[R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
Bill Dunlap
w||||@mwdun|@p @end|ng |rom gm@||@com
Thu Sep 30 19:33:34 CEST 2021
You can define the environment variable R_DONT_USE_TK (to any value) to
avoid this hang caused by code in the tkrplot package. You do not have to
have an X server running if R_DONT_USE_TK is set. This will avoid
potential hangs while installing the 23 packages that depend on tkrplot.
tools::package_dependencies("tkrplot", reverse=TRUE, recursive=TRUE)
$tkrplot
[1] "adoption" "baggingbwsel" "biplotbootGUI"
[4] "cncaGUI" "ConvergenceConcepts" "fisheyeR"
[7] "forensim" "GGEBiplotGUI" "GUIDE"
[10] "idendr0" "InterfaceqPCR" "multibiplotGUI"
[13] "RclusTool" "RcmdrPlugin.FuzzyClust"
"RcmdrPlugin.PcaRobust"
[16] "rriskDistributions" "RVideoPoker" "SyNet"
[19] "tsgui" "uHMM" "GGEBiplots"
[22] "decisionSupport" "geneticae"
E.g.,
> install.packages("forensim", type="source",
INSTALL_opts="--no-byte-compile")
Installing package into ‘/home/bill/R-devel/R-build/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forensim_4.3.tar.gz'
Content type 'application/x-gzip' length 84232 bytes (82 KB)
==================================================
downloaded 82 KB
* installing *source* package ‘forensim’ ...
** package ‘forensim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c auxilary.c -o auxilary.o
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c recursFinal.c -o recursFinal.o
gcc -shared -L/usr/local/lib -o forensim.so auxilary.o recursFinal.o
installing to
/home/bill/R-devel/R-build/site-library/00LOCK-forensim/00new/forensim/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** 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 (forensim)
The downloaded source packages are in
‘/tmp/Rtmp0jqhj9/downloaded_packages’
The relevant code is in tkrplot/src/tcltkimg.c:
EXPORT(int,Rplot_Init)(interp)
Tcl_Interp *interp;
{
/* Added to allow CRAN to disable Tk initialization */
#if !defined(Win32) && !defined(HAVE_AQUA)
if (getenv("R_DONT_USE_TK") != NULL)
return 0;
#endif
-Bill
On Thu, Sep 30, 2021 at 9:35 AM Brodie, Kent <brodie using mcw.edu> wrote:
> Bill-- BINGO. You have found the answer. After some testing on
> one of my environments where it was always hanging, connecting to the same
> server with an X-Sever running on my workstation did indeed allow the
> package to be installed.
>
>
>
> **GOOD LORD THAT’S RIDICULOUS** But---- at least I know. And why it
> doesn’t error out without X running, who knows.
>
>
>
> After a ton more research, I ALSO discovered that there IS a timeout thing
> I can make use of, should I decide to continue just building things and
> ignoring the X-Server requirement for this (and probably some other?)
> packages.
>
>
>
> Before executing R and installing things, set this:
>
>
>
> export _R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_=500
>
>
>
> (value is seconds). So, the previously-hanging R CMD INSTALL inside of
> the install.packages call will eventually die, and then move on to the next
> package.
>
> This is buried in the documentation but- it’s there and I confirmed it
> works. My example above times out a package install at 5 minutes.
>
>
>
> While knowing the X requirement is a huge win (thanks again!), I will
> probably stick with just using the timeout thing for what I’m trying to
> accomplish. Installing EVERYTHING from cran will take forever, and more
> than likely my VPN connection to my data center will be disconnected (thank
> you internal IT department) before it finishes. They have some sort of
> internal “you’ve been connected too long” timer that disconnects things
> overnight. Grr.
>
>
>
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