[Bioc-devel] Pigengene problems reported due to partykit::as.party

Tue Dec 5 21:42:54 CET 2017

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
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    could see something different when you visit the URL(s) above,
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  * It is possible that the problems reported in this report are false
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  * Please check the report again 24h after you've committed your changes
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