R tidyverse package dependencies problem (aleardy solve it, but why this happened?)

English Install/Boot/Login
#1

OS : openSUSE Leap 15.4 n/a (x86-64)
cinnamon V: 4.6.7
kernel : 5.14.21-150400.24.63-default
RStudio V : Version 1.4.1717

1- i try install “tidyverse package” to Rstudio by run install.packages (“tidyverse”) command in RStudio console, it return bunch of error message about dependencies.

2- i think if i run RStudio as root it will own the power to install the dependencies. so i open the terminal, write “su” and hit enter, add the password and hit enter, then run the Rstudio and try install “tidyverse package” to Rstudio by run install.packages (“tidyverse”) command in RStudio console, but it also return bunch of error messages.

3- out from root and run Rstudio as normal user
a- try install the package again.
b- read the error message.
c- find the missed dependencies, search and install them using yast.
d- it need repeat that four times, and every time come with new missed dependencies.
e- finally the “tidyverse package” installed

my Questions:

1- why even when run the Rstudio as root (from terminal, after run su command and enter the root password) it could not install the required dependencies?

2- why face this problem from the beginning?

3- is there’s some more professional way to solve this problem or what i did is good?

thanks in advance.

#2

@naive2021:

Did you, before you began the installation of RStudio, refresh the Zypper databases and, install all the patches and updates needed by your system?

 # zypper refresh --force
 # zypper list-patches
 # zypper patch --- possibly with --optional
 # zypper list-updates
 # zypper update

When you first installed RStudio, did you notice the following?

 # LANG=C zypper install --dry-run rstudio
Loading repository data...
Reading installed packages...
Resolving package dependencies...

The following 2 recommended packages were automatically selected:
  mathjax pandoc

The following 2 packages are suggested, but will not be installed:
  rstudio-desktop rstudio-server

The following 63 NEW packages are going to be installed:
  R-KernSmooth R-MASS R-Matrix R-base R-base-devel R-boot R-class R-cluster R-codetools R-compiler R-core R-core-devel
  R-core-doc R-core-libs R-core-packages R-datasets R-foreign R-grDevices R-graphics R-grid R-lattice R-methods R-mgcv
  R-nlme R-nnet R-parallel R-recommended-packages R-rpart R-spatial R-splines R-stats R-stats4 R-survival R-tcltk
  R-tools R-utils boost-license1_75_0 libboost_chrono1_75_0 libboost_filesystem1_75_0 libboost_iostreams1_75_0
  libboost_program_options1_75_0 libboost_regex1_75_0 libboost_thread1_75_0 libsoci_core4_0 libsoci_postgresql4_0
  libsoci_sqlite3-4_0 mathjax mathjax-ams-fonts mathjax-caligraphic-fonts mathjax-fraktur-fonts mathjax-main-fonts
  mathjax-math-fonts mathjax-sansserif-fonts mathjax-script-fonts mathjax-size1-fonts mathjax-size2-fonts
  mathjax-size3-fonts mathjax-size4-fonts mathjax-typewriter-fonts mathjax-winchrome-fonts mathjax-winie6-fonts pandoc
  rstudio

63 new packages to install.
Overall download size: 133.3 MiB. Already cached: 0 B. After the operation, additional 544.0 MiB will be used.
Continue? [y/n/v/...? shows all options] (y): n
 #

Did you then, follow the “suggested” information and install the following RStudio packages in addition?

# LANG=C zypper install --dry-run rstudio-desktop rstudio-server

AFAICS, installing the “rstudio” and “rstudio-desktop” and “rstudio-server” packages on your system, will normally result in 65 new packages being installed on your system.

#3

@naive2021:

Please note that, for packages such as those associated with RStudio, a proper re-install must be proceeded by a removal with the “–clean-deps” option:

# zypper remove --clean-deps rstudio rstudio-desktop rstudio-server

#4

Correct but, there’s this «not easy to find» requirement of Tidyverse when installing it into RStudio on Linux – reference is here: <https://blog.zenggyu.com/en/post/2018-01-29/installing-r-r-packages-e-g-tidyverse-and-rstudio-on-ubuntu-linux/>

In short, the tidyverse package requires the following non-R packages: libcurl4-openssl-dev, libssl-dev, libxml2-dev.

Next problem:

 > LANG=C zypper search libcurl4-openssl-dev libssl-dev libxml2-dev
Loading repository data...
Reading installed packages...

S | Name                | Summary                                                    | Type
--+---------------------+------------------------------------------------------------+--------
i | libxml2-devel       | Development files for libxml2, an XML manipulation library | package
  | libxml2-devel-32bit | Development files for libxml2, an XML manipulation library | package
 >

In other words, only the libxml2 development files package is available for Leap 15.4.

  • The development files packages for libcurl4-openssl and libssl are currently not available for Leap 15.4 – at least not in the repositories I use and, they can’t be found in <https://software.opensuse.org/>.

I have absolutely no idea as to how you can resolve this issue – you may have to ask the “R packages for data science” folks: <https://www.tidyverse.org/>

#5

Those are Debian packages and do not exist in openSUSE under these names.

#6

1- i had installed R language and Rstudio from two or three months so i don’t remember (but i regularly update the system, so i believe i already refresh and update the system before install the R and Rstudio).

  • i use zupeer ref, zupeer lu, and zupeer up command for update the system.

2- i install R and Rstudio using Yast graphical interface (for last two or three months i was work on Rstudio “learning” without any problem.

#7

1- first time see “LANG=C”, can i ask what it did, is it important?

2- if i understand “–dry-run” it mean you will test if the package (app) will installing without any problem without really install it, is it correct?

#8

there’s R language (programming language)
Rstudio (graphical user interface for the programming language)
packages like “tidyverse” (it’s more like let’s say plugin, and it installed using Rstudio console)

and there’s the dependencies packages (some connect to R lang and Rstudio themself, and installed at the begin when install R lang and Rstudio)

(other dependencies required when try add packages like “tidyverse” to Rstudio, and that’s where the problem happened).

so i do not have problem with R lang, Rstudio, or there’s base dependencies

#9

1- add to those some “jpg” and “png” packages
2- when run the command in Rstudio console the error message show for me the alternative packages for RPM Package Manager, and other package manager (still some package name changes, but when search using other names that for other package manager i found them)

#10

still the main question

if i understand correct, when run the Rstudio as root (from terminal, after run su command and enter the root password) it should have the power (full permission) to install the required dependencies?yes

so why it did not work?

is there’s chance as the error message tell me wrong dependencies names for RPM Package Manager also when Rstuido own the full premission start search using same wrong dependencies names and the result it could not find them and can not install the tidyverse package?

is there’s chance that’s is the main problem (wrong dependencies names for RPM Package Manager ), so with sudo power or without it can not find the dependencies as it search using wrong names.

#11

1- add to those some “jpg” and “png” packages
2- when run the command in Rstudio console the error message show for me the alternative packages for RPM Package Manager, and other package manager (still some package name changes, but when search using other names that for other package manager i found them)

#12

That will make sure that the command line output is using US English, which is best for posting in an English forum.

It is actually --dry-run. (Yes, you probably have that right, but the forum software can make it hard to read what was actually used). This will check for dependencies and conflicts, but it won’t actually install anything. It might not find all possible problems.

#13

On openSUSE, the alternative package names for RPM could, possibly, be the needed packages but,

  • can you please inform us which RPM packages the RStudio console is suggesting.

AFAICS, the openSUSE package “libxml2-devel” has the same content as the Debian package “libxml2-dev” and, the openSUSE package places those files in the same directory as that named in the Debian package: <https://packages.debian.org/en/bullseye/amd64/libxml2-dev/filelist>.

That which is still to be resolved is, the equivalent openSUSE packages for the Debian “libcurl4-openssl-dev” and “libssl-dev” packages.

AFAICS, the openSUSE package “libopenssl-1_1-devel” is, as far as the content is concerned, equivalent to the Debian package “libssl-dev” …

AFAICS, the openSUSE package “libcurl-devel” contains most of the files in the Debian package “libcurl4-openssl-dev” with the following differences:

  • Debian uses the directory ‘/usr/include/x86_64-linux-gnu/’
    openSUSE uses the directory ‘/usr/include/curl/’

  • Debian uses the directory ‘/usr/lib/x86_64-linux-gnu/pkgconfig/’
    openSUSE uses the directory ‘/usr/lib64/pkgconfig/’

  • Debian uses the directory ‘/usr/lib/x86_64-linux-gnu/’
    openSUSE uses the directory ‘/usr/lib64/’
    And, the Debian file ‘libcurl.a’ is missing from the openSUSE ‘/usr/lib64/’ directory.

So, there you have it – take it or leave it …