Crash on install_github remains

[jankowtf]

I have the same problem as described here and also followed the advice with update.packages(checkBuilt = TRUE).

Still, R crashes upon calling install_github():

> install_github("rstudio/packrat")
Installing github repo packrat/master from rstudio
Downloading master.zip from https://github.com/rstudio/packrat/archive/master.zip
Installing package from C:\Users\RAPPST~1\AppData\Local\Temp\RtmpCaiyWW/master.zip
Error in unzip(src, list = TRUE) : 
zip file 'C:\Users\RAPPST~1\AppData\Local\Temp\RtmpCaiyWW/master.zip' cannot be opened
In addition: Warning messages:
1: In mapCurlOptNames(names(.els), asNames = TRUE) :
  Unrecognized CURL options: writedata
2: In mapCurlOptNames(names(.els), asNames = TRUE) :
  Unrecognized CURL options: writedata
3: In unzip(src, exdir = target, unzip = getOption("unzip")) :
  error 1 in extracting from zip file

At first I thought, that my Rtools might not be recognized correctly (zip/unzip), but the tools are attached to my path and I can access them:

> system("unzip")
UnZip 6.00 of 20 April 2009, by Info-ZIP.  Maintained by C. Spieler.  Send
bug reports using http://www.info-zip.org/zip-bug.html; see README for details.
[...]

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

[hadley]

When does it crash?

[jankowtf]

When I run install_github() from R.exe, Rterm.exe, RStudio and via Eclipse/StatET, it crashes. When running it via Rgui.exe, I get the above error, but the console stays "alive".

[jankowtf]

I tried to narrow things down a bit:

1. Tested on a different machine with identical settings, same result.
2. On that other machine, tested with an old installation of R-3.1.0 and thus (possibly) old versions of devtools' package dependencies (I'll have to check that in more detail; the version of devtools itself already was at 1.5 anyway) and everything worked just fine.
3. On that other machine, tested with a new installation of R-3.1.0 and thus latest dependency versions and it failed again.

In all three cases, I used the Rtools 3.1.

So I'm guessing, that it has to do with some package that devtools depends on?

[jankowtf]

Okay, I think I got it narrowed down to being a problem with RCurl version 1.95-4.1 (working) vs. 1.95-4.2 (not working).

Starting from my old installation of R-3.1.0, the only package that devtools depends on and that changed until today is RCurl. After upgrading to version 1.95-4.2, install_github() fails (see details below).

HTH,
Janko

---

## Functions //
getCurrentLibraryState <- function() {
  pkgs <- list.files(R.home("library"))
  vsns <- sapply(pkgs, packageDescription, field="Version")
  vsns[order(names(vsns))]
}
getRepositoryState <- function() {
  vsns <- available.packages()[,"Version"]
  vsns <- vsns[which(names(vsns) %in% list.files(R.home("library")))]
  vsns[order(names(vsns))]
}
getVersionDifferences <- function(vsns) {
  sapply(1:nrow(vsns), function(ii) {
    vsns[ii,1] != vsns[ii,2]
  })
}

## Version overview //
repos <- getRepositoryState()
local <- getCurrentLibraryState()[names(repos)]
vsns <- data.frame(
  local=local,
  repos=repos,
  stringsAsFactors=FALSE
)
vsns$changed <- getVersionDifferences(vsns=vsns)

The only dependency for which a new version is available for R-3.1.0 is package RCurl:

## Devtools dependencies //
deps <- packageDescription("devtools", field="Imports")
deps <- unlist(strsplit(gsub("\\s|\\(.*\\)|\\n", "", deps), split=","))
vsns_2 <- vsns[which(rownames(vsns) %in% deps), ]
> vsns_2
            local    repos changed
digest      0.6.4    0.6.4   FALSE
evaluate    0.5.5    0.5.5   FALSE
httr          0.3      0.3   FALSE
memoise     0.2.1    0.2.1   FALSE
RCurl    1.95-4.1 1.95-4.2    TRUE
whisker     0.3-2    0.3-2   FALSE

Before updating RCurl, everything still works fine:

> require("devtools")
> install_github("rstudio/packrat")
Installing github repo packrat/master from rstudio
Downloading master.zip from https://github.com/rstudio/packrat/archive/master.zip
Installing package from C:\Users\rappster\AppData\Local\Temp\RtmpQT0Exb/master.zip
Installing packrat
"C:/home/apps/r/R-31~1.0/bin/x64/R" --vanilla CMD INSTALL  \
  "C:\Users\rappster\AppData\Local\Temp\RtmpQT0Exb\devtools10c0124774a9\packrat-master"  \
  --library="C:/home/apps/r/R-3.1.0/library" --install-tests 

* installing *source* package 'packrat' ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (packrat)

After the update, the whole thing fails:

> install.packages("RCurl")
--- Please select a CRAN mirror for use in this session ---

  There is a binary version available (and will be installed) but the source version is later:
        binary   source
RCurl 1.95-4.2 1.95-4.3

trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/RCurl_1.95-4.2.zip'
Content type 'application/zip' length 2835598 bytes (2.7 Mb)
opened URL
downloaded 2.7 Mb

package ‘RCurl’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\rappster\AppData\Local\Temp\RtmpYJd16m\downloaded_packages
> packageDescription("RCurl", field="Version")
[1] "1.95-4.2"

> require("devtools")
Loading required package: devtools

Attaching package: ‘devtools’

The following objects are masked from ‘package:utils’:

    ?, help

The following object is masked from ‘package:base’:

    system.file

> install_github("rstudio/packrat")
Installing github repo packrat/master from rstudio
Downloading master.zip from https://github.com/rstudio/packrat/archive/master.zip
Installing package from C:\Users\rappster\AppData\Local\Temp\RtmpYJd16m/master.zip
Error in unzip(src, list = TRUE) : 
  zip file 'C:\Users\rappster\AppData\Local\Temp\RtmpYJd16m/master.zip' cannot be opened
In addition: Warning messages:
1: In mapCurlOptNames(names(.els), asNames = TRUE) :
  Unrecognized CURL options: writedata
2: In mapCurlOptNames(names(.els), asNames = TRUE) :
  Unrecognized CURL options: writedata
3: In unzip(src, exdir = target, unzip = getOption("unzip")) :
  error 1 in extracting from zip file

[hadley]

Maybe try 1.95-4.3? It looks like that was just released - I suspect that was a quick fix for the problem you're seeing in .2.

[jankowtf]

I would like to, but compiling RCurl from source on Windows seems to be a bit tricky with respect to libcurl and its companion DLLs. I gues I'm stuck until the Windows binary for v.1.95-4.3 comes out.

[dacorea1]

Hey there Rappster. I'm actually experiencing the same issue you've been troubleshooting today. I just had to update all my R packages today, leaving me with an RCurl installation that crashes my R session every time I need to use devtools. Seeing as how it's nearing the end of my day, I thought I'd make my way to Stack Overflow, only to find that you already posted this issue there. 👍

Thanks so much for going through the trouble to uncover this troublesome package. I'll let you know if I make any progress on my end, and I'll keep an eye out to see you if make any as well.

[geneorama]

For what it's worth, I found a workaround that works for me;

1. Clone the project that you want to install (I'm assuming this project is an R Package, like devtools)
2. Start a new R Studio project in that project folder
3. Click on the "build" tab
4. Click on the "Build & Reload" button.

The package should be installed.

[dacorea1]

Rappster and Hadley,

Thanks for both of your efforts in understanding this bug. CRAN now has a binary file for v.1.95-4.3 of RCurl hosted on its site.

After downloading it, and building it from source, I have a working version of RCurl on my windows machine again.