1. 安装

> 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 # 设置国内华科镜像 > options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/") > biocLite("pathview") 

2. 安装报错显示

缺一下软件，需要在ubuntu下的系统进行安装，而不是实用R来安装补充

讯享网* 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

3. 安装系统依赖包，实用R来安装，报错

> 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  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’

4. 实用ubuntu下进行安装，最终所有安装成功

讯享网

讯享网$sudo apt-get install r-cran-xml

无效报错依旧

1. 安装

sudo apt-get install libcurl4-openssl-dev sudo apt-get install libxml2-dev # 或者 sudo apt-get install libcurl4-openssl-dev libxml2-dev

1. 加载库成功，说明缺上面的包,问题已解决

讯享网 library(XML) 

1. 继续根据报错安装

sudo apt-get install libssl-dev 

1. 最终安装成功

讯享网library("pathview")