[Bioc-devel] file 'HilbertCurve/DESCRIPTION' does not exist

[Zuguang Gu]

Yes, that is the problem.

Thank you!

On Tue, 8 Oct 2024 at 17:06, Henrik Bengtsson <henrik.bengtsson using gmail.com>
wrote:

> The content of the .Rbuildignore file should be regular expression,
> i.e. it does _not_ used fixed strings or globbing to match files and
> folders. From 'Writing R Extensions': "To exclude files from being put
> into the package, one can specify a list of exclude patterns in file
> .Rbuildignore in the top-level source directory. These patterns should
> be Perl-like regular expressions (see the help for regexp in R for the
> precise details), one per line, to be matched case-insensitively
> against the file and directory names relative to the top-level package
> source directory."
>
> In regular expression terms, '.o' matches any path that comprise a 'o'
> (or 'O' because it's case-insensitive) preceded by any symbol. In
> other words, 'DESCRIPTION' is matched because of the 'IO' part of it.
> There are other files in this package that are dropped as well by the
> '.o' exclusion, e.g.
>
> $ ls -R -1 R/ | grep -i -E ".o"
> 00_S4_generic_methods.R
> GenomicHilbertCurve.R
> hc_polygon.R
> RcppExports.R
>
> There are probably other files in other subfolders that are dropped as
> well.
>
> The proper way to exclude files with file extensions *.o and *.so via
> .Rbuildignore is:
>
> [.]o$
> [.]so$
>
> /Henrik
>
> On Tue, Oct 8, 2024 at 7:22 AM Jennifer Wokaty
> <Jennifer.Wokaty using sph.cuny.edu> wrote:
> >
> > Hi Zuguang,
> >
> > Sorry for the delayed response. `R CMD build` seems to have a problem
> with the second to last line of your .Rbuildignore, which had ".o". I'm not
> sure why but you could try substituting something else in its place to
> target your .o files, such as src/.o, in your .Rbuildignore to get it
> building again.
> >
> >
> > Jennifer Wokaty (they/them)
> >
> > Waldron Lab at CUNY SPH
> > Bioconductor Core Team
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> Zuguang Gu <jokergoo using gmail.com>
> > Sent: Tuesday, September 24, 2024 4:25 AM
> > To: bioc-devel <bioc-devel using r-project.org>
> > Subject: [Bioc-devel] file 'HilbertCurve/DESCRIPTION' does not exist
> >
> > * This email originates from a sender outside of CUNY. Verify the sender
> before replying or clicking on links and attachments. *
> >
> > Dear Bioc,
> >
> > I have been seeing this error from the HilbertCurve package (devel):
> >
> >
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FHilbertCurve%2F__%3B!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8jgvQQvo%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7Cbbb869428c8245ea230f08dcdc72824f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627631609247752%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=hHY%2B%2FwUZlGBvqmh381GvG9jnOjuAywGbzFIDA8lkHRA%3D&reserved=0
> <
> https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/HilbertCurve/__;!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8jgvQQvo$
> >
> >
> > * checking for file ‘HilbertCurve/DESCRIPTION’ ... OK
> > * preparing ‘HilbertCurve’:
> > * checking DESCRIPTION meta-information ... OK
> > * cleaning src
> > * installing the package to build vignettes
> > * creating vignettes ... OK
> > * cleaning src
> > Error in .read_description(ldpath) :
> >   file 'HilbertCurve/DESCRIPTION' does not exist
> > Execution halted
> >
> > I've checked, the DESCRIPTION file is not missing. See the git commit
> >
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fcode.bioconductor.org%2Fbrowse%2FHilbertCurve%2F728edd7e4b127bea4144ddce608602331817153b%2F__%3B!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8dJcAsaA%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7Cbbb869428c8245ea230f08dcdc72824f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627631609268861%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=RM1CuicK1eGZnzU5Ky%2BCvs06ycCRcrAOCJnza2w%2Bjnw%3D&reserved=0
> <
> https://urldefense.com/v3/__https://code.bioconductor.org/browse/HilbertCurve/728edd7e4b127bea4144ddce608602331817153b/__;!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8dJcAsaA$
> >
> > which was checked on bioc.
> >
> > Also the first line "checking for file ‘HilbertCurve/DESCRIPTION’ ... OK"
> > already means the DESCRIPTION file does exist.
> >
> > Thanks!
> > Zuguang Gu
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> >
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> >
> >
> >         [[alternative HTML version deleted]]
> >
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