Error: 'C:\\Users.../data.table_1.14.0.zip' is not a valid R package, it is an empty archive

[etiennebacher]

Hello, I just started using R on a server at work, and I tried to install packages with pak but I always get the same error, whatever the package. Here, with data.table for instance:

> pak::pkg_install(c("data.table"))
v Loading metadata database ... done
                                                                          
> Will install 1 package.
> Will download 1 CRAN package (2.60 MB).
+ data.table   1.14.0 [dl] (2.60 MB)
i Getting 1 pkg (2.60 MB)
v Cached copy of data.table 1.14.0 (windows) is the latest build   
v No downloads needed, all packages are cached                     
Erreur : 'C:\\Users\\etienne\\AppData\\Local\\Temp\\37\\Rtmp67Ykij\\file171c13c23b9f/bin/windows/contrib/4.1/data.table_1.14.0.zip' is not a valid R package, it is an empty archive
Type .Last.error.trace to see where the error occurred

I only get this with pak. If I use install.packages("data.table"), everything works fine. I am using GitHub version (‘0.1.2.9001’). I tried to manually clear C:\\Users\\etienne\\AppData\\Local\\Temp\\37 but it doesn't change anything.

Session info

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252

[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C

[5] LC_TIME=French_France.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods

[7] base
loaded via a namespace (and not attached):
[1] processx_3.5.2    compiler_4.1.0    R6_2.5.0

[4] cli_3.0.0         tools_4.1.0       glue_1.4.2

[7] data.table_1.14.0 callr_3.7.0       ps_1.6.0

[10] pak_0.1.2.9001

[gaborcsardi]

I am sorry for the slow response. Do you still have this issue?

[etiennebacher]

Hello, thank you for coming back to this issue. I still have the same problem, here's the output of .Last.error.trace:

> .Last.error.trace

 Stack trace:

 12. (function (...)  ...
 13. base:::withCallingHandlers(cli_message = function(msg) { ...
 14. get("pkg_install_do_plan", asNamespace("pak"))(...)
 15. pkgdepends::install_package_plan(plan = plan, lib = lib, num_ ...
 16. base:::withCallingHandlers({ ...
 17. pkgdepends:::handle_events(state, events)
 18. pkgdepends:::handle_event(state, i)
 19. proc$get_result()
 20. processx:::process_get_result(self, private)
 21. private$post_process()
 22. pkgdepends:::install_extracted_binary(filename, lib_cache, pk ...
 23. pkgdepends:::verify_extracted_package(filename, pkg_cache)
 24. base:::throw(new_input_error("{filename} is not a valid R pac ...
 25. base:::signalCondition(cond)
 26. (function (e)  ...
 27. base:::stop(e)
 28. (function (e)  ...

 x 'C:\\Users\\etienne\\AppData\\Local\\Temp\\300\\RtmpaAiexJ\\file68dc6538560/bin/windows/contrib/4.1/data.table_1.14.2.zip' is not a valid R package, it is an empty archive 

I checked the zip file indicated in the error message, it is not empty.

[gaborcsardi]

How did you install pak? Can you try the devel version? You can install it like this:

install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel")

Also, what's the output of

getOption("repos")
pak::repo_get()

[etiennebacher]

Reinstalled pak as you indicated, same error. Also tried to install data.table after deleting pak cache, but same error.

Here are the outputs you asked:

> getOption("repos")
                       CRAN 
"https://cran.rstudio.com/" 
attr(,"RStudio")
[1] TRUE

> pak::repo_get()
# A tibble: 5 x 5
  name          url                             type  r_version bioc_version
  <chr>         <chr>                           <chr> <chr>     <chr>       
1 CRAN          https://cran.rstudio.com/       cran  *         NA          
2 BioCsoft      https://bioconductor.org/packa~ bioc  4.1.1     3.14        
3 BioCann       https://bioconductor.org/packa~ bioc  4.1.1     3.14        
4 BioCexp       https://bioconductor.org/packa~ bioc  4.1.1     3.14        
5 BioCworkflows https://bioconductor.org/packa~ bioc  4.1.1     3.14 

[gaborcsardi]

Can you please try a simple source package?

pak::pkg_install("pkgconfig?source")

Can you also try to run these?

system2(system.file(package = "pak", "library", "zip", "bin", "x64", "zip.exe"), "--help")
system2(system.file(package = "pak", "library", "zip", "bin", "x64", "cmdunzip.exe"))

Thanks!

[etiennebacher]

> pak::pkg_install("pkgconfig?source")
 
> Will install 1 package.
> Will download 1 CRAN package (6.08 kB).
+ pkgconfig   2.0.3 [bld][dl] (6.08 kB)

! pkgconfig is loaded in the current R session, you probably need to restart R
after the installation.

i Getting 1 pkg (6.08 kB)
v Got pkgconfig 2.0.3 (source) (6.08 kB)                                
v Downloaded 1 package (6.08 kB)in 494ms                                         
i Building pkgconfig 2.0.3
v Built pkgconfig 2.0.3 (6.9s)                                         
Erreur : 'C:\\Users\\etienne\\AppData\\Local\\Temp\\300\\RtmpURDvy9\\file69845cd73a29/pkgconfig_2.0.3.zip' is not a valid R package, it is an empty archive
Type .Last.error.trace to see where the error occurred

> system2(system.file(package = "pak", "library", "zip", "bin", "x64", "zip.exe"), "--help")
Copyright (c) 1990-2008 Info-ZIP - Type 'zip "-L"' for software license.
Zip 3.0 (July 5th 2008). Usage:
zip [-options] [-b path] [-t mmddyyyy] [-n suffixes] [zipfile list] [-xi list]
  The default action is to add or replace zipfile entries from list, which
  can include the special name - to compress standard input.
  If zipfile and list are omitted, zip compresses stdin to stdout.
  -f   freshen: only changed files  -u   update: only changed or new files
  -d   delete entries in zipfile    -m   move into zipfile (delete OS files)
  -r   recurse into directories     -j   junk (don't record) directory names
  -0   store only                   -l   convert LF to CR LF (-ll CR LF to LF)
  -1   compress faster              -9   compress better
  -q   quiet operation              -v   verbose operation/print version info
  -c   add one-line comments        -z   add zipfile comment
  -@   read names from stdin        -o   make zipfile as old as latest entry
  -x   exclude the following names  -i   include only the following names
  -F   fix zipfile (-FF try harder) -D   do not add directory entries
  -A   adjust self-extracting exe   -J   junk zipfile prefix (unzipsfx)
  -T   test zipfile integrity       -X   eXclude eXtra file attributes
  -!   use privileges (if granted) to obtain all aspects of WinNT security
  -$   include volume label         -S   include system and hidden files
  -e   encrypt                      -n   don't compress these suffixes
  -h2  show more help
  
> system2(system.file(package = "pak", "library", "zip", "bin", "x64", "cmdunzip.exe"))
Usage: \\crc\users\etienne\My Documents\R\R-4.1.1\library\pak\library\zip\bin\x64\cmdunzip.exe zip-file target-dir

[gaborcsardi]

One more shot in the dark:

Sys.which("zip")
Sys.which("unzip")

[etiennebacher]

> Sys.which("zip")
zip 
 "" 
> Sys.which("unzip")
unzip 
   "" 

Is it helpful?

[gaborcsardi]

I am sorry, I have no clue what is going on. What is your exact OS? Do you have rtools40 installed?

[etiennebacher]

I'm using Windows Server 2016 Standard, v. 1607, build 14393.4704. rtools40 is installed.

It's not so important, pak::pkg_install doesn't work but install.packages does so I'm not completely blocked. Thanks for your help anyway. I don't know if I should let this issue open since it isn't solved, so I'll let you close it if necessary

[gaborcsardi]

I would like to understand what is happening here, so thank you for the help! I'll send you a couple of more commands to run soon, if you don't mind.

[owenjonesuob]

In case this is useful - I encountered the same "empty archive" error message just now. I had specified lib with a path to a directory, but I didn't have write permissions on that directory.

After granting write permissions on that directory, pkg_install() worked without issue 😇

[maelle]

I am getting a similar error in a workflow, here for installing brio: https://github.com/cynkra/cynkrablog/actions/runs/6770789485/job/18399890155?pr=23#step:4:1151 but before that the error was on base64enc installation.

[etiennebacher]

I come back to this issue thanks to @maelle's comment. After updating pak, I don't see this issue anymore. I can't tell if this is due to the upgrade or a change on the server I'm using but in any case this is resolved for me.

[gaborcsardi]

@maelle Your default package library is not writeable.

[maelle]

thank you, but what I don't get is why, I haven't tweaked anything I know of. :thinking:

[gaborcsardi]

There is nothing to tweak, on GHA there is no user package library by default, and the site and system libraries are not writeable for the default user. AFAICT.

[gaborcsardi]

We should certainly give a better error message, possibly check that the library is writeable before starting the installation.

[maelle]

Ok, so I'll look into the r-lib/actions examples to see where I need to set the package library. Thank you!!

[gaborcsardi]

Those examples use r-lib/actions/setup-r which configures a writeable library for you. So there is no need to do anything in the examples there.

[maelle]

How embarrassing is it that my workflow didn't have the R setup step :woman_facepalming: Thanks so much!

[gaborcsardi]

Well, GHA machines have R installed, so if that version is OK, you don't to install another one. But then you need to do

dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)

or something like that, first.

[etiennebacher]

Closing since it looks like @maelle fixed her issue