R library() bug

[Stephen P Carrier]

On Fri, Dec 1, 2023 at 3:24 PM Stephen P Carrier <carrier@berkeley.edu>
wrote:

>
>
> On Tue, Nov 28, 2023 at 8:32 PM Marco Atzeri <marco.atzeri@gmail.com>
> wrote:
>
>> On 29.11.2023 02:12, Stephen P Carrier via Cygwin wrote:
>> > I have found another issue with Cygwin R.
>> >
>> > This is for a brand new R installation (4.3.0) on up-to-date Cygwin.  I
>> am
>> > warned when starting R that "stats" package was not found.  Though it
>> was
>> > just a warning I do need the stats package for some things.
>> >
>> > Minimal test case:  I invoke "R" with no arguments and get:
>> >
>> > -----
>> > R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
>> > Copyright (C) 2023 The R Foundation for Statistical Computing
>> > Platform: x86_64-pc-cygwin (64-bit)
>> >
>> > R is free software and comes with ABSOLUTELY NO WARRANTY.
>> > You are welcome to redistribute it under certain conditions.
>> > Type 'license()' or 'licence()' for distribution details.
>> >
>> > R is a collaborative project with many contributors.
>> > Type 'contributors()' for more information and
>> > 'citation()' on how to cite R or R packages in publications.
>> >
>> > Type 'demo()' for some demos, 'help()' for on-line help, or
>> > 'help.start()' for an HTML browser interface to help.
>> > Type 'q()' to quit R.
>> >
>> > During startup - Warning message:
>> > package ‘stats’ in options("defaultPackages") was not found
>> >> library("stats")
>> > Error: package or namespace load failed for ‘stats’ in dyn.load(file,
>> > DLLpath = DLLpath, ...):
>> >   unable to load shared object
>> '/usr/lib/R/library/stats/libs/stats.dll':
>> >    No such file or directory
>> > -----
>> >
>> > However, the file /usr/lib/R/library/stats/libs/stats.dll is very much a
>> > file that exists and is readable by the user running R.  I've looked
>> over
>> > file and folder permissions and don't see an issue.  Other packages in
>> > options('defaultPackages') load without difficulty.
>> >
>> > Could the maintainer have a look?  Thanks.
>> >
>> > --Stephen Carrier
>> >
>>
>> Can you share as attachment the cygcheck.out ?
>>
>> https://www.cygwin.com/problems.html
>>
>> Run
>>     "cygcheck -s -v -r > cygcheck.out"
>> and include that file as an attachment in your report. Please do not
>> compress or otherwise encode the output. Just attach it as a straight
>> text file so that it can be easily viewed.
>>
>
>
> I was able to reproduce on a different windows machine which is more
> convenient for me to troubleshoot on, so I'll send along a new
> cygcheck2.out to capture the few differences between the systems.
>
> I ran R under strace and R does find the "missing" file and tries to load
> it, immediately unloads it, and reports an error that seems to come from
> newlib.
>
> I think there may be a problem in newlib or in the way R tries to use
> newlib?  (or, Windows is changing things again.)  Fixing something like
> this is beyond my abilities.  I hope this report is useful.
>
> I am attaching cygcheck2.out and also strace2_select.out, a selection of
> the strace output that shows the error and points to line 288 of dlfcn.cc
> in the newlib source:
>
>
> https://sourceware.org/git/?p=newlib-cygwin.git;a=history;f=winsup/cygwin/dlfcn.cc;h=fb705247352e46fb8fe408937a6e766fa37760e2;hb=HEAD
>
> I have no idea why this one package is affected and none of the others.
>
> The full strace2.out is too big for e-mail, I can make it available if
> anyone who will look at itt.  I will try any suggestions.  Thanks,
>
> Stephen Carrier
>

Attachments really attached this time.
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