question regarding installation of "enrichplot" with BiocManager
2
0
Entering edit mode
abhisek001 • 0
@6d5973d2
Last seen 8 weeks ago
India

I am trying to install "enrichplot" Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2

I getting many error messages which are the following please help me.

 BiocManager::install("enrichplot")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched
  (2022-11-10 r83330)
Installing package(s) 'enrichplot'
also installing the dependencies ‘systemfonts’, ‘ggforce’, ‘ggraph’, ‘scatterpie’

trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.0.4.tar.gz'
Content type 'application/x-gzip' length 81757 bytes (79 KB)
==================================================
downloaded 79 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggforce_0.4.1.tar.gz'
Content type 'application/x-gzip' length 866336 bytes (846 KB)
==================================================
downloaded 846 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggraph_2.1.0.tar.gz'
Content type 'application/x-gzip' length 3172456 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/scatterpie_0.1.8.tar.gz'
Content type 'application/x-gzip' length 390213 bytes (381 KB)
==================================================
downloaded 381 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/enrichplot_1.18.1.tar.gz'
Content type 'application/x-gzip' length 105722 bytes (103 KB)
==================================================
downloaded 103 KB

* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the fontconfig freetype2 library. Try installing:
 * deb: libfontconfig1-dev (Debian, Ubuntu, etc)
 * rpm: fontconfig-devel (Fedora, EPEL)
 * csw: fontconfig_dev (Solaris)
 * brew: freetype (OSX)
If fontconfig freetype2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.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: fontconfig/fontconfig.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘systemfonts’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/systemfonts’
ERROR: dependency ‘systemfonts’ is not available for package ‘ggforce’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/ggforce’
ERROR: dependency ‘ggforce’ is not available for package ‘ggraph’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/ggraph’
ERROR: dependency ‘ggforce’ is not available for package ‘scatterpie’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/scatterpie’
ERROR: dependencies ‘ggraph’, ‘scatterpie’ are not available for package ‘enrichplot’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/enrichplot’

The downloaded source packages are in
    ‘/tmp/RtmpLPh6p2/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, MASS, Matrix, spatial
Warning messages:
1: In install.packages(...) :
  installation of package ‘systemfonts’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘ggforce’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘ggraph’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘scatterpie’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘enrichplot’ had non-zero exit status
R BiocManager install clusterProfiler GO • 284 views
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2
Entering edit mode
@guillaume-devailly-8722
Last seen 6 weeks ago
Toulouse, France

You are likely to be missing a system dependency. See for example this issue. The important part of the error message is here:

Configuration failed to find the fontconfig freetype2 library. Try installing:
 * deb: libfontconfig1-dev (Debian, Ubuntu, etc)
 * rpm: fontconfig-devel (Fedora, EPEL)
 * csw: fontconfig_dev (Solaris)
 * brew: freetype (OSX)
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0
Entering edit mode

Thank you so much. enrichplot is now installed in R studio.

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