SP3源码安装CRUISER进度,MUMmer4的设置与利用

在近些日子的稿子中,基因组共线性深入分析dotplot图大约整个是用MUMmer大概LAST做的。比较对LAST,MUMmer生成的图就像更为美丽,非常是当fasta id比较长时,last-plot会简单一些id,而mummerplot会全体写出来。可是老实,说自家一贯用的LAST做共线性,因为MUMmer真心不佳安装,坑太多了。但是明天花了大半天时光究竟安装成功,记录下来共享。

httperf autobench gnuplot安装

SUSE Linux Enterprise Server 11 SP3源码编写翻译安装ENVISION-3.2.2经过详解。suse上安装牧马人,进度劳碌,作品里的源码包版本都以友好设置时候所用的版本,不必然必需是该版本。

1、情状设置

一、软件列表

  1. MUMmer4的安装

亟需设置如下源码包:
autobench-2.1.2.tar.gz
gd-2.0.34.tar.bz2
gnuplot-4.2.0.tar.gz
httperf-0.9.0.tar.gz
pcre-7.1.tar.bz2
pcre-devel-4.5-3.2.RHEL4.i386.rpm

总体信任关系:

gcc、gcc-c 、make、cmake、svn

  ImageMagick-6.7.1-0.tar.gz

1.1 安装MUMmer4主程序前,需求先安装gnuplot:

安装前先认可是或不是安装过如下程序:

cairo依赖于X11 , pango依赖于cairo

yum install lzo-devel zlib-devel gcc gcc-c make cmake autoconf automake libtool ncurses-devel openssl-devel

  jmagick-6.4.0-src.tar.gz

从gnuplot的官网 链接到其sourceforge下载页。

gcc gcc-c gcc-g77 flex bison autoconf automake bzip2-devel zlib-devel ncurses-devel libjpeg-devel
libpng-devel libtiff-devel freetype-devel pam-devel pcre pcre-devel

设置顺序X11 -> cairo -> pango

2、jdk的安装

  jpegsrc.v6b.tar.gz

潜心:最新版的gnuplot v5.2.6在持续运行时与MUMmer4只怕不太同盟,会报如下错误:

安装GD2:
cd /usr/local/src
wget
tar xzvf gd-2.0.33.tar.gz
cd gd-2.0.33
./configure --prefix=/usr/local/gd2
make
make install

1.设置编写翻译器

rpm -ivh jdk-8-linux-x64.rpm

  libpng-1.5.4.tar.gz

"sample.gp" line 45: warning: this copy of gnuplot has no mouse support

echo "//usr/local/gd2/lib" >> /etc/ld.so.conf
ldconfig

先看看奥迪Q7网站的片段验证:

vim /etc/profile

   tiff-3.8.2.tar.gz

set mouse format "%.0f" ^

安装texinfo-4.7:
cd /usr/local/src
wget
tar zxvf texinfo-4.8.tar.gz
cd texinfo-4.8
./configure
make && make install

B.6 Using FORTRAN:

export JAVA_HOME=/opt/java/jdk1.7.0_72

   freetype-2.3.11.tar.gz

"sample.gp" line 45: unexpected or unrecognized token

安装gnuplot:
cd /usr/local/src
wget
tar zxvf gnuplot-4.2.0.tar.gz
cd gnupolt-4.2.0
./configure
--prefix=/usr/local/gnuplot
--with-cwdrc --without-row-help
--with-kpsexpand
--with-gd=/usr/local/gd2
make && make install

.................

export JRE_HOME=$JAVA_HOME/jre

   zlib-1.2.5.tar.bz2

WARNING: Unable to run '/path/to/gnuplot-5.2.6/bin/gnuplot sample.gp', Inappropriate ioctl for device

安装httperf:
cd /usr/local/src
wget
tar zxvf httperf-0.8.tar.gz
cd httperf-0.8
./configure --prefix=/usr/local/httperf
make && make install

To compile R, you need a FORTRAN compiler.

export PATH=$JAVA_HOME/bin:$JRE_HOME/bin:$PATH

二、安装进程

此地下载的稳固的老版本gnuplot v4.6.2,读者也得以尝尝任何更加高级中学一年级些的老版本,招待将测量试验结果分享到切磋区。

安装autobench包:
cd /usr/local/src
wget
tar zxvf autobench-2.1.2.tar.gz
cd autobench-2.1.2
make && make install

The default is to search for f95, fort, xlf95, ifort,ifc, efc, pgf95 lf95, gfortran, ftn, g95, f90,

export CLASSPATH=.:$JAVA_HOME/lib:$JAVA_HOME/jre/lib:$JAVA_HOME/lib/dt.jar:$JAVA_HOME/lib/tools.jar

只顾:尽管设置进程中因为gcc导致不能够设置时,使用

mkdir gnuplot && cd gnuplot

vi /etc/profile
在HISTSIZE=一千底下增加一行:
export PATH=/usr/local/bin:/usr/local/gnuplot/bin:/usr/local/httperf/bin:$PATH
source /etc/profile

xlf90, pghpf, pgf90, epcf90, g77, f77, xlf, frt,pgf77, cf77, fort77, fl32, af77 (in that order)56,

3、Maven的安装

yum install gcc*或者yum update

wget

倘使上边编写翻译都没错误,施行上面发号施令:

and use whichever is found first; if none is found, Rcannot be compiled. However,

wget

1、安装jpeg协助软件jpegsrc.v6b.tar.gz

tar -zxvf gnuplot-4.6.2.tar.gz

cp /usr/local/bin/bench2graph /usr/local/bin/bench2png
vi /usr/local/bin/bench2png

SP3源码安装CRUISER进度,MUMmer4的设置与利用。if CC is gcc, the matching FORTRAN compiler (g77 forgcc 3 and gfortran for gcc 4) is used if available

tar -zxvf /opt/apache-maven-3.1.1-bin.tar.gz

   tar zvxf jpegsrc.v6b.tar.gz

./configure --prefix=$PWD

sed -i 's/postscript color/png xffffff/g' /usr/local/bin/bench2png

suse暗中认可是未有gfortran编辑器,所以必要先安装它

vim /etc/peofile

   cd jpeg-6b

make install

 

xz -d gcc-trunk.tar.xz

export M2_HOME=/opt/java/maven/apache-maven-3.1.1

    ./configure --enable-shared --enable-static  

专一:如果有报错,能够尝试晋级gcc版本

测试三个服务器质量,生成tsv文件:

tar -xvf gcc-trunk.tar -C /opt

export PATH=$PATH:$M2_HOME/bin

     make 

姣好后,必要将调换的bin目录加到情形变量中

/usr/local/bin/autobench
--single_host
--host1=192.168.0.2
--port1=80
--quiet
--low_rate=10
--high_rate=100
--rate_step=10
--num_call=1
--num_conn=100
--timeout=10
--file /opt/result.tsv

vi /etc/profile

4、Ant的安装

     make install

export PATH=/path/to/gnuplot/gnuplot-4.6.2/bin:$PATH

把tsv文件用图片表示出来:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/gcc-trunk/lib64:/opt/gcc-trunk/lib

wget

2、安装png匡助软件libpng-1.5.4.tar.gz[安装libpng1.4.0以上包后ImageMagick安装退步](安装扶助软件zlib-1.2.5)

1.2 再来安装mummer4:

/usr/local/bin/bench2png /opt/result.tsv /opt/result.png [ 1 2 3 .... ]

exportLIBRARY_PATH=$LIBRARY_PATH:/opt/gcc-trunk/lib:/opt/gcc-trunk/lib64

tar -zxvf /opt/apache-ant-1.9.4-bin.tar.gz

cd zlib-1.2.5

mkdir MUMmer4.00b2 && cd MUMmer4.00b2

万一对两台服务器进行相比较,则用下边发号施令:

export PATH=$PATH:/opt/gcc-trunk/bin

vim /etc/profile

     CFLAGS="-O3 -fPIC" ./configure   //使用61位元的点子进行编写翻译
      make

# MUMmer4.00b2是其设置目录

/usr/local/bin/autobench
--host1=squid.yhc.com
--port1=80
--host2=nginx.yhc.com
--port2=80
--quiet
--low_rate=100
--high_rate=5000
--rate_step=10
--num_call=1
--num_conn=3000
SP3源码安装CRUISER进度,MUMmer4的设置与利用。--timeout=5
--file /opt/result.tsv

source /etc/profile

export ANT_HOME=/opt/java/ant/apache-ant-1.9.4

make install

从MUMmer GitHub下载最新版mummer-4.0.0beta2,并设置:

再把变化的数额转化成图形:
/usr/local/bin/bench2png /opt/result.tsv /opt/result.png [ 1 2 3 .... ]

which gfortran

export PATH=$PATH:$ANT_HOME/bin

 

wget

注:
[1 2 3 .... ]的值分别表示如下:

/opt/gcc-trunk/bin/gfortran

5、Findbugs的安装

tar zvxf libpng-1.5.4.tar.gz

tar -zxvf mummer-4.0.0beta2.tar.gz

1 dem_req_rate

还索要安装gcc-c

wget

cd libpng-1.5.4

cd mummer-4.0.0beta2

2   req_rate_nginx.yhc.com
3   con_rate_nginx.yhc.com
4   min_rep_rate_nginx.jackbillow.com
5   avg_rep_rate_nginx.jackbillow.com
6   max_rep_rate_nginx.jackbillow.com
7   stddev_rep_rate_yhc.jackbillow.com
8   resp_time_nginx.jackbillow.com
9   net_io_nginx.jackbillow.com
10 errors_nginx.jackbillow.com
11 req_rate_apache.jackbillow.com
12con_rate_apache.jackbillow.com
13 min_rep_rate_squid.jackbillow.com
14 avg_rep_rate_squid.jackbillow.com
15 max_rep_rate_squid.jackbillow.com
16 stddev_rep_rate_squid.jackbillow.com
17 resp_time_squid.jackbillow.com
18 net_io_squid.jackbillow.com
19 errors_squid.jackbillow.com

zypper in gcc-c

tar -zxvf /opt/findbugs-3.0.0.tar.gz

./configure

一经gcc版本过底,运营如下代码,也许会并发上边包车型大巴报错

诸如,我做如下相比:

2.安装Xorg-X11
安装cairo必要xlib援助,全数要求X11支撑,编写翻译揽胜供给X11的libX11和libXt

vim /etc/profile

make 

./configure --prefix=$PWD

2   req_rate_nginx.jackbillow.com
11 req_rate_squid.jackbillow.com
/usr/local/bin/bench2png /opt/result.tsv /opt/result.png [ 2 11 ]

 2.1安装libX11-1.6.5
  依赖关系(a,b-> c  c信赖于a,b):

export FINDBUGS_HOME=/opt/java/findbugs/findbugs-3.0.0

 make install

checking if std::thread::sleep_for is supported... no

3   con_rate_nginx.jackbillow.com
12 con_rate_squid.jackbillow.com
/usr/local/bin/bench2png /opt/result.tsv /opt/result.png [ 3 12 ]
   
4   min_rep_rate_nginx.jackbillow.com
13 min_rep_rate_squid.jackbillow.com
/usr/local/bin/bench2png /opt/Result.tsv /opt/result.png [ 4 13 ]

  (libpthread-stubs-0.3,xcb-proto-1.12,libXau-1.0.4) -> libxcb-1.12

export PATH=$PATH:$FINDBUGS_HOME/bin

3、安装tiff援救软件

configure: error: in `/path/to/MUMmer4.00b2/mummer-4.0.0beta2':

 

  (util-macros-1.19.1,kbproto-1.0.4,xproto-7.0.23,inputproto-2.3.2,xextproto-7.0.3)-> libX11-1.6.5 <- (libxcb-1.12)

6、安装protobuf

tar zvxf tiff-3.8.2.tar.gz

configure: error: Compiler does not support std::this_thread::sleep_for

5   avg_rep_rate_nginx.jackbillow.com 
14 avg_rep_rate_squid.jackbillow.com 
/usr/local/bin/bench2png /opt/resultdef.tsv /opt/resulta5_14.png [ 5 14 ]

  1)安装util-macros-1.19.1

wget

cd tiff-3.8.2

查看本身的gcc版本,是4.8.5版的

6   max_rep_rate_nginx.jackbillow.com
15 max_rep_rate_squid.jackbillow.com
/usr/local/bin/bench2png /opt/Resultabc.tsv /opt/resultaabc6_15.png [ 6 15 ]

  ./configure --prefix=/usr/local

tar -zxvf /opt/protobuf-2.5.0.tar.gz

./configure

图片 1

7   stddev_rep_rate_nginx.jackbillow.com 
16 stddev_rep_rate_squid.jackbillow.com  
/usr/local/bin/bench2png /opt/Resultabc.tsv /opt/resultaabc7_16.png [ 7 16 ]

  make install

cd protobuf-2.5.0

make 

急需重新安装三个新版的gcc,gcc的安装可参见作者的另一篇博文( )。

8   resp_time_nginx.jackbillow.com
17 resp_time_squid.jackbillow.com 
/usr/local/bin/bench2png /opt/resultdef.tsv /opt/resultaabc8_17.png [ 8 17 ]

  2)安装kbproto-1.0.4

./configure --prefix=/usr/local

make install 

本人那边已经安装了二个7.2.0本子的,需先将路线加到意况变量中:

9   net_io_nginx.jackbillow.com
18 net_io_squid.jackbillow.com
/usr/local/bin/bench2png /opt/resultdef.tsv /opt/resultaabc9_18.png [ 9 18 ]

  ./configure --prefix=/usr/local

make && make install

4、安装freetype字体帮忙软件freetype-2.3.11.tar.gz

export PATH=/path/to/gcc-v7.2.0/bin:$PATH

10 errors_nginx.jackbillow.com
19 errors_squid.jackbillow.com
/usr/local/bin/bench2png /opt/Resultabc.tsv /opt/resultaabc10_19.png [ 10 19 ]

  make install

7、编译hadoop源码

tar zxvf freetype-2.3.11.tar.gz

图片 2

图片 3

  3)安装xproto-7.0.23

source /etc/profile

cd freetype-2.3.11

./configure --prefix=$PWD

  ./configure --prefix=/usr/local

7.1修改

./configure --prefix=/usr/local/freetype-2.3.11

make install

  make

修改/root/hadoop-2.2.0-src/hadoop-common-project/hadoop-auth/pom.xml文件,扩张补丁内容,那部分是hadoop2.2.0的bug,假使是其余的2.x的本子,能够视情状而定,内容如下:

make 

mummer套件中任何程序幸而,假设最难搞的mummerplot安装达成,就明表明安装OK。能够因而以下结果来申明是还是不是安装完整。

  make install

<dependency>

make install

图片 4

  4)安装inputproto-2.3.2

<groupId>org.mockito</groupId>

<artifactId>mockito-all</artifactId>

<scope>test</scope>

5、安装ImageMagick-6.7.1-0.tar.gz

  1. MUMmer的运行

  ./configure --prefix=/usr/local

</dependency>

tar zvxf ImageMagick-6.7.1-0.tar.gz

建议将MUMmer的门路写到运营时的shell脚本中,当然也能够二遍性写到$HOME/.bashrc中

  make

<!--新扩展的内容初始 -->

cd ImageMagick-6.7.1-0

export PATH=/path/to/MUMmer4.00b2/mummer-4.0.0beta2/bin:$PATH

  make install

<dependency>

./configure --prefix=/usr/local/ImageMagick --enable-share LDFLAGS="-L/usr/lib" CPPFLAGS="-   I/usr/include" --enable-lzw

# step1: run nucmer for alignment

  5)安装xextproto-7.0.3

<groupId>org.mortbay.jetty</groupId>

<artifactId>jetty-util</artifactId>

<scope>test</scope>

make 

nucmer --threads 32 --mum -D 5 -p <outpfix> <subject> <query>

  ./configure --prefix=/usr/local

</dependency>

make install

# outpfix是出口文件前缀

  make install

<!--新增的剧情甘休 -->

6、JMagick是一个开源API,利用JNI(Java Native Interface)技巧达成了对ImageMagickAPI的Java访问接口。安装jmagick-6.4.0-src.tar.gz

# subject和query是想要相比较的多个体系文件,fasta格式

  6)安装libpthread-stubs-0.3

<dependency>

tar xvfz jmagick-6.4.0-src.tar.gz

# step2: filter alignment result

  ./configure --prefix=/usr/local

<groupId>org.mortbay.jetty</groupId>

<artifactId>jetty</artifactId>

cd 6.4.0

delta-filter -i 85 -l 12000 -o 85 <outpfix>.delta -1 > <outpfix>.best_delta

  make

<scope>test</scope>

./configure --prefix=/usr/local/jmagick-6.4.0 --with-magick-home=/usr/local/ImageMagick --enable-share --enable-static

# 个中-i钦赐最小的alignment相似性阈值

  make install

</dependency>

make 

# -l,注意,这里是字母小写的L,钦命最小的alignment长度

  7)安装xcb-proto-1.12

7.2编译

make install

# -o 和-r,-q相关,能够知晓为alignment coverage

  ./configure --prefix=/usr/local

tar -zxvf /opt/hadoop-2.5.1-src.tar.gz

将JMagic库参加到分享库中

# -1注意,这里是数字1,钦点是还是不是实行一定的比对,三个职位(subject或query上)只找贰个顶尖的比对。极其是对大的基因组必得求加那个选项,不然会要命慢

  make

cd hadoop-2.5.1-src

vi /etc/profile

切切实实的参数能够透过delta-filter -h参见到

  make install

mvn package -Pdist,native,docs -DskipTests -Dtar

Mac OS时: export DYLD_LIBRARY_PATH=

# step3: generate figure using mummerplot

  8)安装libXau-1.0.4

图片 5

$DYLD _LIBRARY_PATH:/usr/local/jmagick-6.4.0/lib:/usr/local/ImageMagick/lib

mummerplot -p <outpfix> <outpfix>.best_delta -t postscript

  ./configure --prefix=/usr/local

末尾的文件就在hadoop-2.5.1-src/hadoop-dist/target中

Linux系统时:export LD_LIBRARY_PATH=

# 选拔上一步过滤后的结果<outpfix>.best_delta画图,这里生成的是ps格式的图,就算-t能够钦定png图,可是结果彰显生成的png图分辨率太低。

  make

时现今天,自身编写翻译的hadoop2.5.1早已产生,经测量检验不会再在运作的时候出现warning了,确实令人开玩笑!

$LD_LIBRARY_PATH:/usr/local/jmagick-6.4.0/lib:/usr/local/ImageMagick/lib

# step4: convert ps format to png

  make install

其余:假诺在编写翻译的时候出现难点,不要紧思考一下jdk的本子以及各类软件的本子的主题素材,作者开始的一段时期用的是jdk8,一贯报错,最终尝试了须臾间jdk7才算成功。

   在export CLASSPATH中加入:/usr/local/jmagick-6.4.0/lib

/usr/bin/ps2pdf <outpfix>.pdf <outpfix>.ps

  9)安装libxcb-1.12

source /etc/profile

convert -density 300 <outpfix>.pdf <outpfix>.png

  ./configure --prefix=/usr/local

三、测试

# ps2pdf能够将ps格式的文书转pdf

  make

convert logo: logo.jpg

# convert是imagemagick包中的三个子主次,能够将pdf转为png图片,况兼高清晰

  make install

convert logo: logo.png

  10)安装libX11-1.6.5

convert logo: logo.gif

 2.2安装libXt-1.1.5
  重视关系(a,b-> c  c信赖于a,b)

convert -geometry 600x200 1503.jpg 1503_small.gif 

  (xtrans-1.3.5,libice_1.0.8,libsm_1.2.1) -> libXt-1.1.5

将其拷贝出来,看是或不是能显得

  1)安装xtrans-1.3.5

四、在JAVA工程中应用Jmagick压缩生成图片

  ./configure --prefix=/usr/local

     将jmagick-6.4.0.jar拷贝至jre的lib /ext下,

  make

比如 /usr/java/jdk1.6.0_12/jre/lib/ext/ jmagick-6.4.0.jar

  make install

五、下载文件

  2)安装libICE-1.0.8

   1、 ImageMagick-6.7.1-0.tar.gz

  ./configure --prefix=/usr/local

    

  make

   2、jmagick-6.4.0-src.tar.gz

  make install

   

  3)安装libsm_1.2.1

  3、jpegsrc.v6b.tar.gz

  ./configure --prefix=/usr/local

   

  make

  4、libpng-1.5.4.tar.gz

  make install

   

  4)安装libXt-1.1.5

  5、tiff-3.8.2.tar.gz

  ./configure --prefix=/usr/local

   

  make

   6、freetype-2.3.11.tar.gz 

  make install

   

3.安装cairo-1.14.8  

   7、zlib-1.2.5.tar.bz2

奇骏网站的辨证:

   

A.2 Useful libraries and programs:

六、linux要安装64位的JDK

..............

   下载地址:

The ‘modern’ version of the X11(), jpeg(), png() andtiff() graphics devices uses the cairo and (optionally) Pango libraries.

Cairo version 1.2.0 or later is required.

Pango needs to be at least version 1.10, and 1.12 isthe earliest version we have tested.

(For Fedora users we believe the pango-devel RPM andits dependencies suffice.)

R checks for pkg-config, and uses that to check firstthat the ‘pangocairo’ package is installed (and if not, ‘cairo’)

and if additional flags are needed for the‘cairo-xlib’ package,

then if suitable code can be compiled.

These tests will fail if pkg-config is notinstalled48, and are likely to fail if cairo was built statically (unusual).

Most systems with Gtk 2.8 or later installed willhave suitable libraries

..............

  须求cairo-xlib的支撑(需求安装逼11)

  依赖关系:(a,b-> c  c重视于a,b)

  (libXext-1.0.1,pixman-0.34.0)-> cairo-1.14.8

  1)安装libXext-1.0.1

  ./configure --prefix=/usr/local

  make

  make install

  2)安装pixman-0.34.0

  ./configure --prefix=/usr/local

  make

  make install

  2)安装cairo-1.14.8

  ./configure --prefix=/usr/local --disable-static --enable-xlib=yes--enable-ft=yes --enable-xlib-xcb=yes -enable-tee

  make

  make install

 configure的结果:

  Thefollowing font backends:

  User:          yes (always builtin)

 FreeType:      yes

 Fontconfig:    yes

  Win32:        no (requires a Win32 platform)

  Quartz:        no (requires CoreGraphics framework)

The following functions:

  PNGfunctions:  yes

  GLXfunctions:  no (not required by anybackend)

  WGLfunctions:  no (not required by anybackend)

  EGLfunctions:  no (not required by anybackend)

  X11-xcbfunctions: yes

  XCB-shmfunctions: yes

The following features and utilities:

 cairo-trace:                yes

 cairo-script-interpreter:  yes

And the following internal features:

  pthread:      yes

  gtk-doc:      no

  gcovsupport:  no

 symbol-lookup: no (requires bfd)

  testsurfaces: no (disabled, use --enable-test-surfaces to enable)

  pstesting:    no (requires libspectre)

  pdftesting:  no (requires poppler-glib>= 0.17.4)

  svgtesting:  no (requires librsvg-2.0 >=2.35.0)

4.安装pango  

依傍关系:(a,b -> c  c注重于a,b):

(libffi-3.2,pcre-8.40 ) ->  glib-2.48.2

(libpng-1.6.28,readline-6.3) ->freetype-2.5.4 -> fontconfig-2.12.0 -> harfbuzz-1.4.0 <-(icu4c-50_1,glib-2.48.2)

harfbuzz-1.4.0 -> pango-1.40.2

  1)编译libpng-1.6.28 

  rpm-ivh --nodeps zlib-devel-1.2.7-7.1.1.x86_64.rpm    --freetype需要

 ./configure --prefix=/usr/local

 make

 make install

  2)编译readline-6.3

 ./configure --prefix=/usr/local

 make

 make install

  3)安装freetype-2.5.4

 ./configure --prefix=/usr/local

 make

 make install

  4)编译fontconfig-2.12.0

  rpm-ivh --nodeps libxml2-devel-2.7.6-0.23.1.x86_64.rpm  --fontconfig需要

 ./configure --sysconfdir=/etc --prefix=/usr/local--mandir=/usr/share/man --enable-libxml2

 make

 make install

  5)编译icu4c-50_1

 ./configure --prefix=/usr/local

 make

 make install

  6)编译libffi-3.2

 ./configure --prefix=/usr/local

 make

 make install

  7)编译pcre-8.40

 ./configure --enable-utf8 --enable-unicode-properties--prefix=/usr/local

 make

 make install

  8)编写翻译glib-2.48.2(最棒是其一版本)

 ./configure --prefix=/usr/local

 make

 make install

  9)编译harfbuzz-1.4.0

 ./configure --prefix=/usr/local

 make

 make install

 configure结果:

 Unicode callbacks (you want at least one):

      Glib:                  true

      ICU:                    true

      UCDN:                  false

  10)编译pango-1.40.2

 ./configure --prefix=/usr/local

 make

 make install

5.安装R-3.2.2
  信任关系(a->b  b信任于a):

 gmp-5.1.3 -> isl-0.13

 mpfr-3.1.5 -> mpc-1.0.2

 jpeg9b

 tiff-4.0.7

  1)安装ncurses-devel(readline的依赖)

 zypper in ncurses-devel

  2)安装gmp-5.1.3

 ./configure --prefix=/usr/local

 make

 make install

  2)安装isl-0.13

 ./configure --prefix=/usr/local

 make

 make install

  3)安装mpfr-3.1.5

 ./configure --prefix=/usr/local

 make

 make install

  4)安装mpc-1.0.2

 ./configure --prefix=/usr/local

 make

 make install

  5)安装jpeg-9b

 ./configure --prefix=/usr/local

 make

 make install

  6)安装tiff-4.0.7

 ./configure --prefix=/usr/local

 make

 make install

  7)安装R-3.2.2

 ./configure --enable-R-shlib --with-readline=yes --with-jpeglib=yes--with-libpng=yes --with-x=yes --with-libtiff=yes --with-cairo=yes--with-ICU=yes --prefix=/opt/R

 make  (若无java遭遇还索要安装java)

 make install

 8)vi /etc/profile

  export PATH=$PATH:/opt/gcc-trunk/bin:/opt/R/bin

  source /etc/profiel

  能够最早使用AMG ONE了

  R

 > capabilities()

      jpeg        png        tiff      tcltk        X11        aqua

      TRUE        TRUE        TRUE      FALSE      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        TRUE        TRUE      FALSE

option
  R安装ggplot2

  依赖于:

 digest, gtable (≥ 0.1.1),  plyr (≥ 1.7.1),reshape2, scales (≥ 0.4.1),  tibble, lazyeval

 Rcpp -> plyr

 stringi,magrittr -> stringr -> reshape2

 lazyeval,assertthat -> tibble

 RColorBrewer,dichromat,(colorspace -> munsell),labeling -> scales

  1)R CMD INSTALL digest_0.6.12.tar.gz

  2)R CMD INSTALL gtable_0.2.0.tar.gz

  3)R CMD INSTALL Rcpp_0.12.9.tar.gz

  4)R CMD INSTALL plyr_1.8.4.tar.gz

  5)R CMD INSTALL stringi_1.1.2.tar.gz

  6)R CMD INSTALL magrittr_1.5.tar.gz

  7)R CMD INSTALL stringr_1.2.0.tar.gz

  8)R CMD INSTALL reshape2_1.4.2.tar.gz

  9)R CMD INSTALL lazyeval_0.2.0.tar.gz

 10)R CMD INSTALL assertthat_0.1.tar.gz

 11)R CMD INSTALL tibble_1.2.tar.gz

 12)R CMD INSTALL RColorBrewer_1.1-2.tar.gz

 13)R CMD INSTALL dichromat_2.0-0.tar.gz

 14)R CMD INSTALL colorspace_1.3-2.tar.gz

 15)R CMD INSTALL munsell_0.4.3.tar.gz

 16)R CMD INSTALL labeling_0.3.tar.gz

 17)R CMD INSTALL scales_0.4.1.tar.gz

 18)R CMD INSTALL ggplot2_2.2.1.tar.gz

 R

>library()

Packages in library ‘/opt/R/lib64/R/library’:

KernSmooth              Functions for Kernel SmoothingSupporting Wand

                        & Jones (1995)

MASS                    Support Functions andDatasets for Venables and

                        Ripley's MASS

Matrix                  Sparse and Dense MatrixClasses and Methods

RColorBrewer            ColorBrewer Palettes

Rcpp                    Seamless R and C Integration

assertthat              Easy pre and post assertions.

base                    The R Base Package

boot                    Bootstrap Functions(Originally by Angelo Canty

                        for S)

class                  Functions for Classification

cluster                "Finding Groups inData": Cluster Analysis

                        Extended Rousseeuw etal.

codetools              Code Analysis Tools for R

colorspace              Color Space Manipulation

compiler                The R Compiler Package

datasets                The R Datasets Package

dichromat              Color Schemes for Dichromats

digest                  Create Compact Hash Digestsof R Objects

foreign                Read Data Stored by Minitab,S, SAS, SPSS,

                        Stata, Systat, Weka,dBase, ...

ggplot2                Create Elegant DataVisualisations Using the

                        Grammar of Graphics

FAQ
在安装奥迪Q5的进度中蒙受的一部分主题素材

1.      R依赖

揽胜极光官方网址表达:

The ‘modern’ version of the X11(), jpeg(),png() and tiff() graphics devices uses the cairo and (optionally) Pangolibraries.

Cairo version 1.2.0 or later is required.

Pango needs to be at least version 1.10,and 1.12 is the earliest version we have tested.

(For Fedora users we believe thepango-devel RPM and its dependencies suffice.)

R checks for pkg-config, and uses that tocheck first that the ‘pangocairo’ package is installed (and if not, ‘cairo’)

and if additional flags are needed for the‘cairo-xlib’ package,

then if suitable code can be compiled.

These tests will fail if pkg-config is notinstalled48,

and are likely to fail if cairo was builtstatically (unusual).

Most systems with Gtk 2.8 or laterinstalled will have suitable libraries

需要pango和cairo,并且cairo需要cairo-xlib支持

2.      --with-x=yes (default) andX11 headers/libs are not available

编译R时报错:

checking X11/Intrinsic.h usability... no

checking X11/Intrinsic.h presence... no

checking for X11/Intrinsic.h... no

configure: error: --with-x=yes (default)and X11 headers/libs are not available

化解办法: install libXt

3.      dchdc.o: could not readsymbols: Bad value

make R时报错:

/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:

../appl/dchdc.o: relocation R_X86_64_32against `.rodata' can not be used when making a shared object; recompile with-fPIC

../appl/dchdc.o: could not read symbols:Bad value

collect2: ld returned 1 exit status

搞定办法: configura时去掉--enable-昂Cora-shlib

4.  error: cairo-xlib.h: No suchfile or directory

编译R时报错:

configure:31534: checking for X

configure:31720: result: disabled

configure:32391: result: using X11 ... no

configure:32501: checking whetherpkg-config knows about cairo and pango

configure:32513: result: yes

configure:32547: checking whether cairoincluding pango is >= 1.2 and works

configure:32570: gcc -std=gnu99 -o conftest-g -O2 -fpic  -I/usr/local/include  -I/usr/include/libxml2-I/usr/local/include/pango-1.0 -I/usr/local/include/cairo-I/usr/local/include/harfbuzz -I/usr/local/include/freetype2-I/usr/local/include -I/usr/local/include/glib-2.0-I/usr/local/lib/glib-2.0/include -I/usr/local/include/pixman-1 -I/usr/local/include/libpng16  -L/usr/local/lib64 conftest.c -lrt -ldl-lm  -L/usr/local/lib -lpangocairo-1.0-lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo  >&5

conftest.c:233:24: error: cairo-xlib.h: Nosuch file or directory

configure:32570: $? = 1

化解办法:那是设置了cairo,然则编写翻译cairo时未有加--enable-xlib=yes参数

5.    /libreadline.so: undefined reference to….

configure R时候readline报错,查看config.log:

configure:20905: checking forrl_callback_read_char in -lreadline

configure:20930: gcc -o conftest -g -O2-I/usr/local/include -L/usr/local/lib64 conftest.c -lreadline  >&5

/usr/local/lib/libreadline.so: undefinedreference to `tputs'

/usr/local/lib/libreadline.so: undefinedreference to `tgoto'

/usr/local/lib/libreadline.so: undefinedreference to `tgetflag'

/usr/local/lib/libreadline.so: undefinedreference to `UP'

/usr/local/lib/libreadline.so: undefinedreference to `tgetent'

/usr/local/lib/libreadline.so: undefinedreference to `tgetnum'

/usr/local/lib/libreadline.so: undefinedreference to `PC'

/usr/local/lib/libreadline.so: undefinedreference to `tgetstr'

/usr/local/lib/libreadline.so: undefinedreference to `BC'

collect2: ld returned 1 exit status

configure:20930: $? = 1

消除办法: zypper in ncurses-devel

6.  error: cannot compile a simple Fortranprogram

configure 宝马X5 时候报错:

checking for Fortran 77 libraries ofgfortran...

checking how to get verbose linking outputfrom gcc -std=gnu99... -v

checking for C libraries of gcc-std=gnu99...  -L/usr/local/lib64-L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64-L/lib/../lib64 -L/usr/lib/../lib64-L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/lib-L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../.. -lgcc_s

checking for dummy main to link withFortran 77 libraries... none

checking for Fortran 77 name-manglingscheme... configure: error: in `/soft/R-3.2.2':

configure: error: cannot compile a simpleFortran program

config.log中搜索"cannotcompile a simple Fortran program":

configure:23745: checking for Fortran 77name-mangling scheme

configure:23758: gfortran -c  conftest.f >&5

/opt/gcc-trunk/bin/../libexec/gcc/x86_64-pc-linux-gnu/7.0.0/f951:error while loading shared libraries: libisl.so.13: cannot open sh

ared object file: No such file or directory

configure:23758: $? = 1

configure: failed program was:

|      subroutine foobar()

|      return

|      end

|      subroutine foo_bar()

|      return

|      end

configure:23891: error: in `/soft/R-3.2.2':

configure:23893: error: cannot compile asimple Fortran program

消除办法:安装isl

7.      undefined reference to….

make R时报错

gcc -std=gnu99 -Wl,--export-dynamic-fopenmp  -L../../lib -L/usr/local/lib64-o R.bin Rmain.o  -lR -lRblas

/opt/gcc-trunk/lib64/libgfortran.so.4:undefined reference to `__cpu_model@GCC_4.8.0'

collect2: ld returned 1 exit status

make[3]: *** [R.bin] Error 1

消除办法:

/etc/profile里添加:

exportLIBRARY_PATH=$LIBRARY_PATH:/opt/gcc-trunk/lib:/opt/gcc-trunk/lib64

source /etc/profile

越来越多SUSE相关新闻见SUSE 专项论题页面 http://www.linuxidc.com/topicnews.aspx?tid=3

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