#1

Hello,

I have also problems installing the agricolae package,

I installed R and various packages using Synaptic. But I couldn't find Agricolae in Synaptic. Thus I installed it as sudo in R :

install.packages("agricolae", lib = "/usr/lib/R/library", dependencies = TRUE)

but agricolae required newer version of dplyr and rlang, I downloaded them from CRAN, and installed them :

install.packages("/home/fred/rlang_1.0.1.tar.gz", lib = "/usr/lib/R/library",repos = NULL, dependencies = TRUE)

install.packages("/home/fred/dplyr_1.0.0.tar.gz", lib = "/usr/lib/R/library",repos = NULL, dependencies = TRUE)

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.

=========================================

Installed R version : R-base 3.6.3-2

DISTRIB_ID=LinuxMint

DISTRIB_RELEASE=20.2

DISTRIB_CODENAME=uma

DISTRIB_DESCRIPTION="Linux Mint 20.2 Uma"

=========================================

What should I do ?

Sincerely

frederic

#2

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.

#3

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

/bin/bash: gfortran : commande introuvable
make: *** [/usr/lib/R/etc/Makeconf:191 : mvt.o] Erreur 127
ERROR: compilation failed for package ‘mvtnorm’

  • removing ‘/usr/lib/R/library/mvtnorm’
    /bin/bash: gfortran : commande introuvable

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.

Blockquote

sincerely
frederic

#4

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.

#5

Hello Andres,

  • 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/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]

Failed with error: ‘no package ‘shiny’ was found’

../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)

Thanks
sincerely
frederic

#6

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.

#7

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’

sincerely
frederic

#8

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.

#9

Hello, I may have found the solution from:

simply running:

sudo apt-get install liblapack-dev

I could install the "car" package.
sincerely
frederic

#10

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