Thank you Simon. Dr Oleg Sklyar Research Technologist AHL / Man Investments Ltd +44 (0)20 7144 3107 oskl...@maninvestments.com
> -----Original Message----- > From: Simon Urbanek [mailto:simon.urba...@r-project.org] > Sent: 14 January 2009 16:11 > To: Sklyar, Oleg (London) > Cc: r-devel@r-project.org > Subject: Re: [Rd] particulars of importing/loading libraries > > > On Jan 14, 2009, at 10:52 , Sklyar, Oleg (London) wrote: > > > Well, this is very reasonable and this is how it should be I would > > say. If it was consistent, there would be no problem as they would > > be easy to nail down. However, the problem is now that if I load > > pack3 only (which imports pack2 only) then as.POSIXct > exported from > > pack1 is NOT available for functions in pack3, > > Because pack3 didn't request it. > > > > but is available for calls from the global env (see example > below). > > It is obviously available for calls from functions in pack2 > as there > > it is imported directly. Although, why also testPosix() of > pack2 is > > then available for calls from the global env as it was only loaded > > as import for pack3? > > > > Global environment is not encapsulated - you have access to anything > that has been attached - sort of implicitly importing anything that > has even been [exported and] attached (there is really no concept of > "importing" for the global environment, but the effect is > analogous). > This is a conceptual difference of the "interactive" use vs package > code. Unlike package code you don't know in advance what you will be > doing when you're working interactively, so I think it makes > sense to > assume that everything is implicitly imported. > > Cheers, > S > > > > In my understanding if pack3 does not depend on pack1 directly, > > functionality of pack1 should not be available anywhere apart from > > functions called from pack2 as well as functions in pack2 should > > only be > > available for calls by functions in pack3 but not in the > global env... > > The semantics seems to be broken here, is it not? > > > >> library(pack3) > > Loading required package: pack2 > > Loading required package: pack1 > >> testPosix() ## from pack2 > > [1] "2009-01-13 15:29:50 UTC" > > [1] "POSIXt" "POSIXct" > > [1] "2009-01-13 15:29:50 UTC" > >> testPosix2() > > Error in as.POSIXct.default(testPosixVal) : > > do not know how to convert 'testPosixVal' to class "POSIXlt" > >> as.POSIXct(pack1::testPosixVal) > > [1] "2009-01-13 15:29:50 UTC" > > > > > > > > Dr Oleg Sklyar > > Research Technologist > > AHL / Man Investments Ltd > > +44 (0)20 7144 3107 > > oskl...@maninvestments.com > > > >> -----Original Message----- > >> From: Simon Urbanek [mailto:simon.urba...@r-project.org] > >> Sent: 14 January 2009 15:38 > >> To: Sklyar, Oleg (London) > >> Cc: r-devel@r-project.org > >> Subject: Re: [Rd] particulars of importing/loading libraries > >> > >> > >> On Jan 14, 2009, at 4:24 , Sklyar, Oleg (London) wrote: > >> > >>> Sorry Simon, you are right. I tried to recreate a problem > >> that I had > >>> with other packages where the packages were added to Depends but > >>> made a mistake. However the problem remains if I do the following. > >>> > >>> Added: pack1 to Depends of pack2. Now I create pack3 with the > >>> following contents: it does not import pack1 directly, nor depends > >>> on it. It rather imports pack2 and depends on pack2. I then expect > >>> the functionality of pack1 to be available still if I only > >> load pack3. > >> > >> > >> That is semantically not a reasonable requirement. pack3 > cannot (and > >> should not) assume anything about the internals of pack2. If > >> it needs > >> a function from pack1, it has to import it from pack1. If pack2 re- > >> exported as.POSIXct then that would make it part of pack2's > >> interface > >> and then you're free to just depend on pack2. > >> > >> Cheers, > >> S > >> > >> > >> > >>> But I > >>> now get errors with pack3 calling the function from > pack1. Does this > >>> mean I need to import and depend on pack1 and methods > explicitly in > >>> pack3. I.e. do I have to import and depend on ALL the > >> packages that > >>> may > >>> be in use, even if they are imported by other that I depend on and > >>> import: > >>> > >>> ---- pack3: DESCRIPTION ----- > >>> > >>> Package: pack3 > >>> Version: 0.0.1 > >>> Date: 12 Jan 2009 > >>> Title: pack1 to test S3/S4 methods compatibility > >>> Author: Oleg Sklyar > >>> Depends: R (>= 2.7.1), pack2 > >>> Maintainer: Oleg Sklyar <oskl...@maninvestments.com> > >>> Description: pack3 > >>> LazyLoad: yes > >>> License: Proprietary > >>> URL: http://www.maninvestments.com > >>> LazyLoad: no > >>> > >>> ---- pack3: NAMESPACE ------ > >>> import(pack2) > >>> exportPattern("^[^\\.]") > >>> > >>> ---- pack3: posix.R ------ > >>> testPosix2 = function() { > >>> z = as.POSIXct(testPosixVal) > >>> print(z) > >>> print(class(z)) > >>> z > >>> } > >>> > >>> Note, that the above function is the same as in pack2, just a > >>> different > >>> name. > >>> > >>> > >>> *** R 2.9.0 (svn -r 46585) > >> [/share/research/R-devel/20081002/lib64/R] > >>> *** > >>>> library(pack3) > >>> Loading required package: pack2 > >>> Loading required package: pack1 > >>>> as.POSIXct(pack1::testPosixVal) > >>> [1] "2009-01-13 15:29:50 UTC" > >>>> testPosxi() ## called from pack2 > >>> [1] "2009-01-13 15:29:50 UTC" > >>> [1] "POSIXt" "POSIXct" > >>> [1] "2009-01-13 15:29:50 UTC" > >>>> testPosix2() ## called from pack3 > >>> Error in as.POSIXct.default(testPosixVal) : > >>> do not know how to convert 'testPosixVal' to class "POSIXlt" > >>> > >>> > >>> > >>> > >>> Dr Oleg Sklyar > >>> Research Technologist > >>> AHL / Man Investments Ltd > >>> +44 (0)20 7144 3107 > >>> oskl...@maninvestments.com > >>> > >>>> -----Original Message----- > >>>> From: Simon Urbanek [mailto:simon.urba...@r-project.org] > >>>> Sent: 14 January 2009 01:51 > >>>> To: Sklyar, Oleg (London) > >>>> Cc: r-devel@r-project.org > >>>> Subject: Re: [Rd] particulars of importing/loading libraries > >>>> > >>>> Oleg, > >>>> > >>>> On Jan 13, 2009, at 11:00 , Sklyar, Oleg (London) wrote: > >>>> > >>>>> Dear List: > >>>>> > >>>>> Sorry for posting maybe a trivial question, but I have a basic > >>>>> understanding problem. If I have say pack1 and pack2, two R > >>>> packages, > >>>>> and pack2 depends on and imports pack1 fully (as in the > >>>> code below), > >>>>> is > >>>>> there a way to make all the functionality of pack1 > >> available for the > >>>>> global and other environments (not only for the functions > >>>> called from > >>>>> withing pack2) by loading pack2 only? I thought if pack2 > >>>> depends on > >>>>> and > >>>>> imports pack1 and essentially reexports everything, one > >>>> should get the > >>>>> full functionality simply by loading pack2. This does not > >>>> seem to be > >>>>> the > >>>>> case or I am missing something trivial in my > NAMESPACE/DESCRIPTION > >>>>> files? > >>>>> > >>>>> If this is documented in Writing R Extensions, I would > be thankful > >>>>> for a > >>>>> page number and maybe a quick fix in my example below as so > >>>> far I have > >>>>> not been able to find a clear explanation. > >>>>> > >>>>> The problem can be illustrated by the following simple > >>>> example (this > >>>>> is > >>>>> a simple code for 2 packages, pack1 and pack2; plus an example). > >>>>> > >>>> > >>>> if you bothered to use R CMD check you would find your bug right > >>>> away: > >>>> * checking package dependencies ... ERROR > >>>> Namespace dependencies not required: > >>>> pack1 > >>>> > >>>> You simply forgot to add pack1 to the Depends: line - that's > >>>> all. Once > >>>> you fix that, you'll see what happens: > >>>> > >>>>> library(pack2) > >>>> Loading required package: pack1 > >>>>> as.POSIXct(pack1::testPosixVal) > >>>> [1] "2009-01-14 01:38:08 UTC" > >>>> > >>>> Cheers, > >>>> S > >>>> > >>>> > >>>>> Thank you for your replies. > >>>>> > >>>>> Dr Oleg Sklyar > >>>>> Research Technologist > >>>>> AHL / Man Investments Ltd > >>>>> +44 (0)20 7144 3107 > >>>>> oskl...@maninvestments.com > >>>>> > >>>>> --- pack1: DESCRIPTION ------ > >>>>> Package: pack1 > >>>>> Version: 0.0.1 > >>>>> Date: 12 Jan 2009 > >>>>> Title: pack1 to test S3/S4 methods compatibility > >>>>> Author: Oleg Sklyar > >>>>> Depends: R (>= 2.7.1), methods > >>>>> Maintainer: Oleg Sklyar <oskl...@maninvestments.com> > >>>>> Description: pack1 > >>>>> LazyLoad: yes > >>>>> License: Proprietary > >>>>> URL: http://www.maninvestments.com > >>>>> LazyLoad: no > >>>>> > >>>>> --- pack1: NAMESPACE ------ > >>>>> import(methods) > >>>>> exportPattern("^[^\\.]") > >>>>> exportClasses(posixTime) > >>>>> exportMethods(as.POSIXct) > >>>>> > >>>>> --- pack1: posix.R ------ > >>>>> setClass("posixTime", "numeric") > >>>>> > >>>>> setGeneric("as.POSIXct") > >>>>> setMethod("as.POSIXct", signature(x="posixTime"), > >>>>> function(x, tz) { > >>>>> z = x...@.data > >>>>> attr(z,"class") = c("POSIXt", "POSIXct") > >>>>> attr(z,"tzone") = "UTC" > >>>>> z > >>>>> } > >>>>> ) > >>>>> > >>>>> testPosixVal = new("posixTime", as.numeric(Sys.time())) > >>>>> > >>>>> --- pack2: DESCRIPTION > >>>>> Package: pack2 > >>>>> Version: 0.0.1 > >>>>> Date: 12 Jan 2009 > >>>>> Title: pack2 to test S3/S4 methods compatibility > >>>>> Author: Oleg Sklyar > >>>>> Depends: R (>= 2.7.1), methods > >>>>> Maintainer: Oleg Sklyar <oskl...@maninvestments.com> > >>>>> Description: pack2 > >>>>> LazyLoad: yes > >>>>> License: Proprietary > >>>>> URL: http://www.maninvestments.com > >>>>> LazyLoad: no > >>>>> > >>>>> --- pack2: NAMESPACE ------ > >>>>> import(pack1) > >>>>> exportPattern("^[^\\.]") > >>>>> > >>>>> --- pack2: posix.R ------ > >>>>> testPosix = function() { > >>>>> z = as.POSIXct(testPosixVal) > >>>>> print(z) > >>>>> print(class(z)) > >>>>> z > >>>>> } > >>>>> > >>>>> ------ test code to run from global env, showing > problems ------- > >>>>> require(pack2) > >>>>> > >>>>> ## use as.POSIXct imported into pack2 from pack1 to do the > >>>>> conversion in > >>>>> the fun > >>>>> testPosix() > >>>>> #~ [1] "2009-01-13 15:29:50 UTC" > >>>>> #~ [1] "POSIXt" "POSIXct" > >>>>> #~ [1] "2009-01-13 15:29:50 UTC" > >>>>> > >>>>> ## now try using it directly from the global env (pack1 was not > >>>>> explicitly loaded) > >>>>> as.POSIXct(pack1::testPosixVal) > >>>>> #~ Error in as.POSIXct.default(pack1::testPosixVal) : > >>>>> #~ do not know how to convert 'pack1::testPosixVal' to class > >>>>> "POSIXlt" > >>>>> > >>>>> ## now require pack1 explicitly and try again > >>>>> require(pack1) > >>>>> as.POSIXct(pack1::testPosixVal) > >>>>> #~ [1] "2009-01-13 15:29:50 UTC" > >>>>> > >>>>> > >>>>> > >>>> > >> > ********************************************************************** > >>>>> Please consider the environment before printing this > email or its > >>>>> attachments. > >>>>> The contents of this email are for the named addressees > >>>> ...{{dropped: > >>>>> 19}} > >>>>> > >>>>> ______________________________________________ > >>>>> R-devel@r-project.org mailing list > >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>>>> > >>>>> > >>>> > >>>> > >>> > >>> > >> > ********************************************************************** > >>> Please consider the environment before printing this email or its > >>> attachments. > >>> The contents of this email are for the named addressees only. It > >>> contains information which may be confidential and privileged. If > >>> you are not the intended recipient, please notify the sender > >>> immediately, destroy this email and any attachments and do not > >>> otherwise disclose or use them. Email transmission is not a secure > >>> method of communication and Man Investments cannot accept > >>> responsibility for the completeness or accuracy of this > >> email or any > >>> attachments. Whilst Man Investments makes every effort to keep its > >>> network free from viruses, it does not accept > >> responsibility for any > >>> computer virus which might be transferred by way of this email or > >>> any attachments. This email does not constitute a request, offer, > >>> recommendation or solicitation of any kind to buy, subscribe, sell > >>> or redeem any investment instruments or to perform other such > >>> transactions of any kind. Man Investments reserves the right to > >>> monitor, record and retain all electronic communications > >> through its > >>> network to ensure the integrity of its systems, for record keeping > >>> and regulatory purposes. > >>> Visit us at: www.maninvestments.com > >>> TG0908 > >>> > >> > ********************************************************************** > >>> > >>> > >> > >> > > > > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
