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

Habil Zare zare at txstate.edu
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
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 =

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:

          d1 <- rbind(aml,mds)

          ## Fiting the trees:
          trees <- make.decision.tree(pigengene=pigengene, Data=d1,
          saveDir="trees", minPerLeaf=15, doHeat=FALSE,verbose=3,
t1 <- trees$c5Trees[["15"]]
> class(t1)
[1] "C5.0"
*> 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

[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

Habil Zare, PhD
Assistant Professor
Department of Computer Science
Texas State University
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:

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org


  * This was the status of your package at the time this email was sent to
    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
    either because another package (from CRAN or Bioconductor) breaks your
    package (if yours depends on it) or because of a Build System problem.
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  * Please check the report again 24h after you've committed your changes
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