tidyverse install fails

wdchild · November 5, 2021, 8:05pm

I usually have no issues on a Mac, but trying to install tidyverse in Linux is giving me fits. I got a message that the package is stored in

/tmp/RtmpboNTou/downloaded_packages

but the install fails no matter what. Here's what the install attempt looked like.

> install.packages("tidyverse", dependencies = TRUE)
Installing package into ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘gargle’, ‘curl’, ‘ids’, ‘openssl’, ‘googledrive’, ‘googlesheets4’, ‘httr’, ‘rvest’, ‘xml2’, ‘covr’

trying URL 'https://cloud.r-project.org/src/contrib/gargle_1.2.0.tar.gz'
Content type 'application/x-gzip' length 313418 bytes (306 KB)
==================================================
downloaded 306 KB

trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.2.tar.gz'
Content type 'application/x-gzip' length 793345 bytes (774 KB)
==================================================
downloaded 774 KB

trying URL 'https://cloud.r-project.org/src/contrib/ids_1.0.1.tar.gz'
Content type 'application/x-gzip' length 91213 bytes (89 KB)
==================================================
downloaded 89 KB

trying URL 'https://cloud.r-project.org/src/contrib/openssl_1.4.5.tar.gz'
Content type 'application/x-gzip' length 1311351 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/googledrive_2.0.0.tar.gz'
Content type 'application/x-gzip' length 1593656 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cloud.r-project.org/src/contrib/googlesheets4_1.0.0.tar.gz'
Content type 'application/x-gzip' length 222038 bytes (216 KB)
==================================================
downloaded 216 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/rvest_1.0.2.tar.gz'
Content type 'application/x-gzip' length 94357 bytes (92 KB)
==================================================
downloaded 92 KB

trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.2.tar.gz'
Content type 'application/x-gzip' length 271876 bytes (265 KB)
==================================================
downloaded 265 KB

trying URL 'https://cloud.r-project.org/src/contrib/covr_3.5.1.tar.gz'
Content type 'application/x-gzip' length 146686 bytes (143 KB)
==================================================
downloaded 143 KB

trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.1.tar.gz'
Content type 'application/x-gzip' length 702779 bytes (686 KB)
==================================================
downloaded 686 KB

* 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/daniel/R/x86_64-pc-linux-gnu-library/3.6/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* 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/daniel/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 ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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 ‘xml2’
* removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6/xml2’
Warning in install.packages :
  installation of package ‘xml2’ had non-zero exit status
ERROR: dependency ‘openssl’ is not available for package ‘ids’
* removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6/ids’
Warning in install.packages :
  installation of package ‘ids’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/daniel/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 ‘httr’ is not available for package ‘gargle’
* removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6/gargle’
Warning in install.packages :
  installation of package ‘gargle’ had non-zero exit status
ERROR: dependencies ‘httr’, ‘xml2’ are not available for package ‘rvest’
* removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6/rvest’
Warning in install.packages :
  installation of package ‘rvest’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘covr’
* removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6/covr’
Warning in install.packages :
  installation of package ‘covr’ had non-zero exit status
ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’
* removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.6/googledrive’
Warning in install.packages :
  installation of package ‘googledrive’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘gargle’, ‘googledrive’, ‘httr’, ‘ids’ are not available for package ‘googlesheets4’
* removing ‘/home/daniel/R/x86_64-pc-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’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/daniel/R/x86_64-pc-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/RtmpboNTou/downloaded_packages’

Any ideas on how to fix this. FWIW, the Linux Mint is running on a VM under Hyper-V. Thanks so much for looking into this.

pcall · November 5, 2021, 11:05pm

I think this is the relevant part of the error:

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)

One of the tidyverse packages, rvest I believe, requires *ssl which is probably causing the failure to install here. So for whatever Linux distribution you're running, look for the appropriate command to install *ssl (probably libssl-dev).

You should be able to install the whole tidyverse after that.

wdchild · November 8, 2021, 2:21pm

Thank you!!!! I had to install a couple of other things, but once you showed me what the message was trying to tell me, I figured it out and was eventually able to install tidyverse.

Wolney · November 8, 2021, 5:20pm

Hi pcall,
Perhaps you can help me; install tidyverse was possible but load it shouw the current error:

library(tidyverse)
Erro: package or namespace load failed for ‘tidyverse’ in dyn.load(file, DLLpath = DLLpath, ...):
impossível carregar objeto compartilhado '/home/usuario/R/x86_64-pc-linux-gnu-library/4.1/xml2/libs/xml2.so':
/home/usuario/R/x86_64-pc-linux-gnu-library/4.1/xml2/libs/xml2.so: symbol htmlReadFile version LIBXML2_2.6.0 not defined in file libxml2.so.2 with link time reference

I'm also using linux and had already installe de libxml2; this problem also appears with loading kableextra and xml2 packages.

Any ideda?

Tks

pcall · November 8, 2021, 6:23pm

Hi, I tried Googling your error message, and I see you've made several other posts about this issue. Unfortunately, I don't have any suggestions beyond what people had already told you to try (remove/reinstall tidyverse, download xml at the command line, update R, update or downgrade your computer etc.) You might have encountered a bonafide error though, and hopefully someone in the xml2 GitHub repo will respond appropriately.

If you don't need the {xml2} package, then I would recommend running the library() command only with the specific tidyverse libraries you need. So library(dplyr), library(ggplot2), etc.

Wolney · November 8, 2021, 6:47pm

That is true, I tried many forums but no results till now. Thanks for the answer. I will keep looking for some correction.

system · November 29, 2021, 6:47pm

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