KEGG通路分析R包安裝失敗解決-pathview

知識 07-01

1. 安裝

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
# 設置國內華科鏡像
> options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/")
> biocLite("pathview")
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2. 安裝報錯顯示

缺一下軟體，需要在ubuntu下的系統進行安裝，而不是實用R來安裝補充

* installing *source* package 『curl』 ...
** package 『curl』 successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc"
to the PKG_CONFIG_PATH environment variable
No package "libcurl" found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc"
to the PKG_CONFIG_PATH environment variable
No package "libcurl" found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that "pkg-config" is in your
PATH and PKG_CONFIG_PATH contains a libcurl.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 『curl』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/curl』
* installing *source* package 『openssl』 ...
** package 『openssl』 successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
------------------------- 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/toucan/R/x86_64-pc-linux-gnu-library/3.4/openssl』
* installing *source* package 『XML』 ...
** package 『XML』 successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package 『XML』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/XML』
ERROR: dependencies 『curl』, 『openssl』 are not available for package 『httr』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/httr』
ERROR: dependency 『XML』 is not available for package 『KEGGgraph』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/KEGGgraph』
ERROR: dependency 『httr』 is not available for package 『KEGGREST』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/KEGGREST』
ERROR: dependencies 『KEGGgraph』, 『XML』, 『KEGGREST』 are not available for package 『pathview』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/pathview』
The downloaded source packages are in
『/tmp/RtmphFHfs8/downloaded_packages』
installation path not writeable, unable to update packages: backports, bindr, bindrcpp, data.table, dplyr, Formula, highr, htmlTable,
htmlwidgets, knitr, munsell, pillar, purrr, Rcpp, reshape2, rlang, stringi, stringr, tibble, tidyr, utf8, viridis, yaml, cluster,
foreign, MASS, Matrix, mgcv, nlme, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『curl』 had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『openssl』 had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『XML』 had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『httr』 had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『KEGGgraph』 had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『KEGGREST』 had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 『pathview』 had non-zero exit status
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3. 安裝系統依賴包，實用R來安裝，報錯

> install.packages("XML")
Installing package into 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4』
(as 『lib』 is unspecified)
trying URL "https://cloud.r-project.org/src/contrib/XML_3.98-1.11.tar.gz"
Content type "application/x-gzip" length 1599533 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
* installing *source* package 『XML』 ...
** package 『XML』 successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package 『XML』
* removing 『/home/toucan/R/x86_64-pc-linux-gnu-library/3.4/XML』
Warning in install.packages :
installation of package 『XML』 had non-zero exit status
The downloaded source packages are in
『/tmp/RtmphFHfs8/downloaded_packages』
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