline char/sequence ........... : lf
\R matches only ANYCRLF ......... : no
EBCDIC coding ................... : no
EBCDIC code for NL .............. : n/a
Rebuild char tables ............. : no
Use stack recursion ............. : yes
POSIX mem threshold ............. : 10
Internal link size .............. : 2
Nested parentheses limit ........ : 250
Match limit ..................... : 10000000
Match limit recursion ........... : MATCH_LIMIT
Build shared libs ............... : yes
Build static libs ............... : yes
Use JIT in pcregrep ............. : no
Buffer size for pcregrep ........ : 20480
Link pcregrep with libz ......... : no
Link pcregrep with libbz2 ....... : no
Link pcretest with libedit ...... : no
Link pcretest with libreadline .. : no
Valgrind support ................ : no
Code coverage ................... : no
checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... no
checking whether PCRE support suffices... configure: error: pcre >= 8.20 library and headers are required
--->UTF-8 support... no
$./configure --prefix=/xxx/yyy/lib/pcre-8.40 -enable-utf8
...
Enable UTF-8/16/32 support ...... : yes
...
...
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes
checking for pcre2-config... no
checking for curl-config... /usr/local/bin/conda/miniconda/bin/curl-config
checking libcurl version ... 7.60.0
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.22.0... no
configure: error: libcurl >= 7.22.0 library and headers are required with support for https
$wget https://curl.haxx.se/download/curl-7.64.1.tar.gz --no-check-certificate
#照旧configure,make,make install.
#但后面R的configure写错了路径, 鄙视一下分心.
...
checking for curl-config... /usr/local/bin/conda/miniconda/bin/curl-config
checking libcurl version ... 7.60.0
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.22.0... yes
checking if libcurl supports https... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
R的configure这关算是过了,但make报错:
...
gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include ...
/usr/bin/ld: warning: libpcre.so.1, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: liblzma.so.5, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
../../lib/libR.so: undefined reference to `lzma_code@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_raw_encoder@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_stream_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_free'
../../lib/libR.so: undefined reference to `lzma_lzma_preset@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_raw_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `libiconv'
../../lib/libR.so: undefined reference to `pcre_version'
../../lib/libR.so: undefined reference to `pcre_exec'
../../lib/libR.so: undefined reference to `pcre_config'
../../lib/libR.so: undefined reference to `libiconv_close'
../../lib/libR.so: undefined reference to `_libiconv_version'
../../lib/libR.so: undefined reference to `pcre_fullinfo'
../../lib/libR.so: undefined reference to `pcre_maketables'
../../lib/libR.so: undefined reference to `libiconv_open'
../../lib/libR.so: undefined reference to `pcre_compile'
../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
../../lib/libR.so: undefined reference to `lzma_end@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_alone_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_version_string@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_crc64@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
../../lib/libR.so: undefined reference to `pcre_study'
../../lib/libR.so: undefined reference to `pcre_free_study'
../../lib/libR.so: undefined reference to `lzma_stream_encoder@XZ_5.0'
collect2: ld returned 1 exit status
j据说是因为gcc版本太低,于是又倒回去折腾gcc
$wget ftp://ftp.gnu.org/gnu/gcc/gcc-4.8.5/gcc-4.8.5.tar.gz
#编译安装 GCC 需要依赖 mpc，mpfr，gmp，isl 包。前四个包是 GNU 软件，$ ./contrib/download_prerequisites下载；
#最后一个 isl 不是 GNU 项目，需要我们手动去下载。
$ wget http://isl.gforge.inria.fr/isl-0.14.tar.gz
$ tar zvxf isl-0.14.tar.gz
$ ln -s lsl isl-0.14
#为了避免在编译过程中，受原来系统自定义的一堆环境影响，建议先 unset 这些环境设置：
$ unset LIBRARY_PATH CPATH C_INCLUDE_PATH PKG_CONFIG_PATH CPLUS_INCLUDE_PATH INCLUDE
$ ABSOLUTE_PATH/configure -enable-checking=release -enable-languages=c,c++ -disable-multilib --prefix=/xxx/yyy/gcc-4.8.5
$ make
$ make install
configure必须用绝对路径,否则make install时报错:
/bin/sh: line 3: cd: ./fixincludes: No such file or directory
make[1]: *** [install-fixincludes] Error 1Wed Feb 03 21:08:13 321 gcc-4.8.5/gcc-build-4.8.5
$make -j 48
Wed Feb 03 21:16:59 322 gcc-4.8.5/gcc-build-4.8.5
48core真快, 耗时8:46
gcc-4.8.5/bin/gcc -dumpversion
4.8.5
$./configure CC=/xxx/tools/gcc-4.8.5/bin/gcc CXX=/home/yangming/tools/gcc-4.8.5/bin/c++ --enable-R-shlib --with-libpng --with-jpeglib --with-libtiff --with-x --prefix=/xxx/tools/R/R-3.6.0 LDFLAGS="-L.../lib" CPPFLAGS="-I.../include"
还是报同样的错误.
gcc-4.8.5/bin/gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L"...
/usr/bin/ld: warning: libpcre.so.1, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: liblzma.so.5, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
../../lib/libR.so: undefined reference to `lzma_code@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_raw_encoder@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_stream_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_free'
../../lib/libR.so: undefined reference to `lzma_lzma_preset@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_raw_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `libiconv'
../../lib/libR.so: undefined reference to `pcre_version'
../../lib/libR.so: undefined reference to `pcre_exec'
../../lib/libR.so: undefined reference to `pcre_config'
../../lib/libR.so: undefined reference to `libiconv_close'
../../lib/libR.so: undefined reference to `_libiconv_version'
../../lib/libR.so: undefined reference to `pcre_fullinfo'
../../lib/libR.so: undefined reference to `pcre_maketables'
../../lib/libR.so: undefined reference to `libiconv_open'
../../lib/libR.so: undefined reference to `pcre_compile'
../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
../../lib/libR.so: undefined reference to `lzma_end@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_alone_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_version_string@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_crc64@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
../../lib/libR.so: undefined reference to `pcre_study'
../../lib/libR.so: undefined reference to `pcre_free_study'
../../lib/libR.so: undefined reference to `lzma_stream_encoder@XZ_5.0'
collect2: error: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
此时因修改$vim Makeconf
LDFLAGS = -L/...
-Wl,-rpath=/xxx/yyy/lib/pcre-8.40/lib
-Wl,-rpath=/xxx/yyy/lib/xz-5.2.3/lib
上面错误消失,变成了
gcc-4.8.5/bin/gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L"../../lib" -L ... -Wl,-rpath=/xxx/yyy/lib/pcre-8.40/lib -Wl,-rpath=/xxx/yyy/lib/xz-5.2.3/lib -o R.bin Rmain.o -lR -lRblas
../../lib/libR.so: undefined reference to `libiconv'
../../lib/libR.so: undefined reference to `libiconv_close'
../../lib/libR.so: undefined reference to `_libiconv_version'
../../lib/libR.so: undefined reference to `libiconv_open'
collect2: error: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
$locate libiconv.so.2出来的几个版本都不对,
libiconv.so.2.6.0
libiconv.so.2.5.1
下原码:
$wget https://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz
...
$./configure --prefix=/xxx/yyy/lib/libiconv-1.14
make & make install
...
R-3.6.0
$vim Makeconf
...
算是编译过了.
下面错误JAVA没装SDK
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
...
configuring Java ...
Java interpreter : /usr/bin/java
Java version : 1.7.0_221
Java home path : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.221.x86_64/jre
Java compiler : not present
Java headers gen.:
Java archive tool:
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
make[2]: Entering directory `/tmp/Rjavareconf.buCQwx'
...
conftest.c:1:17: fatal error: jni.h: No such file or directory
#include <jni.h>
^
compilation terminated.
make[2]: *** [conftest.o] Error 1
make[2]: Leaving directory `/tmp/Rjavareconf.buCQwx'
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 :
Done.
make[1]: Leaving directory xxxx但在拷贝NEWS.pdf时又出现问题:
$make install
...
/usr/bin/install: cannot stat `NEWS.pdf': No such file or directory
/usr/bin/install: cannot stat `NEWS.pdf': No such file or directory
make[1]: *** [install-sources2] Error 1
make[1]: Leaving directory xxx
make: *** [install] Error 1
这个问题搞了我好久,但至少R是装好了:
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE FALSE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE TRUE TRUE
NLS profmem cairo ICU long.double libcurl
TRUE FALSE TRUE FALSE TRUE TRUE
> q('no')
最后简单粗暴解决:
R-3.6.0
$cp doc/NEWS doc/NEWS.pdf
然后$make install成功.
但这还不算完, 装ggplot2时报错, 需要改/usr/lib64/libstdc++.so.6的指向
$ll /usr/lib64/libstdc++.so.6
lrwxrwxrwx. 1 root root 19 Jun 2 2019 /usr/lib64/libstdc++.so.6 -> libstdc++.so.6.0.13
$strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH
$strings /xxx/yyy/gcc-4.8.5/lib64/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH
$sudo ln -sf /xxx/tools/gcc-4.8.5/lib64/libstdc++.so.6.0.19 /usr/lib64/libstdc++.so.6
$strings /usr/lib64/libstdc++.so.6 | grep GLIBC
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBC_2.3
GLIBC_2.2.5
GLIBC_2.3.2
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH
至此,算是经过九九八十一难完成.
下面加入环境变量
$export R_HOME=/xxx/yyy/tools/R/R-3.6.0
$export R_LIBS=/xxx/yyy/tools/R/R-3.6.0/lib64/R/library/
$export LD_LIBRARY_PATH=$R_HOME/lib:$LD_LIBRARY_PATH
$export PATH=$R_HOME/bin:$PATH
参考:
https://blog.csdn.net/weixin_36118025/article/details/112664193
https://blog.51cto.com/191226139/2066137
https://www.jianshu.com/p/5bfe154f1aa4?from=timeline
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