由于R,Rstudio,Shiny都已经安装好了,那么我就直接进入服务器,进行安装。人在墙外,因此无需设置cran repos和Bioc_mirror(其实人在哪无所谓,关键是云服务器在哪)
R #启动R,这是一个啥也没装的R install.packages("BiocManager")
BiocManager::install("scater")
直接报错,我们跟着jimmy教程的思路,可能是linux的库文件缺失,检查发现,是没有安装Java的,如下
java -version # 查看是否安装
cat /etc/issue # 查看ubuntu的版本号 # Ubuntu 18.04.4 LTS \n \l
sudo apt update # 更新本地软件包 # 111个packages可以安装 sudo apt-get dist-upgrade # 升级
开始安装java
sudo apt install default-jre # 安装OpenJDK
java -version # version 11.0.6 sudo apt install default-jdk
javac -version # 检查Java编译器的javac版本,来验证是否已安装JDK # javac 11.0.6 # 进入R,安装scater R
BiocManager::install('scater') # 报错 ------------------------- ANTICONF ERROR --------------------------- Configuration failed because openssl was not found. Try installing: * deb: libssl-dev (Debian, Ubuntu, etc) * rpm: openssl-devel (Fedora, CentOS, RHEL) * csw: libssl_dev (Solaris) * brew: openssl@1.1 (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed for package 'openssl’ * removing '/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.6/openssl’
The downloaded source packages are in '/tmp/RtmpWg4YTU/downloaded_packages’ Warning message: In install.packages("openssl") : installation of package 'openssl’ had non-zero exit status
这里尝试先安装openssl,再安装scater 但是还是提示同样的错误 - Configuration failed because openssl was not found
如何解决呢,参考了stack overflow的一个帖子,帖子里第一种方法不可行,但是第二种是可行的 # 先退出R,运行以下代码 sudo apt-get install libssl-dev # 之后,再次进入R,安装openssl提示成功,进而安装scater也没有阻碍
同样的,安装Seurat还是报错
解决的方法同scater,这里我有个疑问,因为忘了存图了,因此只能文字描述了: 在server上已经安装好了miniconda,但是安装seurat的时候,提示没有安装python,进而提示安装miniconda 感觉不是很理解,不知道有没有朋友知道是为啥
BiocManager::install("monocle")
# 直接上错误信息 ERROR: configuration failed for package 'XML’
直接上解决方案
# 先退出R,运行以下代码 sudo apt-get update
sudo apt-get install libxml2-dev # 之后,再次进入R,安装XML提示成功,进而安装monocle,最终安装成功
OK!全部搞定,可以开始分析了
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