But then, when I attached agricolae, I had an error message :
Erreur : package or namespace load failed for ‘agricolae’:
l'objet ‘faststack’ n'est pas exporté par 'namespace:fastmap'
thus I reinstalled the fastmap package through Synaptic, but it reinstalled an older version of dplyr or rlang, after 2 or 3 hours trying to remove and reinstall various versions, I did not get the package Agricolae to work.
If there is no precompiled binary on the Synaptic repository, then it is very likely that the CRAN version is not going to compatible with the rest of packages.
I would recommend updating your R version (yours is quite old) from the CRAN repository (since Linux Mint is Ubuntu based, the Ubuntu repositories might work Ubuntu Packages For R - Brief Instructions) and installing all your packages from CRAN.
Dear Andres,
thanks for your quick reply. I made all whats was in "Ubuntu Packages For R - Brief Instructions)", but I couldn't install any supplementary package from R as sudo, except gtools, gmodels & car. There seem to be a problem with a "release" file:
Blockquote
sudo apt-get update
Ign :9 /cloud.r-project.org/bin/linux/ubuntu uma-cran40/ InRelease
Err :10 Ubuntu Packages For R - Brief Instructions uma-cran40/ Release
404 Not Found [IP : 2600:9000:219c:e400:6:c2d3:f940:93a1 443]
Lecture des listes de paquets... Fait
E: Le dépôt Ubuntu Packages For R - Brief Instructions uma-cran40/ Release n'a pas de fichier Release.
N: Les mises à jour depuis un tel dépôt ne peuvent s'effectuer de manière sécurisée, et sont donc désactivées par défaut.
N: Voir les pages de manuel d'apt-secure(8) pour la création des dépôts et les détails de configuration d'un utilisateur.
Blockquote
installing packages seem to fail because a gfortran problem :
Blockquote
when I try to install agricolae, I get this additional error :
Blockquote
In file included from RS-PQescape.c:7:
RS-PostgreSQL.h:23:14: fatal error: libpq-fe.h: Aucun fichier ou dossier de ce type
23 | # include "libpq-fe.h"
| ^~~~~~~~~~~~
compilation terminated.
There is not Ubuntu Uma version so that repository doesn't exists, I believe Linux Mint Uma is based on Ubuntu Focal so you should try with the "Focal" repository, so the repository should be
deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
Once you have that sorted out, you can install the new R version.
This on the other hand, is a different problem, you are missing a system library, install the required compilers with
sudo apt install build-essential
Note: Please post the console output in English, I don't speak French so you are making a little harder for me to help you.
concerning the deb, ok, I made a mistake, I didn't replace the" $(lsb_release -cs)" by the version. I desinstalled all what I could and reinstalled r-base.
to get rid of the fortran warning, I reinstalled "build-essential" from synaptic, and installed also gfortran.
However, I have still a lot of errors, for example installing car or alr4 through: install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE)
1: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘nloptr’ had non-zero exit status
2: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘RcppEigen’ had non-zero exit status
3: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘quantreg’ had non-zero exit status
4: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘lme4’ had non-zero exit status
5: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘pbkrtest’ had non-zero exit status
6: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘effects’ had non-zero exit status
7: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘car’ had non-zero exit status
8: in install.packages("alr4", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘alr4’ had non-zero exit status
I had tried to paste here the errors i could see in the output :
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
gcc -std=gnu99 -std=gnu11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o quantreg.so akj.o boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crqf.o crqfnb.o dsel05.o etime.o extract.o frand.o grexp.o idmin.o iswap.o kuantile.o kuantiles.o linpack.o mcmb.o penalty.o pfnb.o powell.o profnb.o pwxy.o qfnb.o qselect.o quantreg_init.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sakj.o sparskit2.o srqfn.o srqfnc.o srtpai.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld : cannot find -llapack
/usr/bin/ld : cannot find -lblas
iswap.f:40:72:
40 | IF (INCX-1) 5,20,60
| 1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
srtpai.f:19:72:
19 | 10 P(1, I) = I
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
../inst/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
232 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
You are missing some more system dependencies, that causes the installation of several R package dependencies to fail, install those first and see if you still get error messages.
Hello,
I was looking for the llapack package, but I then understood it was the "lapack' package which was installed:
liblapack3 3.9.0-1build1 and liblas3 . I uninstalled completely both packages using synaptic. But it did not help.
I tried to install gtools through install.packages("gtools", lib = "/usr/lib/R/library", dependencies = TRUE)
but still several errors on dependencies:
ERROR: dependency ‘httr’ is not available for package ‘plotly’
removing ‘/usr/lib/R/library/plotly’
ERROR: dependency ‘solrium’ is not available for package ‘ritis’
removing ‘/usr/lib/R/library/ritis’
ERROR: dependencies ‘httr’, ‘WikipediR’, ‘WikidataQueryServiceR’ are not available for package ‘WikidataR’
removing ‘/usr/lib/R/library/WikidataR’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
removing ‘/usr/lib/R/library/pbkrtest’
ERROR: dependencies ‘Cairo’, ‘plotly’, ‘quantreg’, ‘sn’ are not available for package ‘SGP’
removing ‘/usr/lib/R/library/SGP’
ERROR: dependencies ‘WikidataR’, ‘xml2’ are not available for package ‘wikitaxa’
removing ‘/usr/lib/R/library/wikitaxa’
ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘lme4’ are not available for package ‘car’
removing ‘/usr/lib/R/library/car’
ERROR: dependencies ‘xml2’, ‘ape’, ‘bold’, ‘rotl’, ‘ritis’, ‘wikitaxa’, ‘phangorn’ are not available for package ‘taxize’
removing ‘/usr/lib/R/library/taxize’
I could not install package 'car, and got still the lapack and blas errors': ==========
1: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘nloptr’ had non-zero exit status
2: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘RcppEigen’ had non-zero exit status
3: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘quantreg’ had non-zero exit status
4: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘rgl’ had non-zero exit status
5: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘lme4’ had non-zero exit status
6: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘pbkrtest’ had non-zero exit status
7: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘effects’ had non-zero exit status
8: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘car’ had non-zero exit status
9: Dans install.packages("car", lib = "/usr/lib/R/library", dependencies = TRUE) :
installation of package ‘alr4’ had non-zero exit status
================= errors:
In file included from pixmap.cpp:16:
pngpixmap.h:3:10: fatal error: png.h: Aucun fichier ou dossier de ce type
3 | #include <png.h>
| ^~~~~~~
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
gcc -std=gnu99 -std=gnu11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o quantreg.so akj.o boot.o
/usr/bin/ld : ne peut trouver -llapack
/usr/bin/ld : ne peut trouver -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10 : RcppEigen.so] Erreur 1
ERROR: compilation failed for package ‘RcppEigen’
It is the same problem, R can't find lapack and openblas on the specified locations, I'm sorry but since I'm not a Linux mint user I don't know how to install and configure those system libraries on it.