is not a valid R package, it is an empty archive

[royfrancis]

Getting this error with some packages. As an example;

>> pak::pkg_install("patchwork")

→ Will install 1 package.
→ Will download 1 CRAN package (3.19 MB).
+ patchwork   1.1.2 [bld][dl] (3.19 MB)
ℹ Getting 1 pkg (3.19 MB)
✔ Got patchwork 1.1.2 (source) (3.19 MB)                               
✔ Downloaded 1 package (3.19 MB)in 946ms                               
ℹ Building patchwork 1.1.2
✔ Built patchwork 1.1.2 (4.1s)                                       
Error:                                                                 
! error in pak subprocess
Caused by error in `verify_extracted_package(filename, pkg_cache)`:
! '/tmp/Rtmp7LxpdS/file95fd9c3dbb/patchwork_1.1.2_R_x86_64-pc-linux-gnu.tar.gz' is not a valid R package, it is an empty archive

It works with install.packages().

>> install.packages("patchwork")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/patchwork_1.1.2.tar.gz'
Content type 'application/x-gzip' length 3192018 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

* installing *source* package ‘patchwork’ ...
** package ‘patchwork’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location

** testing if installed package keeps a record of temporary installation path
* DONE (patchwork)

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

>> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

loaded via a namespace (and not attached):
 [1] prettyunits_1.1.1 pak_0.5.1         ps_1.7.5         
 [4] crayon_1.5.2      rprojroot_2.0.3   pkgdepends_0.5.0 
 [7] R6_2.5.1          jsonlite_1.8.4    zip_2.3.0        
[10] cli_3.6.1         rstudioapi_0.14   callr_3.7.3      
[13] filelock_1.0.2    desc_1.4.2        tools_4.2.3      
[16] glue_1.6.2        compiler_4.2.3    processx_3.8.1   
[19] pkgbuild_1.4.0    lpSolve_5.6.18  

>> options("repos")
$repos
                                                    CRAN 
                          "https://cloud.r-project.org/" 
                                                BioCsoft 
           "https://bioconductor.org/packages/3.16/bioc" 
                                                 BioCann 
"https://bioconductor.org/packages/3.16/data/annotation" 
                                                 BioCexp 
"https://bioconductor.org/packages/3.16/data/experiment" 
                                               CRANextra 
                   "https://www.stats.ox.ac.uk/pub/RWin" 

Running in RStudio Server in a docker container.

RStudio Server 2023.03.0 Build 386

[gaborcsardi]

Are you sure that you are not running out of disk space?

[royfrancis]

As far as I can see, there is plenty of disk space. Even if it was the disk space, the regular install.packages() command works immediately after.

[gaborcsardi]

Pak uses more disk space because it has a cache and it creates a binary package first.

[royfrancis]

It's a new laptop and there is more than a TB of space. I am hoping the docker container I am running has access to all that. I haven't defined any restrictions.

[gaborcsardi]

What OS do you have on the host? Ie on the laptop itself?

[royfrancis]

It's a MacBook Pro M2.

aarch64-apple-darwin20.0.0 (64-bit)
macOS Ventura 13.4.1

[gaborcsardi]

Then Docket does not have access to that space. You can see the amount of empty space and you can also make it bigger in the Docker dashboard. And/or you can run 'docker system prune' to remove unused images and containers.

If this does not work then can you please share your Dockerfile?

[royfrancis]

Interesting! So, I looked into disk usage and it was by default set to 64GB. But only 43GB of 64GB was used. So, it probably shouldn't be limiting. Anyhow, I increased it to 200GB. Restarted docker and the container and tried the installation again. Same error! I will put together a Dockerfile that I can share.

[royfrancis]

Tried again with a new Dockerfile, image and container and it works!

[gaborcsardi]

It would be good to know why the first file didn't work. Do you think you can share that?