An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20130304/5a5d6104/attachment.pl>
[Bioc-devel] avoiding call to ".find.package"
4 messages · Andreas Heider, Antti Honkela, Laurent Gatto +1 more
According to the build logs my package (tigre) appears to have the same problem, but I cannot reproduce this on my own install of R-devel (r62117). Perhaps this is just an R bug that has since been fixed? Antti
On 04/03/13 10:52, Andreas Heider wrote:
Dear mailing list, how can I solve the warning during the CHECK of the examples in my virtualArray package that states: Warning: ?.find.package? is deprecated.
From what function call does it originate?
Thanks, Andreas [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Antti Honkela antti.honkela at hiit.fi - http://www.hiit.fi/u/ahonkela/
On 4 March 2013 09:57, Antti Honkela <antti.honkela at hiit.fi> wrote:
According to the build logs my package (tigre) appears to have the same problem, but I cannot reproduce this on my own install of R-devel (r62117). Perhaps this is just an R bug that has since been fixed?
I believe the warnings result from changes to R r62077 prefer loaded namepaces in find.package deprecate .find.package and .path.package Biobase and affy (which our packages rely on) use .find.package. $ grep .find.package Biobase/R/* Biobase/R/packages.R: pkgpath <- .find.package(package) Biobase/R/vignettes.R: vigrds = file.path(.find.package(pkgs), "Meta", "vignette.rds") Biobase/R/vignettes.R: vigs = file.path(.find.package(pkgName), "doc", vigMtrx[, "PDF"]) $ grep .find.package affy/R/* affy/R/getCDFenv.R: if (length(.find.package(cdfname, lib.loc=lib, quiet=TRUE)) == 0) I suspect that's were the warnings come from and were the fix should be applied. Hope this helps. Best wishes, Laurent
Antti On 04/03/13 10:52, Andreas Heider wrote:
Dear mailing list, how can I solve the warning during the CHECK of the examples in my virtualArray package that states: Warning: ?.find.package? is deprecated.
From what function call does it originate?
Thanks,
Andreas
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Antti Honkela antti.honkela at hiit.fi - http://www.hiit.fi/u/ahonkela/
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Mon, Mar 4, 2013 at 2:22 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
On 4 March 2013 09:57, Antti Honkela <antti.honkela at hiit.fi> wrote:
According to the build logs my package (tigre) appears to have the same problem, but I cannot reproduce this on my own install of R-devel (r62117). Perhaps this is just an R bug that has since been fixed?
I believe the warnings result from changes to R r62077 prefer loaded namepaces in find.package deprecate .find.package and .path.package Biobase and affy (which our packages rely on) use .find.package. $ grep .find.package Biobase/R/* Biobase/R/packages.R: pkgpath <- .find.package(package) Biobase/R/vignettes.R: vigrds = file.path(.find.package(pkgs), "Meta", "vignette.rds") Biobase/R/vignettes.R: vigs = file.path(.find.package(pkgName), "doc", vigMtrx[, "PDF"]) $ grep .find.package affy/R/* affy/R/getCDFenv.R: if (length(.find.package(cdfname, lib.loc=lib, quiet=TRUE)) == 0) I suspect that's were the warnings come from and were the fix should be applied. Hope this helps.
I've fixed all BioC packages that were calling .find.package(); they now call find.package(). Dan
Best wishes, Laurent
Antti On 04/03/13 10:52, Andreas Heider wrote:
Dear mailing list, how can I solve the warning during the CHECK of the examples in my virtualArray package that states: Warning: ?.find.package? is deprecated.
From what function call does it originate?
Thanks,
Andreas
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Antti Honkela antti.honkela at hiit.fi - http://www.hiit.fi/u/ahonkela/
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel