Installation of package ‘Rmpfr’ had non-zero exit status in R
If you surf to Rmpfr part of the CRAN repository, you will notice that this package requires gmp and mpfr as system requirements installed prior to installing the R package.
What worked for me on Fedora 30 was that I made sure that I had the -devel versions installed, so:
sudo dnf install gmp-devel mpfr-devel
First I tried installing the package:
$ R
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
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> install.packages("Rmpfr")
Installing package into ‘/home/romunov/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependency ‘gmp’
trying URL 'https://cran.wu.ac.at/src/contrib/gmp_0.5-13.5.tar.gz'
Content type 'application/x-gzip' length 133364 bytes (130 KB)
==================================================
downloaded 130 KB
trying URL 'https://cran.wu.ac.at/src/contrib/Rmpfr_0.7-2.tar.gz'
Content type 'application/x-gzip' length 626031 bytes (611 KB)
==================================================
downloaded 611 KB
* installing *source* package ‘gmp’ ...
** package ‘gmp’ successfully unpacked and MD5 sums checked
** using staged installation
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... no
configure: error: GNU MP not found, or not 4.1.4 or up, see http://gmplib.org
ERROR: configuration failed for package ‘gmp’
* removing ‘/home/romunov/R/x86_64-redhat-linux-gnu-library/3.6/gmp’
ERROR: dependency ‘gmp’ is not available for package ‘Rmpfr’
* removing ‘/home/romunov/R/x86_64-redhat-linux-gnu-library/3.6/Rmpfr’
The downloaded source packages are in
‘/tmp/RtmpstRn5N/downloaded_packages’
Warning messages:
1: In install.packages("Rmpfr") :
installation of package ‘gmp’ had non-zero exit status
2: In install.packages("Rmpfr") :
installation of package ‘Rmpfr’ had non-zero exit status
Installing gmp-devel
$ sudo dnf install gmp-devel
Last metadata expiration check: 0:59:19 ago on Tue 24 Dec 2019 09:44:08 AM CET.
Dependencies resolved.
=========================================================================================================================================================================
Package Architecture Version Repository Size
=========================================================================================================================================================================
Installing:
gmp-devel x86_64 1:6.1.2-10.fc30 fedora 173 k
Installing dependencies:
gmp-c++ x86_64 1:6.1.2-10.fc30 fedora 17 k
Transaction Summary
=========================================================================================================================================================================
Install 2 Packages
Total download size: 191 k
Installed size: 402 k
Is this ok [y/N]: y
Downloading Packages:
(1/2): gmp-c++-6.1.2-10.fc30.x86_64.rpm 36 kB/s | 17 kB 00:00
(2/2): gmp-devel-6.1.2-10.fc30.x86_64.rpm 214 kB/s | 173 kB 00:00
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 107 kB/s | 191 kB 00:01
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : gmp-c++-1:6.1.2-10.fc30.x86_64 1/2
Installing : gmp-devel-1:6.1.2-10.fc30.x86_64 2/2
Running scriptlet: gmp-devel-1:6.1.2-10.fc30.x86_64 2/2
Verifying : gmp-c++-1:6.1.2-10.fc30.x86_64 1/2
Verifying : gmp-devel-1:6.1.2-10.fc30.x86_64 2/2
Installed:
gmp-devel-1:6.1.2-10.fc30.x86_64 gmp-c++-1:6.1.2-10.fc30.x86_64
Complete!
Ooops, not enough.
> install.packages("Rmpfr")
Installing package into ‘/home/romunov/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependency ‘gmp’
trying URL 'https://cran.wu.ac.at/src/contrib/gmp_0.5-13.5.tar.gz'
Content type 'application/x-gzip' length 133364 bytes (130 KB)
==================================================
downloaded 130 KB
trying URL 'https://cran.wu.ac.at/src/contrib/Rmpfr_0.7-2.tar.gz'
Content type 'application/x-gzip' length 626031 bytes (611 KB)
==================================================
downloaded 611 KB
* installing *source* package ‘gmp’ ...
** package ‘gmp’ successfully unpacked and MD5 sums checked
** using staged installation
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c apply.cc -o apply.o
...
checking mpfr.h presence... no
checking for mpfr.h... no
configure: error: Header file mpfr.h not found; maybe use --with-mpfr-include=INCLUDE_PATH
ERROR: configuration failed for package ‘Rmpfr’
* removing ‘/home/romunov/R/x86_64-redhat-linux-gnu-library/3.6/Rmpfr’
The downloaded source packages are in
‘/tmp/Rtmpaz2MNH/downloaded_packages’
Warning message:
In install.packages("Rmpfr") :
installation of package ‘Rmpfr’ had non-zero exit status
Installing mpfr-devel.
$ sudo dnf install mpfr-devel
Fedora Modular 30 - x86_64 21 kB/s | 23 kB 00:01
Fedora Modular 30 - x86_64 - Updates 32 kB/s | 22 kB 00:00
Fedora 30 - x86_64 - Updates 28 kB/s | 22 kB 00:00
Fedora 30 - x86_64 18 kB/s | 23 kB 00:01
google-chrome-beta 16 kB/s | 1.3 kB 00:00
google-chrome 3.4 kB/s | 1.3 kB 00:00
RPM Fusion for Fedora 30 - Free - Updates 61 kB/s | 10 kB 00:00
RPM Fusion for Fedora 30 - Free 12 kB/s | 10 kB 00:00
RPM Fusion for Fedora 30 - Nonfree - Steam 54 kB/s | 9.6 kB 00:00
RPM Fusion for Fedora 30 - Nonfree - Updates 51 kB/s | 10 kB 00:00
RPM Fusion for Fedora 30 - Nonfree 61 kB/s | 11 kB 00:00
Dependencies resolved.
=========================================================================================================================================================================
Package Architecture Version Repository Size
=========================================================================================================================================================================
Installing:
mpfr-devel x86_64 3.1.6-4.fc30 fedora 76 k
Transaction Summary
=========================================================================================================================================================================
Install 1 Package
Total download size: 76 k
Installed size: 122 k
Is this ok [y/N]: y
Downloading Packages:
mpfr-devel-3.1.6-4.fc30.x86_64.rpm 283 kB/s | 76 kB 00:00
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 66 kB/s | 76 kB 00:01
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : mpfr-devel-3.1.6-4.fc30.x86_64 1/1
Running scriptlet: mpfr-devel-3.1.6-4.fc30.x86_64 1/1
Verifying : mpfr-devel-3.1.6-4.fc30.x86_64 1/1
Installed:
mpfr-devel-3.1.6-4.fc30.x86_64
Complete!
Trying again
> install.packages("Rmpfr")
Installing package into ‘/home/romunov/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cran.wu.ac.at/src/contrib/Rmpfr_0.7-2.tar.gz'
Content type 'application/x-gzip' length 626031 bytes (611 KB)
==================================================
downloaded 611 KB
* installing *source* package ‘Rmpfr’ ...
** package ‘Rmpfr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc -m64
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 -m64 accepts -g... yes
...
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rmpfr)
The downloaded source packages are in
‘/tmp/Rtmp4K9VTv/downloaded_packages’