Docker Rstudio 镜像安装包报错解决办法

第一次安装包

BiocManager::install("genefilter")

报错：

io_utils.c:16:10: fatal error: zlib.h: No such file or directory
   16 | #include <zlib.h>
      |          ^~~~~~~~
compilation terminated.
make: *** [/usr/local/lib/R/etc/Makeconf:168: io_utils.o] Error 1
ERROR: compilation failed for package ‘XVector’
* removing ‘/usr/local/lib/R/site-library/XVector’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/usr/local/lib/R/site-library/annotate’
ERROR: dependency ‘XVector’ is not available for package ‘Biostrings’
* removing ‘/usr/local/lib/R/site-library/Biostrings’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/usr/local/lib/R/site-library/genefilter’

The downloaded source packages are in
    ‘/tmp/RtmpTwafK0/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/local/lib/R/library
  packages:
    Matrix, mgcv
Warning messages:
1: In .inet_warning(msg) : download of package ‘AnnotationDbi’ failed
2: In .inet_warning(msg) :
  installation of package ‘XVector’ had non-zero exit status
3: In .inet_warning(msg) :
  installation of package ‘annotate’ had non-zero exit status
4: In .inet_warning(msg) :
  installation of package ‘Biostrings’ had non-zero exit status
5: In .inet_warning(msg) :
  installation of package ‘genefilter’ had non-zero exit status

在终端输入命令：

groups
sudo su
apt-get update
apt-get install zlib1g-dev

解决Ubuntu下make error：fatal error: zlib.h: No such file or directory_InWho的博客-CSDN博客

第二次安装包：

BiocManager::install("genefilter")

报错：

Error: package or namespace load failed for ‘XML’:
 .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
  libxml2.so.2: cannot open shared object file: No such file or directory
Error: package ‘XML’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘annotate’
* removing ‘/usr/local/lib/R/site-library/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/usr/local/lib/R/site-library/genefilter’

The downloaded source packages are in
    ‘/tmp/RtmpO5AUIa/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/local/lib/R/library
  packages:
    Matrix, mgcv
Warning messages:
1: In grSoftVersion() :
  unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
  libXt.so.6: cannot open shared object file: No such file or directory
2: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
3: In .inet_warning(msg) :
  installation of package ‘annotate’ had non-zero exit status
4: In .inet_warning(msg) :
  installation of package ‘genefilter’ had non-zero exit status

继续终端输入命令：

apt-get install libxt6

查看的资料：
libXt.so.6在哪安装啊？谢谢 - Ubuntu中文论坛

apt-get install libxml2
apt-get install libxml2-dev

查看的资料：
Ubuntu下libxml2的安装和使用_wangrl的博客-CSDN博客
设置镜像：

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
options(repos=structure(c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/")))

查看的资料如下：
R install.packages() 设置国内CRAN镜像_明顯有閒-CSDN博客
bioconductor | 镜像站使用帮助 | 清华大学开源软件镜像站 | Tsinghua Open Source Mirror

举一反三：

BiocManager::install("clusterProfiler")

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/local/lib/R/site-library/igraph/libs/igraph.so':
  libglpk.so.40: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘enrichplot’
* removing ‘/usr/local/lib/R/site-library/enrichplot’
ERROR: dependency ‘enrichplot’ is not available for package ‘clusterProfiler’
* removing ‘/usr/local/lib/R/site-library/clusterProfiler’

The downloaded source packages are in
    ‘/tmp/RtmpO5AUIa/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/local/lib/R/library
  packages:
    Matrix, mgcv, survival
Warning messages:
1: In .inet_warning(msg) :
  installation of package ‘enrichplot’ had non-zero exit status
2: In .inet_warning(msg) :
  installation of package ‘clusterProfiler’ had non-zero exit status
> library("clusterProfiler")
Error in library("clusterProfiler") : 
  there is no package called ‘clusterProfiler’

直接在谷歌上检索：libglpk.so.40，得到可以找到对应包的链接：https://packages.ubuntu.com/search?searchon=contents&keywords=libglpk.so&mode=filename&suite=focal&arch=any根据查看，得知libglpk.so.40对应libglpk40这个包：

image.png
在终端上输入：

apt-get install libglpk40

控制台输入

BiocManager::install("clusterProfiler")

现在安装啥都OK啦！！！感谢张琼老师的耐心指导！！！