argument to 'which' is not logical

[dejmail]

Hi all

I have been trying to export graphs generated using shiny-phyloseq, which is a great little program by the way. However no matter which graph I generate, I am getting a Error: argument to 'which' is not logical. I can't seem to find anything on the net that indicates other people have or are having the same problem.

Does this seem like an issue with the source data or with the shiny-phyloseq application ?

Thanks

[spholmes]

This is an issue with the newer version of shiny-phyloseq and not with the original phyloseq commands.

It is a recent issue and we'll try and track it down.

Susan

On Wed, Apr 20, 2016 at 8:26 AM, Liam_Thompson notifications@github.com wrote:

Hi all

I have been trying to export graphs generated using shiny-phyloseq, which is a great little program by the way. However no matter which graph I generate, I am getting a Error: argument to 'which' is not logical. I can't seem to find anything on the net that indicates other people have or are having the same problem.

Does this seem like an issue with the source data or with the shiny-phyloseq application ?

Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/64

Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[dejmail]

Hi Susan. Thanks for the reply. I tried just the normal Bioconductor (phyloseq) and shiny-phyloseq versions but it doesn't change, perhaps that is what you meant.

The output from an attempt is the following, I don't if its helpful, perhaps it is not verbose enough.

---

Error in which(sapply(eventlog[ctxlogs], function(x) { : 
  argument to 'which' is not logical
Warning: Error in which: argument to 'which' is not logical
Stack trace (innermost first):
    77: which
    76: reactive event_code [panels/panel-server-provenance.R#116]
    65: event_code
    64: writeLines
    63: reactive write_temp_record_files [panels/panel-server-provenance.R#165]
    52: write_temp_record_files
    51: download$func [panels/panel-server-provenance.R#182]
     3: runApp
     2: runUrl
     1: shiny::runGitHub

[joey711]

This should be resolved with the latest version (which requires latest version of R, phyloseq, etc.). Follow the normal instructions for shiny-phyloseq and it should tell you or attempt install. Updating R you'll have to do yourself.

Meanwhile, I will close for now. Please re-post if you're still having a problem.

[arnonl]

Hi there,

I encountered a similar problem to the one dejmail reported. While trying to save code thorough the Provenance tab, I get the following error: "argument to 'which' is not logical". No code is presented at the right side of the screen.

Here is my sessionInfo() > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.9.5 (Mavericks)

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 grid stats graphics grDevices utils datasets methods base

other attached packages: [1] doParallel_1.0.10 iterators_1.0.8 foreach_1.4.3 scales_0.4.0 RColorBrewer_1.1-2
[6] png_0.1-7 rmarkdown_1.0 markdown_0.7.7 gridExtra_2.2.1 genefilter_1.54.2
[11] networkD3_0.2.13 data.table_1.9.6 ggplot2_2.1.0 shinythemes_1.0.1 biomformat_1.0.2
[16] BiocInstaller_1.22.3 shiny_0.13.2 phyloseq_1.16.2

loaded via a namespace (and not attached): [1] Biobase_2.32.0 jsonlite_1.0 splines_3.3.1 Formula_1.2-1
[5] stats4_3.3.1 latticeExtra_0.6-28 yaml_2.1.13 RSQLite_1.0.0
[9] lattice_0.20-33 chron_2.3-47 digest_0.6.10 GenomicRanges_1.24.2
[13] XVector_0.12.1 colorspace_1.2-6 htmltools_0.3.5 httpuv_1.3.3
[17] Matrix_1.2-6 plyr_1.8.4 DESeq2_1.12.4 XML_3.98-1.4
[21] zlibbioc_1.18.0 xtable_1.8-2 BiocParallel_1.6.6 annotate_1.50.0
[25] mgcv_1.8-14 IRanges_2.6.1 SummarizedExperiment_1.2.3 nnet_7.3-12
[29] BiocGenerics_0.18.0 survival_2.39-5 magrittr_1.5 mime_0.5
[33] evaluate_0.9 nlme_3.1-128 MASS_7.3-45 foreign_0.8-66
[37] vegan_2.4-0 tools_3.3.1 stringr_1.1.0 S4Vectors_0.10.3
[41] locfit_1.5-9.1 munsell_0.4.3 cluster_2.0.4 AnnotationDbi_1.34.4
[45] Biostrings_2.40.2 ade4_1.7-4 GenomeInfoDb_1.8.3 rhdf5_2.16.0
[49] htmlwidgets_0.7 igraph_1.0.1 labeling_0.3 gtable_0.2.0
[53] codetools_0.2-14 multtest_2.28.0 DBI_0.5 reshape2_1.4.1
[57] R6_2.1.3 Hmisc_3.17-4 permute_0.9-0 ape_3.5
[61] stringi_1.1.1 Rcpp_0.12.6 geneplotter_1.50.0 rpart_4.1-10
[65] acepack_1.3-3.3

Thank you for your help, Arnon