[Bioc-devel] Pigengene problems reported due to partykit::as.party
Martin Morgan
martin.morgan at roswellpark.org
Wed Dec 6 10:37:04 CET 2017
Remember that Bioconductor uses the current (3.4.3) or devel version of
R, and the corresponding versions of packages enforced by
BiocInstaller::biocValid().
Below you are using 3.3.3, which is not current. The first step then is
to get a current installation of R and Bioconductor.
Also
> qq <- eval(parse(text =
> (as.character(partykit::as.party(c5Tree))[3])))[[1]]
eval(parse(text=)) is almost never necessary, so think carefully about
what you are trying to accomplish; maybe you're looking for
fitted(as.party(c5Text)[3])
Martin
On 12/05/2017 03:42 PM, Habil Zare wrote:
> Hi Bioconductor team,
>
> The 3.6 build of my Pigengene package failed with the following error
> message. I do not get this error on my local machine. So, I am out of idea
> how to proceed. Can you please help?
>
> * creating vignettes ... ERROR
> Quitting from lines 114-116 (Pigengene_inference.Rnw)
> Error: processing vignette 'Pigengene_inference.Rnw' failed with
> diagnostics:
> no applicable method for 'as.party' applied to an object of class "C5.0"
> Execution halted
> =====================
>
> The error is caused by the following line in the get.fitted.leaf function:
>
> qq <- eval(parse(text =
> (as.character(partykit::as.party(c5Tree))[3])))[[1]]
>
> However, on my local machine with the latest version of partykit (1.1.1), I
> have no problem in running partykit::as.party function on an object of
> class "C5.0" as shown in a minimal example below:
>
> library(Pigengene)
> data(aml)
> data(mds)
> data(pigengene)
> d1 <- rbind(aml,mds)
>
> ## Fiting the trees:
> trees <- make.decision.tree(pigengene=pigengene, Data=d1,
> saveDir="trees", minPerLeaf=15, doHeat=FALSE,verbose=3,
> toCompact=FALSE)
> t1 <- trees$c5Trees[["15"]]
>> class(t1)
> [1] "C5.0"
> partykit::as.party(t1)
> ===================
> *> sessionInfo()*
> R version 3.3.3 (2017-03-06)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X Mavericks 10.9.5
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] Pigengene_1.3.8 graph_1.52.0 BiocGenerics_0.20.0
>
> loaded via a namespace (and not attached):
> [1] robust_0.4-18 Rcpp_0.12.12 mvtnorm_1.0-6
> [4] lattice_0.20-35 GO.db_3.4.0 digest_0.6.12
> [7] foreach_1.4.3 plyr_1.8.4 backports_1.1.0
> [10] acepack_1.4.1 pcaPP_1.9-72 dynamicTreeCut_1.63-1
> [13] stats4_3.3.3 RSQLite_2.0 ggplot2_2.2.1
> [16] rlang_0.1.2 lazyeval_0.2.0 data.table_1.10.4
> [19] Rgraphviz_2.18.0 blob_1.1.0 S4Vectors_0.12.2
> [22] rpart_4.1-11 Matrix_1.2-11 *partykit_1.1-1 *
> [25] checkmate_1.8.3 preprocessCore_1.36.0 splines_3.3.3
> [28] stringr_1.2.0 foreign_0.8-69 htmlwidgets_0.9
> [31] pheatmap_1.0.8 bit_1.1-12 munsell_0.4.3
> [34] pkgconfig_2.0.1 base64enc_0.1-3 C50_0.1.0-24
> [37] htmltools_0.3.6 nnet_7.3-12 tibble_1.3.4
> [40] gridExtra_2.2.1 htmlTable_1.9 Hmisc_4.0-3
> [43] IRanges_2.8.2 codetools_0.2-15 matrixStats_0.52.2
> [46] rrcov_1.4-3 MASS_7.3-47 grid_3.3.3
> [49] gtable_0.2.0 DBI_0.7 magrittr_1.5
> [52] scales_0.5.0 stringi_1.1.5 impute_1.48.0
> [55] doParallel_1.0.10 latticeExtra_0.6-28 robustbase_0.92-7
> [58] fastcluster_1.1.24 Formula_1.2-2 WGCNA_1.61
> [61] bnlearn_4.2 RColorBrewer_1.1-2 iterators_1.0.8
> [64] tools_3.3.3 bit64_0.9-7 Biobase_2.34.0
> [67] DEoptimR_1.0-8 fit.models_0.5-14 survival_2.41-3
> [70] AnnotationDbi_1.36.2 colorspace_1.3-2 cluster_2.0.6
> [73] memoise_1.1.0 knitr_1.17
>
>
> Thanks,
> Habil Zare, PhD
> Assistant Professor
> Department of Computer Science
> Texas State University
> http://cs.txstate.edu/~h_z14/
> Principal Investigator of Oncinfo Lab <http://oncinfo.org>
> Cellphone: 206 612 7830
>
> ---------- Forwarded message ----------
> From: <BBS-noreply at bioconductor.org>
> Date: Mon, Dec 4, 2017 at 2:14 PM
> Subject: Pigengene problems reported in the Multiple platform build/check
> report for BioC 3.6
> To: zare at txstate.edu
>
>
> [This is an automatically generated email. Please don't reply.]
>
> Hi Pigengene maintainer,
>
> According to the Multiple platform build/check report for BioC 3.6,
> the Pigengene package has the following problem(s):
>
> o ERROR for 'R CMD build' on malbec1. See the details here:
> https://master.bioconductor.org/checkResults/3.6/bioc-
> LATEST/Pigengene/malbec1-buildsrc.html
>
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
>
> Notes:
>
> * This was the status of your package at the time this email was sent to
> you.
> Given that the online report is updated daily (in normal conditions) you
> could see something different when you visit the URL(s) above,
> especially if
> you do so several days after you received this email.
>
> * It is possible that the problems reported in this report are false
> positives,
> either because another package (from CRAN or Bioconductor) breaks your
> package (if yours depends on it) or because of a Build System problem.
> If this is the case, then you can ignore this email.
>
> * Please check the report again 24h after you've committed your changes
> to the
> package and make sure that all the problems have gone.
>
> * If you have questions about this report or need help with the
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>
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