UpSetR 关联的 venneuler 包安装笔记

2021-10-15 13:45:33 浏览数 (1)

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背景

R 语言中的 venneuler 是一个用于计算并显示韦恩图和欧拉图的包，这个包在 CRAN 上的最后一个版本是 1.1.0，发布于 2011-08-10，它是一个基于 rJava 依赖的 R 包。

代码语言：javascript复制
vd <- venneuler(c(A=0.3, B=0.3, C=1.1, "A&B"=0.1, "A&C"=0.2, "B&C"=0.1 ,"A&B&C"=0.1))
plot(vd)

# same as c(A=1, `A&B&C`=1, C=1)
m <- data.frame(elements=c("1","2","2","2","3"), sets=c("A","A","B","C","C"))
v <- venneuler(m)
plot(v)

m <- as.matrix(data.frame(A=c(1.5, 0.2, 0.4, 0, 0),
                          B=c(0 , 0.2, 0 , 1, 0),
                          C=c(0 , 0 , 0.3, 0, 1)))
# without weights
v <- venneuler(m > 0)
plot(v)

# with weights
v <- venneuler(m)
plot(v)

在 venneuler 包，作者引入了一个的用于描述集合交集的向量，这一点后来也被UpSetR所借鉴，即UpSetR中的fromExpression。UpSetR接受三种类型的数据输入：

  • 表格数据，即 R 语言里面的数据框。行表示元素，列表示数据集分配和额外信息。
  • 元素名的集合(fromList)。
  • venneuler包引入的用于描述集合交集的向量 (fromExpression)。

早在 18 年 6 月的时候，我公众号上写过一篇关于UpSetR的学习笔记《UpSetR：多数据集绘图可视化处理利器》，提到过一下venneuler，当时也没怎么留意，直到前不久有个读者在使用UpSetR的时候给我了一个截图。

  • 其实，这个截图中的fromExpression拼写错了，如果UpSetR安装好了，函数 fromExpression 也拼写对了，截图中导入集合交集向量数据的问题也就迎刃而解。
  • rJava，venneuler包的安装并没有想象中的那么好安装，尤其是venneuler。

问题

使用conda install r-venneuler安装完venneuler包后，library(venneuler)加载时出现动态库异常。

代码语言：javascript复制
> library(venneuler)
Loading required package: rJava
Error occurred during initialization of VM
Unable to load native library: /usr/local/software/miniconda3/libjava.so: cannot open shared object file: No such file or directory
代码语言：javascript复制
$ R CMD javareconf
Java interpreter : /usr/local/software/miniconda3/bin/java
Java version     : 1.8.0_192
Java home path   : /usr/local/software/miniconda3/jre
Java compiler    : /usr/local/software/miniconda3/bin/javac
Java headers gen.: /usr/local/software/miniconda3/bin/javah
Java archive tool: /usr/local/software/miniconda3/bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
x86_64-conda_cos6-linux-gnu-cc -I"/usr/local/software/miniconda3/lib/R/include" -DNDEBUG -I/usr/local/software/miniconda3/jre/../include -I/usr/local/software/miniconda3/jre/../include/linux  -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/software/miniconda3/include -I/usr/local/software/miniconda3/include -Wl,-rpath-link,/usr/local/software/miniconda3/lib  -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/software/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1576190804673/work=/usr/local/src/conda/r-base-3.6.2 -fdebug-prefix-map=/usr/local/software/miniconda3=/usr/local/src/conda-prefix  -c conftest.c -o conftest.o
x86_64-conda_cos6-linux-gnu-cc -shared -L/usr/local/software/miniconda3/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/software/miniconda3/lib -Wl,-rpath-link,/usr/local/software/miniconda3/lib -L/usr/local/software/miniconda3/lib -Wl,-rpath-link,/usr/local/software/miniconda3/lib -o conftest.so conftest.o -L/usr/local/software/miniconda3/jre/lib/amd64/server -ljvm -L/usr/local/software/miniconda3/lib/R/lib -lR


JAVA_HOME        : /usr/local/software/miniconda3/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /usr/local/software/miniconda3/lib/R
Done.

$ cd /usr/local/software/miniconda3
$ find ./ -name libjava.so
./pkgs/openjdk-8.0.192-h516909a_1004/jre/lib/amd64/libjava.so
./jre/lib/amd64/libjava.s

即使使用LD_LIBRARY_PATH添加完目标动态库后，后面出现的"java/lang/NoClassDefFoundError: java/lang/Object"异常也依然没办法解决。

代码语言：javascript复制
$ export LD_LIBRARY_PATH=/usr/local/software/miniconda3/jre/lib/amd64:$LD_LIBRARY_PATH
$ R

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(venneuler)
Loading required package: rJava
Error occurred during initialization of VM
java/lang/NoClassDefFoundError: java/lang/Object

为了避免 base 环境的影响，使用 conda create -n r-3.6.2 r-base=3.6.2创建的新环境中发现，conda install -r r-venneuler会同时执行 openjdk，r-rjava，r-venneuler三个包的安装，并解决它们其中的依赖，但即使安装过程没有任何问题，在使用library(venneuler)后上面提到的问题也仍然会出现。

conda环境中openjdk，r-rjava，r-venneuler都可以安装成功，但就是用不了，这是我在 conda 中遇到的问题，暂时没找到解决方法。

解决

抛弃了 conda 后，用最原始的方法，终于可以解决这个问题，下面是记录。

1. 安装二进制的 java

在 Java SE 7 Archive Downloads 页面下载 jdk-7u80-linux-x64.tar.gz，解压缩。

代码语言：javascript复制
$ tar zvxf jdk-7u80-linux-x64.tar.gz
$ mv jdk1.7.0_80 /usr/local/software

2. Java 环境配置

把下面的内容添加到~/.bashrc最后，source ~/.bashrc执行环境变量更新。

代码语言：javascript复制
export PATH=/usr/local/software/jdk1.7.0_80/bin:$PATH
export JAVA_HOME=/usr/local/software/jdk1.7.0_80
export JRE_HOME=/usr/local/software/jdk1.7.0_80/jre
export LD_LIBRARY_PATH=/usr/local/software/jdk1.7.0_80/lib/amd64:/usr/local/software/jdk1.7.0_80/jre/lib/amd64:$LD_LIBRARY_PATH

3. 更新 R 的 java 配置

如果没有更新 R 语言的java支持配置，直接执行isntall.packages(rJava)可能会引发以下问题：

代码语言：javascript复制
checking whether JNI programs run... configure: error: Unable to run a simple JNI program. 
Make sure you have configured R with Java support (see R documentation) and check config.log for failure reason.

所以，请使用下面的命令更新 R 语言的 java 支持配置：

代码语言：javascript复制
$ /usr/local/software/miniconda3/bin/R CMD javareconf
Java interpreter : /usr/local/software/jdk1.7.0_80/jre/bin/java
Java version     : 1.7.0_80
Java home path   : /usr/local/software/jdk1.7.0_80
Java compiler    : /usr/local/software/jdk1.7.0_80/bin/javac
Java headers gen.: /usr/local/software/jdk1.7.0_80/bin/javah
Java archive tool: /usr/local/software/jdk1.7.0_80/bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
x86_64-conda_cos6-linux-gnu-cc -I"/usr/local/software/miniconda3/lib/R/include" -DNDEBUG -I/usr/local/software/jdk1.7.0_80/include -I/usr/local/software/jdk1.7.0_80/include/linux  -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/software/miniconda3/include -I/usr/local/software/miniconda3/include -Wl,-rpath-link,/usr/local/software/miniconda3/lib  -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/software/miniconda3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1576190804673/work=/usr/local/src/conda/r-base-3.6.2 -fdebug-prefix-map=/usr/local/software/miniconda3=/usr/local/src/conda-prefix  -c conftest.c -o conftest.o
x86_64-conda_cos6-linux-gnu-cc -shared -L/usr/local/software/miniconda3/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/software/miniconda3/lib -Wl,-rpath-link,/usr/local/software/miniconda3/lib -L/usr/local/software/miniconda3/lib -Wl,-rpath-link,/usr/local/software/miniconda3/lib -o conftest.so conftest.o -L/usr/local/software/jdk1.7.0_80/jre/lib/amd64/server -ljvm -L/usr/local/software/miniconda3/lib/R/lib -lR


JAVA_HOME        : /usr/local/software/jdk1.7.0_80
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/local/software/miniconda3/lib/R
Done.

4. 安装 rJava 和 venneuler

上面的步骤完成后，在 R 中使用rJava和venneuler，发现一切正常。

代码语言：javascript复制
install.packages("rJava")
install.packages("venneuler")

后话

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