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

[Simon Urbanek]

Also if you just want to "fix" the file, you can simply change the second byte using R:

fn = "myfile.dbf"
sz = file.info(fn)$size
r = readBin(fn, raw(), sz)
r[2] = as.raw(121) ## make it 2021 instead of 2022
writeBin(r, fn)



> On Feb 12, 2022, at 12:38 PM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
> 
> FWIW this seems to be a known issue (for some definition of known):
> 
> https://bugs.astron.com/view.php?id=316
> 
> 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%7Ce242631c41c342f47d8908d9edb008b8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637802163497599994%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Z77T09j1sONATxupZGSmkayrpjt3Ra1g%2FS6vxQq8CJs%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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> 
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