[R-pkg-devel] shapefile .dbf recognised as executable

[Murray Efford]

Amazing. Who would have thought? This works:

OVforest <- sf::st_read("OVforest.shp")
sf::st_write(OVforest, "OVforest3.shp", layer_options = "DBF_DATE_LAST_UPDATE=2021-12-31")

$ file OVforest3.dbf
OVforest3.dbf: FoxBase+/dBase III DBF, 3 records * 12, update-date 121-12-31, codepage ID=0x57, at offset 65 1st record "          0           1           2\032"

Murray

________________________________________
From: Simon Urbanek <simon.urbanek using R-project.org>
Sent: 12 February 2022 12:38
To: Murray Efford
Cc: Duncan Murdoch; R-package-devel using r-project.org
Subject: Re: [R-pkg-devel] shapefile .dbf recognised as executable

FWIW this seems to be a known issue (for some definition of known):

https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbugs.astron.com%2Fview.php%3Fid%3D316&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7Cf4c62a1b8f424575c75608d9edb7aa72%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637802195379474238%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=EGkZIRKQNcdcqXqHJaN7i%2FhCbaJn8r%2FosFUTrPE39ts%3D&reserved=0

A fix is to set your date when writing the DBF file to year 2021 instead of 2022 (which also explains why it worked last year ;)).

Cheers,
Simon





> On Feb 12, 2022, at 12:33 PM, Murray Efford <murray.efford using otago.ac.nz> wrote:
>
> Many thanks for your guidance. Indeed there is a radical change:
>
> $ file OVforest.dbf
> OVforest.dbf: FoxBase+/dBase III DBF, 3 records * 22, update-date 95-7-26, at offset 97 1st record "beech        beech    leftnonbeech nonbeech rightnonbeechnonbeech"
>
> $ file OVforest2.dbf
> OVforest2.dbf: amd 29k coff prebar executable
>
> I don't recognize the file descriptors (amd, coff, prebar). I guess I need to call in help from the GIS people...
>
> Murray
>
> ________________________________________
> From: Duncan Murdoch <murdoch.duncan using gmail.com>
> Sent: 12 February 2022 11:44
> To: Murray Efford; R-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] shapefile .dbf recognised as executable
>
> On 11/02/2022 5:22 p.m., Murray Efford wrote:
>> I have long distributed a small spatial ESRI shapefile as demonstration data in the extdata directory of 'secr'. It comprises the three files OVforest.shp, OVforest.dbf and OVforest.shx. I wanted to make minor changes (adding a coordinate reference system, dropping an attribute). I find that after merely reading (sf::st_read("OVforest.shp") and re-writing the same (sf::st_write("OVforest.shp")) the .dbf file is recognised by R CMD check as executable and raises a Warning (on GNU/Linux, but not in Windows).
>>
>> No doubt this can be blamed on specifics of the driver used by sf::st_write, but I have been unable to find any settings that might change the behaviour.
>>
>> I would like to know: Is this a false positive, and if not, How can I remove the executable component(s)? Can I apply the test used by R CMD check outside of R CMD check?
>
> It's not easy to run just that test, but you can see it if you look here:
>
> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fwch%2Fr-source%2Fblob%2F988077a792e628677bd5884b351fe08b2c17b8c8%2Fsrc%2Flibrary%2Ftools%2FR%2Fcheck.R%23L4866-L4941&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7Cf4c62a1b8f424575c75608d9edb7aa72%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637802195379474238%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=1SkmfSqsvOpA%2Brs3DNCU86VJi6YXuGcSDxLIpjsQ720%3D&reserved=0
>
> The basic idea is that it uses the "file" command.  There are some known
> false positives.
>
> If you are on Linux, try running "file OVforest.dbf" and see what it says.
>
> Duncan Murdoch
>
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