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
