A Bioconductor package cannot depend on act version of a package that is not available in Bioconductor or CRAN. So he needs to make sure this new version if available in CRAN ASAP.
On February 25, 2016 8:48:49 AM PST, Luca De Sano <l.des...@campus.unimib.it> wrote: >I think that the answer of Marco Scutari, the maintainer of bnlearn, is >the >best solution. >Using bnlearn 4.0-20160212 everything works in the right way: > >Status: 0 ERROR, 0 WARNINGs, 0 NOTE > >Thank you > > >Marco Scutari says: > > > > > > > > > > > >*Hi Morgan, Hi Luca, this problem is known to me and I have fixed it >in my >developmentsnapshots at www.bnlearn.com <http://www.bnlearn.com/>. I >have >basically given up on trying tobe elegant and I try-catch all the calls >to >setMethods() and createthe generics as needed. The fix will eventually >make >its way to CRAN,I expect sometime in late spring or early >summer.Cheers, >Marco* > > >Martin Morgan says: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >*This reproduces the problem> loadNamespace('graph')<environment: >namespace:graph>> loadNamespace('bnlearn')Error: .onLoad failed in >loadNamespace() for 'bnlearn', details: call: setMethod("nodes", cl, >function(object) .nodes(object)) error: no existing definition for >function 'nodes'and it's because of the way bnlearn loads itself if >("graph" %!in% loadedNamespaces()) { setGeneric("nodes", >function(object, ...) standardGeneric("nodes")) >setGeneric("nodes<-", >function(object, value) standardGeneric("nodes<-")) >setGeneric("degree", >function(object, Nodes, ...) standardGeneric("degree")) }#THEN # add >the >methods. for (cl in bnlearn.classes) { setMethod("nodes", cl, >function(object) .nodes(object)) setMethod("nodes<-", cl, >function(object, value) .relabel(object, value)) setMethod("degree", >cl, >function(object, Nodes) .degree(object, Nodes)) }#FORgraph is loaded >but >not attached, so the generic that it defines is not visible to >bnlearn.I'm >ccing the bnlearn maintainer* > > >-- >Luca De Sano >tel: +393337177338 >email: l.des...@campus.unimib.it >PEC: luca.des...@pec.it > >On 25 February 2016 at 17:36, Joris Meys <joris.m...@ugent.be> wrote: > >> Also not an expert, but I've looked at the dependencies and realized >the >> following: >> >> The problem is likely due to import of Rgraphviz before bnlearn. >Rgraphviz >> is dependent on graph, and graph also has a nodes generic. When >bnlearn >> gets loaded, the nodes generic from the graph package is not visible >for >> some reason (I hope some R guru can explain this a bit more >correctly) >> >> So you have to make sure anything from bnlearn is imported before >> Rgraphviz. If you use Roxygen, you'll only get that working by >importing >> bnlearn and not just those two functions. >> >> You also should split the file tronco.R in different files, one >function >> each. Say you have the file tronco.capri.R and tronco.plot.R >> >> Then you can add to the file tronco.plot.R a tag >> @include tronco.capri.R >> >> to make sure that file is processed before tronco.plot. >> >> Last option is changing the namespace file manually, and then >configure >> Roxygen2 to leave your namespace file alone. You can do that in >RStudio by >> clicking on Project Options > build Tools and then the big >"Configure" >> button next to "generate documentation with Roxygen". >> >> Or, on the command line: >> roxygen2::roxygenize(roclets = "rd") >> >> This leaves your namespace file alone. >> >> On a sidenote: if you import from the bnlearn package in the >NAMESPACE >> file, you should add it to the field Imports and not Depends in the >> DESCRIPTION file. If you add it to the Depends field, the complete >package >> is attached before your package is loaded. If you add it to the >fields >> Imports on the other hand, its namespace is imported but not >attached. >> >> See also Writing R Extensions: >> >> >https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies >> >> >> Cheers >> Joris >> >> On Thu, Feb 25, 2016 at 4:56 PM, Luca De Sano ><l.des...@campus.unimib.it> >> wrote: >> >>> The problem is that the NAMESPACE is regenerated every time I >execute the >>> document() command. >>> >>> At the moment, in the description file I've added bnlean >>> >>> Depends: >>> R (>= 3.1), >>> bnlearn, >>> doParallel, >>> >>> to prevent this: >>> >>> > library(devtools) >>> > document() >>> Updating TRONCO documentation >>> Loading TRONCO >>> Loading required package: doParallel >>> Loading required package: foreach >>> foreach: simple, scalable parallel programming from Revolution >Analytics >>> Use Revolution R for scalability, fault tolerance and more. >>> http://www.revolutionanalytics.com >>> Loading required package: iterators >>> Loading required package: parallel >>> Warning messages: >>> 1: .onLoad failed in loadNamespace() for 'bnlearn', details: >>> call: setMethod("nodes", cl, function(object) .nodes(object)) >>> error: no existing definition for function ‘nodes’ >>> 2: .onLoad failed in loadNamespace() for 'bnlearn', details: >>> call: setMethod("nodes", cl, function(object) .nodes(object)) >>> error: no existing definition for function ‘nodes’ >>> 3: .onLoad failed in loadNamespace() for 'bnlearn', details: >>> call: setMethod("nodes", cl, function(object) .nodes(object)) >>> error: no existing definition for function ‘nodes’ >>> 4: .onLoad failed in loadNamespace() for 'bnlearn', details: >>> call: setMethod("nodes", cl, function(object) .nodes(object)) >>> error: no existing definition for function ‘nodes’ >>> >>> With this configuration I can build and check the package, but the >>> warnings >>> mentioned above still remain. >>> >>> >>> >>> >>> -- >>> Luca De Sano >>> tel: +393337177338 >>> email: l.des...@campus.unimib.it >>> PEC: luca.des...@pec.it >>> >>> On 25 February 2016 at 16:23, Vincent Carey ><st...@channing.harvard.edu> >>> wrote: >>> >>> > I am evidently not expert in this topic. However I was able to >get past >>> > the warning/halt you identified by moving the >importFrom(bnlearn,...) >>> > statements to the top of the NAMESPACE. I cannot see in the WRE >manual >>> how >>> > the order of namespace imports/exports should be controlled. >Other >>> minds >>> > will be needed to set this straight. >>> > >>> > On Thu, Feb 25, 2016 at 6:06 AM, Luca De Sano < >>> l.des...@campus.unimib.it> >>> > wrote: >>> > >>> >> This is my sessionInfo(), I've the current stable release of >bnlearn >>> >> (3.9). >>> >> >>> >> > sessionInfo() >>> >> R version 3.2.3 (2015-12-10) >>> >> Platform: x86_64-pc-linux-gnu (64-bit) >>> >> Running under: Ubuntu 14.04.3 LTS >>> >> >>> >> locale: >>> >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> >> [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8 >>> >> [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> >> [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C >>> >> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> >> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C >>> >> >>> >> attached base packages: >>> >> [1] parallel stats graphics grDevices utils datasets >methods >>> >> [8] base >>> >> >>> >> other attached packages: >>> >> [1] TRONCO_2.4.0 bnlearn_3.9 doParallel_1.0.10 >>> iterators_1.0.8 >>> >> >>> >> [5] foreach_1.4.3 devtools_1.10.0 >>> >> >>> >> loaded via a namespace (and not attached): >>> >> [1] igraph_1.0.1 graph_1.44.1 Rcpp_0.12.3 >>> >> [4] magrittr_1.5 roxygen2_5.0.1 BiocGenerics_0.12.1 >>> >> [7] munsell_0.4.3 xtable_1.8-2 colorspace_1.2-6 >>> >> [10] stringr_1.0.0 plyr_1.8.3 tools_3.2.3 >>> >> [13] grid_3.2.3 gtable_0.1.2 R.oo_1.20.0 >>> >> [16] withr_1.0.1 digest_0.6.9 gridExtra_2.0.0 >>> >> [19] RColorBrewer_1.1-2 Rgraphviz_2.10.0 reshape2_1.4.1 >>> >> [22] ggplot2_2.0.0 cgdsr_1.2.5 codetools_0.2-14 >>> >> [25] memoise_1.0.0 stringi_1.0-1 R.methodsS3_1.7.1 >>> >> [28] scales_0.3.0 stats4_3.2.3 >>> >> >>> >> >>> >> -- >>> >> Luca De Sano >>> >> tel: +393337177338 >>> >> email: l.des...@campus.unimib.it >>> >> PEC: luca.des...@pec.it >>> >> >>> >> On 25 February 2016 at 12:03, Vincent Carey < >>> st...@channing.harvard.edu> >>> >> wrote: >>> >> >>> >>> sessionInfo might help. my guess is that you have an outofdate >>> bnlearn >>> >>> installed? >>> >>> >>> >>> On Thu, Feb 25, 2016 at 5:57 AM, Luca De Sano < >>> l.des...@campus.unimib.it >>> >>> > wrote: >>> >>> >>> >>>> Hi all, >>> >>>> I'm working on a package named TRONCO ( >>> >>>> http://bioconductor.org/packages/devel/bioc/html/TRONCO.html ) >which >>> >>>> was >>> >>>> released last year on bioconductor. Everytime I run R CMD check >I get >>> >>>> these >>> >>>> two warnings: >>> >>>> >>> >>>> * checking whether the namespace can be loaded with stated >>> dependencies >>> >>>> ... >>> >>>> WARNING >>> >>>> Error: .onLoad failed in loadNamespace() for 'bnlearn', >details: >>> >>>> call: setMethod("nodes", cl, function(object) .nodes(object)) >>> >>>> error: no existing definition for function ‘nodes’ >>> >>>> Execution halted >>> >>>> >>> >>>> * checking whether the namespace can be unloaded cleanly ... >WARNING >>> >>>> Error: .onLoad failed in loadNamespace() for 'bnlearn', >details: >>> >>>> call: setMethod("nodes", cl, function(object) .nodes(object)) >>> >>>> error: no existing definition for function ‘nodes’ >>> >>>> Execution halted >>> >>>> >>> >>>> I've searched informations about these errors and I've only >found >>> some >>> >>>> old >>> >>>> posts on StackOverflow which suggested to change the order of >the >>> >>>> import. >>> >>>> I've tried to do it with no result. At the moment I can't >figure out >>> >>>> what >>> >>>> those warnings mean! >>> >>>> >>> >>>> Any suggestions? >>> >>>> >>> >>>> Warnings can be reproduced with the code listed below: >>> >>>> >>> >>>> git clone https://github.com/BIMIB-DISCo/TRONCO.git >>> >>>> R CMD build TRONCO >>> >>>> R CMD check TRONCO_2.3.0.tar.gz >>> >>>> >>> >>>> Thank you >>> >>>> >>> >>>> -- >>> >>>> Luca De Sano >>> >>>> tel: +393337177338 >>> >>>> email: l.des...@campus.unimib.it >>> >>>> PEC: luca.des...@pec.it >>> >>>> >>> >>>> [[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 >> >> >> >> >> -- >> Joris Meys >> Statistical consultant >> >> Ghent University >> Faculty of Bioscience Engineering >> Department of Mathematical Modelling, Statistics and Bio-Informatics >> >> tel : +32 9 264 59 87 >> joris.m...@ugent.be >> ------------------------------- >> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php >> > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioc-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Sent from my Android device with K-9 Mail. 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