*** installing help indices
Warning in file.copy(file.path(R.home("doc"), "html", "R.css"), outman) :
problem copying /usr/share/doc/R/html/R.css to /usr/lib64/R/library/00LOCK-textshaping/00new/textshaping/html/R.css: No such file or directory
converting help for package ‘textshaping’
finding HTML links ... done
get_font_features html
shape_text html
text_width html
finding level-2 HTML links ... done
textshaping-package html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (textshaping)
Warning in file.create(f.tg) :
cannot create file '/usr/share/doc/R/html/packages.html', reason 'No such file or directory'
Warning in utils::make.packages.html(.Library, docdir = R.home("doc")) :
cannot update HTML package index
* installing *source* package ‘ragg’ ...
** package ‘ragg’ successfully unpacked and MD5 sums checked
** using staged installation
Package libtiff-4 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libtiff-4.pc'
to the PKG_CONFIG_PATH environment variable
Package 'libtiff-4', required by 'virtual:world', not found
Package 'libjpeg', required by 'virtual:world', not found
Package libtiff-4 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libtiff-4.pc'
to the PKG_CONFIG_PATH environment variable
Package 'libtiff-4', required by 'virtual:world', not found
Package 'libjpeg', required by 'virtual:world', not found
Using PKG_CFLAGS=
Using PKG_LIBS=-lfreetype -lpng16 -ltiff -lz -ljpeg -lbz2
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find one of freetype2 libpng libtiff-4 libjpeg. Try installing:
* deb: libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev (Debian, Ubuntu, etc)
* rpm: freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel (Fedora, CentOS, RHEL)
* csw: libfreetype_dev libpng16_dev libtiff_dev libjpeg_dev (Solaris)
If freetype2 libpng libtiff-4 libjpeg is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a freetype2 libpng libtiff-4 libjpeg.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 MESSAGE] ---------------------------
<stdin>:1:10: fatal error: ft2build.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘ragg’
* removing ‘/usr/lib64/R/library/ragg’
ERROR: dependency ‘ragg’ is not available for package ‘pkgdown’
* removing ‘/usr/lib64/R/library/pkgdown’
ERROR: dependency ‘pkgdown’ is not available for package ‘devtools’
* removing ‘/usr/lib64/R/library/devtools’
The downloaded source packages are in
‘/tmp/RtmpccHk8a/downloaded_packages’
Updating HTML index of packages in '.Library'
Old packages: 'boot', 'class', 'cluster', 'codetools', 'data.table', 'dplyr',
'forcats', 'foreign', 'fs', 'future', 'gargle', 'ggplot2', 'ggrepel',
'httpuv', 'igraph', 'KernSmooth', 'lattice', 'lubridate', 'MASS', 'mgcv',
'nlme', 'nnet', 'RcppArmadillo', 'RcppTOML', 'readr', 'readxl', 'rgeos',
'rpart', 'RSQLite', 'rvcheck', 'sourcetools', 'spatial', 'spatstat.geom',
'survival', 'tidygraph', 'tinytex', 'utf8', 'xfun'
Warning messages:
1: In install.packages(...) :
installation of package ‘ragg’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘pkgdown’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘devtools’ had non-zero exit status
4: In file.create(f.tg) :
cannot create file '/usr/share/doc/R/html/packages.html', reason 'No such file or directory'
5: In make.packages.html(.Library) : cannot update HTML package index
从48行开始,有报错信息,但39-48行有解决安装失败的方法,我的系统是fedora,所以重点看42行,执行 dnf install -y freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel
安装成功后,再次执行R -e "BiocManager::install('devtools')"