The slowness is due to the methods package. We're working on it. Michael
On Wed, Dec 31, 2014 at 8:47 AM, Peng Yu <pengyu...@gmail.com> wrote: > On Wed, Dec 31, 2014 at 9:41 AM, Martin Morgan <mtmor...@fredhutch.org> > wrote: > > On 12/24/2014 07:31 PM, Maintainer wrote: > >> > >> Hi, > >> > >> Many bioconductor packages Depends on other packages but not Imports > >> other packages. (e.g., IRanges Depends on BiocGenerics.) Imports is > >> usually preferred to Depends. > >> > >> > >> > http://stackoverflow.com/questions/8637993/better-explanation-of-when-to-use-imports-depends > >> http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/ > >> > >> Could the unnecessary Depends be forced to be replaced by Imports? > >> This should improve the package load time significantly. > > > > > > R package symbols and other objects are collated at build time into a > 'name > > space'. When used, > > > > - Import: loads the name space from disk. > > - Depends: loads the name space from disk, and attaches it to the > search() > > path. > > > > Attaching is very inexpensive compared to loading, so there is no speed > > improvement gained by Import'ing instead of Depend'ing. > > Yes. For example, changing Depends to Imports does not improve the > package load time much. > > But loading a package in 4 sec seems to be too long. > > > system.time(suppressPackageStartupMessages(library(MBASED))) > user system elapsed > 4.404 0.100 4.553 > > For example, it only takes 10% of the time to load ggplot2. It seems > that many bioconductor packages have similar problems. > > > system.time(suppressPackageStartupMessages(library(ggplot2))) > user system elapsed > 0.394 0.036 0.460 > > > The main reason to Depend: on a package is because the symbols defined by > > the package are needed by the end-user. Import'ing a package is > appropriate > > when the package provides functionality only relevant to the package > author. > > What causes the load time to be too long? Is it because exporting too > many functions from all dependent packages to the global namespace? > > > There are likely to be specific packages that mis-use Depends; packages > such > > as IRanges, GenomicRanges, etc use Depends: as intended, to provide > > functions that are useful to the end user. > > > > Maintainers are certainly encouraged to think carefully about adding > > packages providing functionality irrelevant to the end-user to the > Depends: > > field. The codetoolsBioC package (available from svn, see > > http://bioconductor.org/developers/how-to/source-control/) provides some > > mostly reliable hints to package authors about correctly formulating a > > NAMESPACE file to facilitate using Imports: instead of Depends:. > > > > General questions about Bioconductor packages should be addressed to the > > support forum https://support.bioconductor.org. > > > > Questions about Bioconductor development (such as this) should be > addressed > > to the bioc-devel mailing list (subscription required) > > https://stat.ethz.ch/mailman/listinfo/bioc-devel. > > > > I have cc'd the bioc-devel mailing list; I hope that is ok. > > > > -- > Regards, > Peng > > _______________________________________________ > 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
