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[Bioc-devel] `as.list` and import `image` warnings
3 messages · Levi Waldron, Diego Diez, Martin Morgan
Hi Levi, I had a similar issue with my package (codelink). The problem was the importFrom call in the NAMESPACE file. In my case importFrom(annotate, lookUp, htmlpage). I could temporarily avoid the warnings by commenting out that line and moving package annotate from Imports to Depends in the DESCRIPTION file. However, I imagine it is better to solve the original problem which I am not sure where it is. At least the following thread seems to be related (although it was supposed to be fixed). https://stat.ethz.ch/pipermail/r-devel/2012-April/063802.html Hope this helps, Diego
Diego Diez, PhD Assistant Professor Bioinformatics and Genomics Laboratory, WPI Immunology Frontier Research Center (IFReC) 8F Integrated Life Science Building, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan Phone: +81-6-6879-4266 Fax: +81-6-6879-4272 diez at ifrec.osaka-u.ac.jp On Wed, Sep 26, 2012 at 12:55 AM, Levi Waldron <lwaldron at hsph.harvard.edu> wrote: > I am getting warnings for the ffpe package, about previous base package > functions, that I could really use some help in resolving: > > * installing *source* package ?ffpe? ... > ** R > ** inst > ** preparing package for lazy loading > Warning: found methods to import for function ?as.list? but not the > generic itself > Warning: replacing previous import ?image? when loading ?graphics? > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ?ffpe.Rnw? > ** testing if installed package can be loaded > Warning: found methods to import for function ?as.list? but not the > generic itself > Warning: replacing previous import ?image? when loading ?graphics? > * DONE (ffpe) > > I really apologize for not noticing this until it was pointed out to me, > but I will resolve it right away as soon as I know how. > > Sincerely, > Levi > > > > On Fri, Sep 21, 2012 at 8:07 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > >> Hello, >> >> This is a courtesy warning because your package is currently being >> affected by warnings or errors in the build system. You can see the >> current report here (updated daily): >> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/ >> >> According to our release schedule, all packages are expected to be free >> of errors by the 17th (that was last week), and free of warnings by the >> 24th (this is next Monday). Packages that are not cleaned up by this >> time may be excluded from the upcoming release, which is why you are >> receiving this courtesy email as a warning. In case you have questions >> about the release schedule, you can see our release schedule at this link: >> >> http://www.bioconductor.org/developers/release-schedule/ >> >> Your packages are important to the Bioconductor project, so please let >> me know if I can help you to meet these deadlines. >> >> >> Marc >> >> > > > -- > Levi Waldron > Post-doctoral fellow > Department of Biostatistics, Harvard School of Public Health > Department of Biostatistics and Computational Biology, Dana-Farber Cancer > Institute > Building 1, room 412C > 655 Huntington Avenue > Boston, Massachusetts 02115 > mobile: (617) 851-6849 > fax: (617) 432-5619 > http://www.hsph.harvard.edu/research/levi-waldron/ > > > > -- > Levi Waldron > Post-doctoral fellow > Department of Biostatistics, Harvard School of Public Health > Department of Biostatistics and Computational Biology, Dana-Farber Cancer > Institute > Building 1, room 412C > 655 Huntington Avenue > Boston, Massachusetts 02115 > mobile: (617) 851-6849 > fax: (617) 432-5619 > http://www.hsph.harvard.edu/research/levi-waldron/ > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel >
On 09/25/2012 09:05 AM, Diego Diez wrote:
Hi Levi, I had a similar issue with my package (codelink). The problem was the importFrom call in the NAMESPACE file. In my case importFrom(annotate, lookUp, htmlpage). I could temporarily avoid the warnings by commenting out that line and moving package annotate from Imports to Depends in the DESCRIPTION file. However, I imagine it is better to solve the original problem which I am not sure where it is. At least the following thread seems to be related (although it was supposed to be fixed). https://stat.ethz.ch/pipermail/r-devel/2012-April/063802.html
Please IGNORE the warning Warning: found methods to import for function "as.list" but not the generic itself (possibly with a different method listed). There are many false positives, and there is a fix (now in R-patched, but not in the R used by the build systems or in use by most users). Diego you are right that the error should be corrected, not the symptom, so you do NOT want to comment out the importFrom or change the Depends: versus Imports: tag in the DESCRIPTION file. Martin
Hope this helps, Diego
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