How to install Bibliometric related packages (Bibliometrix and Biblioshiny) in RStudio version 3.6.3 on Linux Mint 20.1?

Mazlee · February 15, 2021, 6:13pm

I was unable to install Bibliometric related packages (bibliometrix and biblioshiny) in Rstudio version 3.6.3 on Linux Mint 20.1. I really hope somebody can advise me on this matter. Thanks in advance.

andresrcs · February 15, 2021, 9:33pm

Can you be more specific? What command you have used? What error message you get?

Mazlee · February 16, 2021, 12:31pm

#BIBLIOMETRIC
install.packages("bibliometrix", dependencies = TRUE)
library(bibliometrix)

Console:

> install.packages("bibliometrix", dependencies = TRUE)
Installing package into ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openssl’, ‘rstatix’, ‘httr’, ‘ggpubr’, ‘car’, ‘rentrez’, ‘XML’, ‘curl’, ‘dimensionsR’, ‘factoextra’, ‘FactoMineR’, ‘pubmedR’, ‘rio’, ‘rscopus’, ‘plotly’

trying URL 'https://cloud.r-project.org/src/contrib/openssl_1.4.3.tar.gz'
Content type 'application/x-gzip' length 1207708 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.0.tar.gz'
Content type 'application/x-gzip' length 402481 bytes (393 KB)
==================================================
downloaded 393 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.2.tar.gz'
Content type 'application/x-gzip' length 159950 bytes (156 KB)
==================================================
downloaded 156 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggpubr_0.4.0.tar.gz'
Content type 'application/x-gzip' length 2689307 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/car_3.0-10.tar.gz'
Content type 'application/x-gzip' length 501293 bytes (489 KB)
==================================================
downloaded 489 KB

trying URL 'https://cloud.r-project.org/src/contrib/rentrez_1.2.3.tar.gz'
Content type 'application/x-gzip' length 84042 bytes (82 KB)
==================================================
downloaded 82 KB

trying URL 'https://cloud.r-project.org/src/contrib/Older/XML_3.99-0.3.tar.gz'
Content type 'application/x-gzip' length 968543 bytes (945 KB)
==================================================
downloaded 945 KB

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.tar.gz'
Content type 'application/x-gzip' length 673779 bytes (657 KB)
==================================================
downloaded 657 KB

trying URL 'https://cloud.r-project.org/src/contrib/dimensionsR_0.0.2.tar.gz'
Content type 'application/x-gzip' length 30227 bytes (29 KB)
==================================================
downloaded 29 KB

trying URL 'https://cloud.r-project.org/src/contrib/factoextra_1.0.7.tar.gz'
Content type 'application/x-gzip' length 1386480 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.4.tar.gz'
Content type 'application/x-gzip' length 2822993 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://cloud.r-project.org/src/contrib/pubmedR_0.0.3.tar.gz'
Content type 'application/x-gzip' length 20497 bytes (20 KB)
==================================================
downloaded 20 KB

trying URL 'https://cloud.r-project.org/src/contrib/rio_0.5.16.tar.gz'
Content type 'application/x-gzip' length 420489 bytes (410 KB)
==================================================
downloaded 410 KB

trying URL 'https://cloud.r-project.org/src/contrib/rscopus_0.6.6.tar.gz'
Content type 'application/x-gzip' length 70609 bytes (68 KB)
==================================================
downloaded 68 KB

trying URL 'https://cloud.r-project.org/src/contrib/plotly_4.9.3.tar.gz'
Content type 'application/x-gzip' length 3846165 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

trying URL 'https://cloud.r-project.org/src/contrib/bibliometrix_3.0.4.tar.gz'
Content type 'application/x-gzip' length 458045 bytes (447 KB)
==================================================
downloaded 447 KB

* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
--------------------------- [ANTICONF] --------------------------------
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 MESSAGE] ---------------------------
tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory
    1 | #include <openssl/opensslv.h>
      |          ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
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
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/mazlee/R/x86_64-pc-linux-gnu-library/3.6/XML’
Warning in install.packages :
  installation of package ‘XML’ had non-zero exit status
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
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/mazlee/R/x86_64-pc-linux-gnu-library/3.6/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
ERROR: dependency ‘curl’ is not available for package ‘rio’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/rio’
Warning in install.packages :
  installation of package ‘rio’ had non-zero exit status
ERROR: dependency ‘rio’ is not available for package ‘car’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependencies ‘XML’, ‘httr’ are not available for package ‘rentrez’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/rentrez’
Warning in install.packages :
  installation of package ‘rentrez’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘dimensionsR’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/dimensionsR’
Warning in install.packages :
  installation of package ‘dimensionsR’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘rscopus’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/rscopus’
Warning in install.packages :
  installation of package ‘rscopus’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘plotly’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/plotly’
Warning in install.packages :
  installation of package ‘plotly’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/rstatix’
Warning in install.packages :
  installation of package ‘rstatix’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/FactoMineR’
Warning in install.packages :
  installation of package ‘FactoMineR’ had non-zero exit status
ERROR: dependencies ‘rentrez’, ‘XML’ are not available for package ‘pubmedR’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/pubmedR’
Warning in install.packages :
  installation of package ‘pubmedR’ had non-zero exit status
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/ggpubr’
Warning in install.packages :
  installation of package ‘ggpubr’ had non-zero exit status
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/factoextra’
Warning in install.packages :
  installation of package ‘factoextra’ had non-zero exit status
ERROR: dependencies ‘dimensionsR’, ‘factoextra’, ‘FactoMineR’, ‘pubmedR’, ‘rio’, ‘rscopus’ are not available for package ‘bibliometrix’
* removing ‘/home/mazlee/R/x86_64-pc-linux-gnu-library/3.6/bibliometrix’
Warning in install.packages :
  installation of package ‘bibliometrix’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmpa8s9qX/downloaded_packages’
> library(bibliometrix)
Error in library(bibliometrix) : 
  there is no package called ‘bibliometrix’

system · April 11, 2021, 4:31pm

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