Maybe dropbox can make things worse, if your package library happens
to be in Dropbox. (I would think this is not a good idea.)
But it does happen without Dropbox, and if you install packages
frequently, e.g. if you develop a bunch of packages, then it is a
familiar error, it does happen all the time.
Gabor
On Tue, Nov 5, 2019 at 9:02 AM Hugh Parsonage <hugh.parson...@gmail.com> wrote:
>
> I wonder if Dropbox “smartsync” is the culprit here. I’ve noticed this
> feature can create confusion between programs when Dropbox provides (a link
> to) the file when it is opened but only when it recognizes the file is being
> opened.
>
> On Tue, 5 Nov 2019 at 7:46 pm, Gábor Csárdi <csardi.ga...@gmail.com> wrote:
>>
>> I am not sure what the first issue was, but the second is an old R
>> issue. It happens when you update a package while its package (or
>> help) database, the rdb file mentioned in the error message, is open
>> in the current R session, i.e. when the package is loaded. The
>> database keeps an index to the objects within the database on the
>> disk. And when the package is updated, this index will be invalid,
>> which R detects as a corrupt rdb file. Restarting R solves the
>> problem.
>>
>> Btw. would R core be interested in a patch for this? I am not sure if
>> the situation is fixable, because the package is already loaded, and
>> we can't just reload it, but R could give a better error message. For
>> the help database, it might make sense to just re-open the database?
>>
>> Gabor
>>
>> On Tue, Nov 5, 2019 at 12:53 AM Rolf Turner <r.tur...@auckland.ac.nz> wrote:
>> >
>> >
>> > I've just heard from another member of the client group and he cannot
>> > reproduce the problem. I.e. he can install both the source package and
>> > the binary that I sent out, without error.
>> >
>> > So the problem seems to be in the system used by that first member of
>> > the client group who contacted me.
>> >
>> > Sorry for the noise.
>> >
>> > cheers,
>> >
>> > Rolf
>> >
>> > On 5/11/19 12:37 PM, Rolf Turner wrote:
>> > >
>> > > I am developing a package ("ldEst" --- lethal dose estimation) for a
>> > > group of consulting clients. (The package may in the future be released
>> > > upon the unsuspecting public, but for the moment it has to stay
>> > > confidential, sad to say.)
>> > >
>> > > The clients run Windoze (sad to say). In the past I have sent them the
>> > > source of the package, which they have the facilities to install. The
>> > > latest release of the package however threw an error:
>> > >
>> > >>> install.packages("C:/Users/abel122/Dropbox/PFR/ldEst_3.0-12.tar.gz",
>> > >>> repos = NULL, type = "source")
>> > >>
>> > >> Error in rawToChar(block[seq_len(ns)]) : embedded nul in string:
>> > >> '\037‹\b\0\0\0\0\0\0\003ì}\a`\024ÕÖ0‚\200,HGºN–¶\033&›ì¦\001aÁ\220Є„\022\b\201\020p³;I\006¶„-)T\021P\024\005,
>> > >> \002Š" E¤ƒ\024\001)‚"*J\023”&\210R\024\vEšÿ=·LÙ’„÷ž¼ïû~xÏìîÌ'
>> > >> Warning in install.packages :
>> > >> installation of package
>> > >> ‘C:/Users/abel122/Dropbox/PFR/ldEst_3.0-12.tar.gz’ had non-zero exit
>> > >> status
>> > >
>> > > Flummoxed by this I thought I'd just get Uwe Ligges' win-builder to
>> > > build a Windoze binary, and sent that to the clients. The win-build
>> > > went without problem, but when I sent the binary to one of the clients
>> > > he got the error:
>> > >
>> > >> Error: package or namespace load failed for ‘ldEst’ in get(method,
>> > >> envir = home):
>> > >> lazy-load database
>> > >> 'C:/Users/abel122/Documents/R/win-library/3.6/ldEst/R/ldEst.rdb' is
>> > >> corrupt
>> > >> In addition: Warning messages:
>> > >> 1: In .registerS3method(fin[i, 1], fin[i, 2], fin[i, 3], fin[i, 4], :
>> > >> restarting interrupted promise evaluation
>> > >> 2: In get(method, envir = home) :
>> > >> restarting interrupted promise evaluation
>> > >> 3: In get(method, envir = home) : internal error -3 in R_decompress1
>> > >
>> > > I (sad to say) have no idea what any of this really means.
>> > >
>> > > The package installs, loads, and runs just fine on my Ubuntu system,
>> > > and builds without error on win-builder.
>> > >
>> > > Can any suggest a way that I might track down what's causing the
>> > > error(s).
>> > >
>> > > I realise this is a big ask without your having the package to
>> > > experiment on, but I thought that someone clever out there might be able
>> > > to offer some insight. E.g. what might I do to find out what is
>> > > triggering that "embedded nul in string" business?
>> > >
>> > > Thanks for any tips.
>> >
>> > ______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
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