Unable to install any packages - "Package which is only available in source form, and may need compilation" - "installation of package ‘...’ had non-zero exit status"

rahelb · September 22, 2020, 8:22am

I'm trying to install packages but it doesn't work and I don't know why. I use the install.packages() function.

install.packages("ggplot2")

And then I get:

also installing the dependencies ‘isoband’, ‘rlang’
There are binary versions available but the source versions are later:
binary source needs_compilation
rlang 0.1.6 0.4.7 TRUE
ggplot2 2.2.1 3.3.2 FALSE

Do you want to install from sources the package which needs compilation?
y/n: y

and after that:

Package which is only available in source form, and may need compilation
of C/C++/Fortran: ‘isoband’
Do you want to attempt to install these from sources?
y/n: y

It doesn't matter if I select yes or no, it always does the same and in the end it says:

Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in ‘/private/var/folders/87/5r3pmptj43l2kkcv9nvhqchr0000gn/T/RtmpkqxLoS/downloaded_packages’

When I then type

library(ggplot2)

I get the warning that there is no ggplot2 installed.
I used ggplot2 as an example but it is the same with any package I try to install. I'm using an older MacBook.

Thanks a lot for any advice!

omar1 · September 22, 2020, 8:52am

Must be some error in the internet connection. Please try again later sometime.

rahelb · September 22, 2020, 3:54pm

thanks a lot for your reply. I think it's unlikely that it's the internet connection, I have a stable connection and tried several times also after restarting the laptop and re-installing R Studio.

EconomiCurtis · September 22, 2020, 4:04pm

I've run into this type of error before, and seen others with it.

I've often found that if I individually install the packages the error message is complaining about, I'm then able to get my end-goal package installed. And if I'm struggling to get those dependencies installed, I'll at least get a bit more information about what is causing the trouble.

So, I'd suggest

install.packages("isoband")
install.packages("rlang")

Windows: Also, very likely, you need to install Rtools.
These error messages ("Package which is only available in source form, and may need compilation") may mean your machine doesn't have a compiler. If that's the case, install Rtools

Mac UPDATE, sorry, you said you're on a Mac -- Rtools is for Windows.
You'll want to make sure you have Xcode. Instructions on installing that here
https://www.r-project.org/nosvn/pandoc/devtools.html

rahelb · September 22, 2020, 6:07pm

Thanks a lot for the suggestion! Unfortunately, that didn't work either. When I try

install.packages("isoband")
install.packages("rlang")

I get the same error message:

install.packages("isoband")
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘isoband’
Do you want to attempt to install these from sources?
y/n: y
installing the source package ‘isoband’
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed
100 2242k 100 2242k 0 0 6653k 0 --:--:-- --:--:-- --:--:-- 6633k
Warnung in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz)
unknown timezone 'zone/tz/2020a.1.0/zoneinfo/Europe/Zurich'

installing source package ‘isoband’ ...
** Paket ‘isoband’ erfolgreich entpackt und MD5 Summen überprüft
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘isoband’

removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status

The downloaded source packages are in ‘/private/var/folders/87/5r3pmptj43l2kkcv9nvhqchr0000gn/T/RtmpxvP5Pf/downloaded_packages’

And then I tried installing Xcode, but again, for that I would need to install the package "devtools" which gives the same error message... it's kind of a vicious circle :')

mara · September 22, 2020, 6:10pm

You don't need devtools to install XCode or Xcode Command Line Tools. Those are part of the toolchain on your OS, not part of your R installation or R packages.

The line involving devtools here is just one way you can check and see if you have the necessary system requirements, it's not actually related to installing what you need:
https://rstats.wtf/set-up-an-r-dev-environment.html#macos-system-prep

rahelb · September 22, 2020, 7:31pm

Thanks a lot! I will see if it works when I have installed Xcode then.

pmeise · October 7, 2020, 7:45am

Hi, rahelb!
Have you managed to solve the problem? I have the same

rahelb · October 7, 2020, 6:57pm

hey there, no, not yet, because I have problems installing Xcode (or Xcode Command Line Tools)... what kind of notebook do you use?

pmeise · October 7, 2020, 8:59pm

I'm using an old macbook air (mid 2012, 1.8Ghz i5, 4gb, 128, Catalina 10.15.7)
I've managed to install Xcode via Appstore, but have no idea what should I do next

EconProf · October 7, 2020, 9:19pm

Check out this link
https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/

Pick the link at the top of that page based on your version of R

pmeise · October 8, 2020, 11:53am

Seems, like I've managed, rahelb.
I made next (surpisingly simple) things:

registered on AppStore and downleaded Xcode.
downloaded the last version of R language, that is 4.0.2
deleted and installed Rstudio.
installed needed packages (devtools and tidyverse(choosed n to compiling) )

pmeise · October 8, 2020, 11:54am

Thank you, EconProf! I'll check it.

pmeise · October 8, 2020, 12:14pm

After described operations it possible to install packages you've mentioned: isoband and rlang(yes to compiling, but decided not to restart R from Rstudio, beacuse begins endless cycle).

> install.packages("isoband")
пробую URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/isoband_0.2.2.tgz'
Content type 'application/x-gzip' length 4016637 bytes (3.8 MB)
==================================================
downloaded 3.8 MB


The downloaded binary packages are in
	/var/folders/_p/_lmvdgh976g_f1t83hx_bl9h0000gn/T//Rtmp56sEI1/downloaded_packages

> install.packages("rlang")
Error in install.packages : Updating loaded packages

Restarting R session...

> install.packages("rlang")
Error in install.packages : Updating loaded packages

Restarting R session...

> install.packages("rlang")
Error in install.packages : Updating loaded packages

Restarting R session...

> install.packages("rlang")
Error in install.packages : Updating loaded packages

Restarting R session...

> install.packages("rlang")
Error in install.packages : Updating loaded packages
> install.packages("rlang")

  There is a binary version available but the source version is
  later:
      binary source needs_compilation
rlang  0.4.7  0.4.8              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘rlang’

пробую URL 'https://cran.rstudio.com/src/contrib/rlang_0.4.8.tar.gz'
Content type 'application/x-gzip' length 847517 bytes (827 KB)
==================================================
downloaded 827 KB

* installing *source* package ‘rlang’ ...
** пакет ‘rlang’ удачно распакован, MD5 sums проверены
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./lib/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c capture.c -o capture.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./lib/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c export.c -o export.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./lib/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c internal.c -o internal.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./lib/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c lib.c -o lib.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./lib/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c version.c -o version.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rlang.so capture.o export.o internal.o lib.o version.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)

The downloaded source packages are in
	‘/private/var/folders/_p/_lmvdgh976g_f1t83hx_bl9h0000gn/T/RtmpucH7nJ/downloaded_packages’
> libra("rlang")
Ошибка в libra("rlang") :не могу найти функцию "libra"
> library("rlang")
Ошибка: package or namespace load failed for ‘rlang’ in get(method, envir = home):
 lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rlang/R/rlang.rdb' is corrupt
Вдобавок: Предупреждение:
В get(method, envir = home) : internal error -3 in R_decompress1

rahelb · October 9, 2020, 11:35am

Thanks a lot for the update! And great to hear that it worked for you. I will try it again – what is R language?

pmeise · October 9, 2020, 12:17pm

Sorry, I don't understand the question. Do you mean which version?

rahelb · October 9, 2020, 12:30pm

Sorry, no, I don't know what you mean by "I downloaded R language". Is that an application or something you downloaded in Xcode?

pmeise · October 9, 2020, 12:57pm

Oh, sorry for my english. I mean the software for the R language itself.
https://www.r-project.org/

rahelb · October 9, 2020, 1:16pm

And now I finally found out what my problem was! Even though I had the newest version of Rstudio, I did not install the newest version of R (I didn't use this laptop for a few years and didn't think about updating this one).
Problem solved

system · October 30, 2020, 1:16pm

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