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

[Habil Zare]

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_1.52.0BiocGenerics_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_1.8.4backports_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_0.2.0data.table_1.10.4
[19] Rgraphviz_2.18.0  blob_1.1.0S4Vectors_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_0.8-69htmlwidgets_0.9
[31] pheatmap_1.0.8bit_1.1-12munsell_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_1.1.24Formula_1.2-2 WGCNA_1.61
[61] bnlearn_4.2   RColorBrewer_1.1-2iterators_1.0.8
[64] tools_3.3.3   bit64_0.9-7   Biobase_2.34.0
[67] DEoptimR_1.0-8fit.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 
Cellphone: 206 612 7830

-- Forwarded message --
From: 
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: z...@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

Re: [Bioc-devel] Data package timeouts

[Sean Davis]

Thanks, Leo.

It turns out that that accession is not "public" yet; the "file" that
GEOquery gets is just an HTML page saying so.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1062236

I'll work on fix to catch such problems.

Sean


On Tue, Dec 5, 2017 at 1:48 PM, Leonardo Collado Torres 
wrote:

> Hi Sean,
>
> I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release.
> Here's a quick example:
>
> library('GEOquery')
> getGEO('GSM1062236', getGPL = FALSE)
>
> I found it from
> https://github.com/leekgroup/recount/blob/master/tests/
> testthat/test-misc.R#L19
>
> Best,
> Leo
>
>
> > library('GEOquery')
> Loading required package: Biobase
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, sd, var, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
> colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
> grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
> rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
> table, tapply, union, unique, unsplit, which, which.max, which.min
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material; view with
> 'browseVignettes()'. To cite Bioconductor, see
> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Setting options('download.file.method.GEOquery'='auto')
> Setting options('GEOquery.inmemory.gpl'=FALSE)
> > getGEO('GSM1062236', getGPL = FALSE)
> File stored at:
> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//RtmpAyQR3U/
> GSM1062236.soft
> ## Force terminate after a long running time
> ^C
> > sessionInfo()
> R version 3.4.2 (2017-09-28)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRblas.0.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
>
> 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] GEOquery_2.46.10Biobase_2.38.0  BiocGenerics_0.24.0
> [4] colorout_1.1-2
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.14 tidyr_0.7.2  dplyr_0.7.4  assertthat_0.2.0
>  [5] R6_2.2.2 magrittr_1.5 rlang_0.1.4  bindrcpp_0.2
>  [9] limma_3.34.2 xml2_1.1.1   readr_1.1.1  glue_1.2.0
> [13] purrr_0.2.4  hms_0.4.0compiler_3.4.2   pkgconfig_2.0.1
> [17] bindr_0.1tibble_1.3.4
>
>
> On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
>  wrote:
> >
> > Thanks Sean! I was seeing timeouts also in recount related to GEOquery
> which I just recently looked into.
> >
> > On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis  wrote:
> >>
> >>
> >> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith 
> wrote:
> >>
> >> > Thanks for the speedy response Sean.  I'll switch back to the version
> >> > using a file name shortly.
> >> >
> >>
> >> No problem. Let me know if it does not work as expected.
> >>
> >> Sean
> >>
> >>
> >>
> >> >
> >> > Cheers,
> >> > Mike
> >> >
> >> > On 30 November 2017 at 11:20, Sean Davis  wrote:
> >> >
> >> >> Thanks for the report, Mike.
> >> >>
> >> >> The problem was (specifically) in parsing a GSEMatrix file using a
> >> >> filename. This should be fixed in versions 2.46.10 (release) and
> 2.47.12
> >> >> (devel).
> >> >>
> >> >> Sean
> >> >>
> >> >>
> >> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith 
> wrote:
> >> >>
> >> >>> Hi Mike,
> >> >>>
> >> >>> I was experiencing similar problems with the BeadArrayUseCases
> vignette,
> >> >>> where using getGEO() from GEOquery was getting stuck in a
> (seemingly)
> >> >>> infinite loop processing a GSE series matrix file.  It looks like
> both of
> >> >>> your examples try to do this too, so I suspect it's a similar
> issue.  I
> >> >>> think the format of those files has changed recently and it seems
> to be
> >> >>> causing a fair few issues with GEOquery.
> >> >>>
> >> >>> I temporarily settled a solution by getting querying GEO directly
> rather
> >> >>> than using a local file, but it would be nice to get it back
> working as
> >> >>> intended.
> >> >>>
> >> >>> Mike
> >> >>>
> >> >>> On 29 November 2017 at 18:56, 

Re: [Bioc-devel] Data package timeouts

[Leonardo Collado Torres]

Hi Sean,

I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release.
Here's a quick example:

library('GEOquery')
getGEO('GSM1062236', getGPL = FALSE)

I found it from
https://github.com/leekgroup/recount/blob/master/tests/testthat/test-misc.R#L19

Best,
Leo


> library('GEOquery')
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> getGEO('GSM1062236', getGPL = FALSE)
File stored at:
/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//RtmpAyQR3U/GSM1062236.soft
## Force terminate after a long running time
^C
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] GEOquery_2.46.10Biobase_2.38.0  BiocGenerics_0.24.0
[4] colorout_1.1-2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14 tidyr_0.7.2  dplyr_0.7.4  assertthat_0.2.0
 [5] R6_2.2.2 magrittr_1.5 rlang_0.1.4  bindrcpp_0.2
 [9] limma_3.34.2 xml2_1.1.1   readr_1.1.1  glue_1.2.0
[13] purrr_0.2.4  hms_0.4.0compiler_3.4.2   pkgconfig_2.0.1
[17] bindr_0.1tibble_1.3.4


On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
 wrote:
>
> Thanks Sean! I was seeing timeouts also in recount related to GEOquery which 
> I just recently looked into.
>
> On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis  wrote:
>>
>>
>> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith  wrote:
>>
>> > Thanks for the speedy response Sean.  I'll switch back to the version
>> > using a file name shortly.
>> >
>>
>> No problem. Let me know if it does not work as expected.
>>
>> Sean
>>
>>
>>
>> >
>> > Cheers,
>> > Mike
>> >
>> > On 30 November 2017 at 11:20, Sean Davis  wrote:
>> >
>> >> Thanks for the report, Mike.
>> >>
>> >> The problem was (specifically) in parsing a GSEMatrix file using a
>> >> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
>> >> (devel).
>> >>
>> >> Sean
>> >>
>> >>
>> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith  wrote:
>> >>
>> >>> Hi Mike,
>> >>>
>> >>> I was experiencing similar problems with the BeadArrayUseCases vignette,
>> >>> where using getGEO() from GEOquery was getting stuck in a (seemingly)
>> >>> infinite loop processing a GSE series matrix file.  It looks like both of
>> >>> your examples try to do this too, so I suspect it's a similar issue.  I
>> >>> think the format of those files has changed recently and it seems to be
>> >>> causing a fair few issues with GEOquery.
>> >>>
>> >>> I temporarily settled a solution by getting querying GEO directly rather
>> >>> than using a local file, but it would be nice to get it back working as
>> >>> intended.
>> >>>
>> >>> Mike
>> >>>
>> >>> On 29 November 2017 at 18:56, Michael Love 
>> >>> wrote:
>> >>>
>> >>> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
>> >>> > both release and devel machines (release was fine leading up to the
>> >>> > Bioc release).
>> >>> >
>> >>> > Not sure what's the issue, I haven't changed these packages in a
>> >>> > while. I checked these out and these both build fine and in ~30s on my
>> >>> > machine (devel branch).
>> >>> >
>> >>> > Here are the reports for release:
>> >>> >
>> >>> > http://bioconductor.org/checkResults/release/data-
>> >>> >