[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 18:36:37 CEST 2021 

I tried this a second time, but with --no-byte-compile, and it hung with a
slightly different traceback

(gdb) where
#0  0x00007f95bc4c6689 in __fxstat64 () from
/usr/lib/x86_64-linux-gnu/libc.so.6
#1  0x00007f95bc497050 in opendir () from
/usr/lib/x86_64-linux-gnu/libc.so.6
#2  0x00007f95b935f1e0 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#3  0x00007f95b9311242 in Tcl_FSMatchInDirectory () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#4  0x00007f95b92f3e2b in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#5  0x00007f95b92f34c5 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#6  0x00007f95b92f29d8 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#7  0x00007f95b92565f2 in TclNRRunCallbacks () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#8  0x00007f95b932bcd9 in Tcl_PkgRequireProc () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#9  0x00007f95b932bb06 in Tcl_PkgRequireEx () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#10 0x00007f95b96bdbe8 in Rplot_Init (interp=0x5625117460d0) at
tcltkimg.c:465

and when I killed the R subprocess doing the lazyload prep I got a
quasi-infinite stream of error messages:

...
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl:
too many nested evaluations (infinite loop?)
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl:
too many nested evaluations (infinite loop?)
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl:
too many nested evaluations (infinite loop?)
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl:
can't find package tile
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl:
too many nested evaluations (infinite loop?)
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl:
too many nested evaluations (infinite loop?)
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl:
too many nested evaluations (infinite loop?)
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl:
can't find package tile
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl:
can't find package tile
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl:
can't find package tile
error reading package index file
/home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl:
can't find package tile
...

-Bill


On Thu, Sep 30, 2021 at 9:00 AM Bill Dunlap <williamwdunlap using gmail.com>
wrote:

> I just tried installing forensim on R-devel/Ubuntu 20.04/WSL-2.0 without
> an X server (hence DISPLAY was not set).  Loading tktcl gives a warning
> that Tk is not available because DISPLAY is not set.  The installation hung
> after the byte-compile message:
> installing to
> /home/bill/R-devel/R-build/site-library/00LOCK-tkrplot/00new/tkrplot/libs
> ** R
> ** byte-compile and prepare package for lazy loading
> Warning message:
> no DISPLAY variable so Tk is not available
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded from temporary location
> Warning: no DISPLAY variable so Tk is not available
> Warning: loading Rplot failed
> ** checking absolute paths in shared objects and dynamic libraries
> ** testing if installed package can be loaded from final location
> Warning: no DISPLAY variable so Tk is not available
> Warning: loading Rplot failed
> ** testing if installed package keeps a record of temporary installation
> path
> * DONE (tkrplot)
> * 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
> ** byte-compile and prepare package for lazy loading
> [hang]
>
> gdb gives a traceback that I think indicates that the package is trying to
> plot something via tcltk at this point:
>
> Attaching to process 9310
> [New LWP 9315]
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> 0x00007fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
> (gdb) where
> #0  0x00007fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/
> libtcl8.6.so
> #1  0x00007fe20a50f5f2 in TclNRRunCallbacks () from
> /usr/lib/x86_64-linux-gnu/libtcl8.6.so
> #2  0x00007fe20a5e4cd9 in Tcl_PkgRequireProc () from
> /usr/lib/x86_64-linux-gnu/libtcl8.6.so
> #3  0x00007fe20a5e4b06 in Tcl_PkgRequireEx () from
> /usr/lib/x86_64-linux-gnu/libtcl8.6.so
> #4  0x00007fe20a976be8 in Rplot_Init (interp=0x55ae6437a6c0) at
> tcltkimg.c:465
> #5  0x00007fe20a5d1ee3 in ?? () from /usr/lib/x86_64-linux-gnu/
> libtcl8.6.so
> #6  0x00007fe20a50f5f2 in TclNRRunCallbacks () from
> /usr/lib/x86_64-linux-gnu/libtcl8.6.so
> #7  0x00007fe20b04d7f0 in dotTclObjv (args=0x55ae6489d210) at
> /mnt/c/R/R-svn/trunk/src/library/tcltk/src/tcltk.c:250
> #8  0x000055ae611cd5a8 in do_External (call=0x55ae6440a270,
> op=0x55ae61fe1338, args=0x55ae6489d210, env=0x55ae6489d3d0)
>     at /mnt/c/R/R-svn/trunk/src/main/dotcode.c:576
> #9  0x000055ae6122a0b3 in bcEval (body=0x55ae6440a190, rho=0x55ae6489d3d0,
> useCache=TRUE)
>     at /mnt/c/R/R-svn/trunk/src/main/eval.c:7128
> #10 0x000055ae6121644a in Rf_eval (e=0x55ae6440a190, rho=0x55ae6489d3d0)
> at /mnt/c/R/R-svn/trunk/src/main/eval.c:740
> #11 0x000055ae61215fda in forcePromise (e=0x55ae6489d398) at
> /mnt/c/R/R-svn/trunk/src/main/eval.c:568
> #12 0x000055ae61220b80 in FORCE_PROMISE (value=0x55ae6489d398,
> symbol=0x55ae62282a08, rho=0x55ae6489d248,
>     keepmiss=FALSE) at /mnt/c/R/R-svn/trunk/src/main/eval.c:5149
> #13 0x000055ae61220d2f in getvar (symbol=0x55ae62282a08,
> rho=0x55ae6489d248, dd=FALSE, keepmiss=FALSE,
>     vcache=0x7fe20b2ec1f0, sidx=1) at
> /mnt/c/R/R-svn/trunk/src/main/eval.c:5190
>
> Henrik, can you reproduce this if you undefine DISPLAY?
>
> -Bill
>
>
>
>
> On Wed, Sep 29, 2021 at 7:48 PM Henrik Bengtsson <
> henrik.bengtsson using gmail.com> wrote:
>
>> I just tried on an up-to-date CentOS 7 with R 4.1.1 built from source
>> using gcc 8.3.1 (from SCL devtoolset-8; so not the default gcc 4.8.5),
>> and it works there.  If of any help, here's the output when installing
>> to user's personal package library:
>>
>> > chooseCRANmirror(ind = 1)
>> > install.packages("forensim")
>> Installing package into
>> ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
>> (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"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
>> -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c auxilary.c -o
>> auxilary.o
>> gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
>> -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c recursFinal.c -o
>> recursFinal.o
>> gcc -shared -L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib
>> -L/usr/local/lib64 -o forensim.so auxilary.o recursFinal.o
>> -L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib -lR
>> installing to
>> /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/00LOCK-forensim/00new/forensim/libs
>> ** R
>> ** data
>> ** inst
>> ** byte-compile and prepare 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
>>     ‘/scratch/henrik/RtmpYFlQyS/downloaded_packages’
>>
>> You could also try to install it via 'R CMD INSTALL' and try with
>> different options disabled to maybe narrow in on what's going on.
>>
>> My $.02
>>
>> /Henrik
>>
>> On Wed, Sep 29, 2021 at 6:37 PM Brodie, Kent via R-help
>> <r-help using r-project.org> wrote:
>> >
>> > Hey everyone!  So, I've been asked by one of our researchers to install
>> "all" cran packages on one of our servers.    Yeah, it's a bit much (and
>> clearly, not everything will install correctly due to various missing
>> tidbits), but it will go a long way to having to constantly respond to
>> install requests of various packages.  OK, fine.
>> >
>> > Anyway, I have tried this, and things proceed nicely for several hours
>> until the process gets completely and absolutely stuck.   I have tried
>> several things, for example trying newer versions of R, and even repeating
>> the process on a CentOS 8 server instead of where my stuff is now (CentOS
>> 7).
>> >
>> > While re-trying one of my newer attempts at this, I decided to focus on
>> the very first place where it hangs.   It dies on package "forensim".
>> It's a slightly older package, and I don't see anything particularly
>> special about it.    The text below is where it hangs.    The install "R"
>> process doing this is whizzing at 100%,  but no progress, no output, no
>> errors.  Nothing in the system logs.
>> >
>> > On new "R" installs, with either operating system (CentOS 7, CentOS 8)
>> and even different versions of "R" (up to including 4.1.1), I get the same
>> result when just attempting to install this ONE package.    (and my guess,
>> there's more packages out there that may bite me the same way).
>> >
>> > I am seeking any recommendations on how I can get past this?   A debug
>> option?  A timeout of sorts so things will  move along to the next package
>> when attempting to install a ton, or...?   I'm of course willing to try
>> anything.   It's stupidly frustrating.    I'd be OK if it errored out and
>> moved on.   But it...  hangs.
>> >
>> > Here's the latter part of the install attempt of this one package.
>>  This latest attempt has been stuck on that last line now for 5 hours and
>> counting.
>> >
>> > * DONE (tkrplot)
>> > Making 'packages.html' ... done
>> > * installing *source* package 'forensim' ...
>> > ** package 'forensim' successfully unpacked and MD5 sums checked
>> > ** using staged installation
>> > ** libs
>> > gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic
>> -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
>> -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong
>> -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
>> -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic
>> -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c
>> auxilary.c -o auxilary.o
>> > gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic
>> -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
>> -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong
>> -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
>> -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic
>> -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c
>> recursFinal.c -o recursFinal.o
>> > gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now
>> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o forensim.so auxilary.o
>> recursFinal.o -L/usr/lib64/R/lib -lR
>> > installing to /usr/lib64/R/library/00LOCK-forensim/00new/forensim/libs
>> > ** R
>> > ** data
>> > ** inst
>> > ** byte-compile and prepare package for lazy loading
>> >
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> ______________________________________________
>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

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