Options: 1) Don't use roxygen2 2) after running document(), move the bnlearn imports to the top of the imports section of the NAMESPACE. 3) Report a bug to the roxygen2 authors.
I tried to put #' @import bnlearn before any other imports in tronco.R, but it still ended up after the Rgraphviz import in the generated NAMESPACE, which causes this problem. Dan ----- Original Message ----- > From: "Luca De Sano" <l.des...@campus.unimib.it> > To: "Vincent Carey" <st...@channing.harvard.edu> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Thursday, February 25, 2016 7:56:58 AM > Subject: Re: [Bioc-devel] R CMD check problems > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
