想使用geoChina，需要安装AnnoProbe包。
> install.pakages('AnnoProbe')
.........
checking whether the C++ compiler works... yes
checking whether g++ -std=gnu++11 accepts -g... yes
.........
.........
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/lme4’
Warning in install.packages :
installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/pbkrtest’
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/rstatix’
Warning in install.packages :
installation of package ‘rstatix’ had non-zero exit status
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/ggpubr’
Warning in install.packages :
installation of package ‘ggpubr’ had non-zero exit status
ERROR: dependency ‘ggpubr’ is not available for package ‘AnnoProbe’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/AnnoProbe’
Warning in install.packages :
installation of package ‘AnnoProbe’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpXnnNVL/downloaded_packages’
报错。缺少nloptr包。
install.packages('nloptr')
Installing package into ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.sjtug.sjtu.edu.cn/cran/src/contrib/nloptr_2.0.1.tar.gz'
Content type 'application/gzip' length 2219799 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
...................
- sudo port install cmake (MacOS; inside a terminal with MacPorts)
Alternatively install CMake from: <https://cmake.org/>
-------------------------------------------------------
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/qmh/R/x86_64-pc-linux-gnu-library/4.0/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpXnnNVL/downloaded_packages’
继续报错。于linux环境中安装nloptr
zlzx@zlzx-PowerEdge-T640:~$ sudo apt install cmake
zlzx@zlzx-PowerEdge-T640:~$ sudo apt-get install libnlopt-dev
重新安装包。成功。
> install.pakages('AnnoProbe')
........
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AnnoProbe)
The downloaded source packages are in
‘/tmp/RtmpXnnNVL/downloaded_packages’
> library(AnnoProbe)
AnnoProbe v 0.1.6 welcome to use AnnoProbe!
If you use AnnoProbe in published research, please acknowledgements:
We thank Dr.Jianming Zeng(University of Macau), and all the members of his bioinformatics team, biotrainee, for generously sharing their experience and codes.