Yes, that is the problem. Thank you!
On Tue, 8 Oct 2024 at 17:06, Henrik Bengtsson <henrik.bengts...@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.wok...@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-boun...@r-project.org> on behalf of > Zuguang Gu <joker...@gmail.com> > > Sent: Tuesday, September 24, 2024 4:25 AM > > To: bioc-devel <bioc-devel@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@r-project.org mailing list > > > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8pSz4r9c%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7Cbbb869428c8245ea230f08dcdc72824f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627631609277706%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=NIBADQRao0bPSQgSs1R88Eib%2B1NQiKz1G2PW27sfByI%3D&reserved=0 > < > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!L3HQzp8CISFrmAsM8ur1f-zLgGoLOB08aAK0PEKUVnaKjfDh-VN-J88FyYSEbCv6OzsHglCEvZGyrc3IXJ-8pSz4r9c$ > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
