Rstudio tidyverse installation error

General
1

Hi,

I'm trying to install tidyverse in Rstudio, but i get insted an error. I have tried to remove rstudio and R, and make a reinstall, but, still get the same error. Its seems something wrong with openssl but i'm not sure.

Here is the log:

install.packages("tidyverse")
Installing package into ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘gargle’, ‘ids’, ‘openssl’, ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’

probando la URL 'https://cran.rstudio.com/src/contrib/gargle_1.2.1.tar.gz'
Content type 'application/x-gzip' length 312943 bytes (305 KB)

downloaded 305 KB

...

  • installing source package ‘openssl’ ...
    ** package ‘openssl’ successfully unpacked and MD5 sums checked
    ** using staged installation
    Using PKG_CFLAGS=
    Using PKG_LIBS=-lssl -lcrypto
    ** libs
    rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c aes.c -o aes.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base64.c -o base64.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c bignum.c -o bignum.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c cert.c -o cert.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c compatibility.c -o compatibility.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c diffie.c -o diffie.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c envelope.c -o envelope.o

...

/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../libcrypto.a(x86_64cpuid.o): relocation R_X86_64_PC32 against symbol `OPENSSL_cpuid_setup' can not be used when making a shared object; recompile con -fPIC
/usr/bin/ld: falló el enlace final: Valor erróneo
collect2: error: ld devolvió el estado de salida 1
make: *** [openssl.so] Error 1
ERROR: compilation failed for package ‘openssl’

  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/openssl’
    Warning in install.packages :
    installation of package ‘openssl’ had non-zero exit status
    ERROR: dependency ‘openssl’ is not available for package ‘ids’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/ids’
    Warning in install.packages :
    installation of package ‘ids’ had non-zero exit status
    ERROR: dependency ‘openssl’ is not available for package ‘httr’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/httr’
    Warning in install.packages :
    installation of package ‘httr’ had non-zero exit status
    ERROR: dependency ‘httr’ is not available for package ‘gargle’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/gargle’
    Warning in install.packages :
    installation of package ‘gargle’ had non-zero exit status
    ERROR: dependency ‘httr’ is not available for package ‘rvest’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/rvest’
    Warning in install.packages :
    installation of package ‘rvest’ had non-zero exit status
    ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/googledrive’
    Warning in install.packages :
    installation of package ‘googledrive’ had non-zero exit status
    ERROR: dependencies ‘gargle’, ‘googledrive’, ‘httr’, ‘ids’ are not available for package ‘googlesheets4’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/googlesheets4’
    Warning in install.packages :
    installation of package ‘googlesheets4’ had non-zero exit status
    ERROR: dependencies ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’ are not available for package ‘tidyverse’
  • removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/tidyverse’
    Warning in install.packages :
    installation of package ‘tidyverse’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpDjgANA/downloaded_packages’

Any suggestions?

2

What happens if you try to install the openssl package on its own? If asked if you want to compile from source, say No (or FALSE)—the pre-compiled binaries should be easier to install.

3

Hi,

I try this: install.packages("openssl"), and get a similar error:

install.packages("openssl")
Installing package into ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
probando la URL 'https://cran.rstudio.com/src/contrib/openssl_2.0.2.tar.gz'
Content type 'application/x-gzip' length 1203211 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
** libs
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c aes.c -o aes.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c base64.c -o base64.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c bignum.c -o bignum.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c cert.c -o cert.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c compatibility.c -o compatibility.o

...

info.c: En la función ‘R_openssl_fips_mode’:
info.c:38:3: aviso: declaración implícita de la función ‘FIPS_mode’ [-Wimplicit-function-declaration]
   int enabled = FIPS_mode();
   ^
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c keygen.c -o keygen.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c keys.c -o keys.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c onload.c -o onload.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c openssh.c -o openssh.o
openssh.c: En la función ‘R_ecdsa_pubkey_build’:
openssh.c:208:3: aviso: declaración implícita de la función ‘EC_KEY_set_public_key_affine_coordinates’ [-Wimplicit-function-declaration]
   if(!EC_KEY_set_public_key_affine_coordinates(pubkey, new_bignum_from_r(x), new_bignum_from_r(y)))

...

/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../libcrypto.a(x86_64cpuid.o): relocation R_X86_64_PC32 against symbol `OPENSSL_cpuid_setup' can not be used when making a shared object; recompile con -fPIC
/usr/bin/ld: falló el enlace final: Valor erróneo
collect2: error: ld devolvió el estado de salida 1
make: *** [openssl.so] Error 1
ERROR: compilation failed for package ‘openssl’
* removing ‘/home/neuro/R/x86_64-redhat-linux-gnu-library/3.6/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status
4

OK. Well, the good news is, it looks like my hypothesis that the openssl installation was the problem was right. The bad news is that I'm not totally sure how to fix it (but at least this should narrow down your problem a little bit).

The most informative part of the error seems to be the following:

Is any of this on a shared drive?

I'm going to move this topic into general and tag it with package-installation, since that's the real issue. I'd recommend taking a look at other questions re. installing openssl (e.g. I can't install this package - Install.packages("openssl"), though I'm not sure the issue is the same).

Hopefully someone will be able to whittle down the issue a bit more than I've been able to.

5

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.