[Bioc-devel] Vignette building error in multiGSEA

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed Nov 4 16:53:22 CET 2020

I made sure I was using Bioc-3.13 and that my packages were valid

> BiocManager::version()
[1] '3.13'
> BiocManager::valid()
[1] TRUE

I then ran purl() and source(), eventually arriving at the error on the build system

> knitr::purl("multiGSEA.rmd")
[1] "multiGSEA.R" 
> source("multiGSEA.R", echo=TRUE, max = Inf)

> knitr::kable(
+     df %>%
+     dplyr::arrange( combined_padj) %>%
+     dplyr::filter( !is.na(metabolome_padj) ) %>%
+     dplyr::select( c( pa .... [TRUNCATED]
Error: Problem with `filter()` input `..1`.
✖ object 'metabolome_padj' not found
ℹ Input `..1` is `!is.na(metabolome_padj)`.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning messages:
1: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (79.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
2: In (function (..., deparse.level = 1)  :
  number of columns of result is not a multiple of vector length (arg 2312)

When I look at the column names of df, I see

> names(df)
 [1] "pathway"             "transcriptome_pval1" "transcriptome_pval2"
 [4] "transcriptome_padj1" "transcriptome_padj2" "proteome_pval1"
 [7] "proteome_pval2"      "proteome_padj1"      "proteome_padj2"
[10] "metabolome_pval1"    "metabolome_pval2"    "metabolome_padj1"
[13] "metabolome_padj2"    "combined_pval"       "combined_padj"

where the appended '1' and '2' suggest a merge that went in an unexpected direction?

Also like Vince I saw many hundreds of lines of ` 'select()' returned 1:many mapping between keys and columns`, which suggests to me that some code is calling `select()` or mapIds()` once for each entry, rather than once for a vector of entries. Also this

snapshotDate(): 2020-11-02
loading from cache


On 11/4/20, 8:02 AM, "Bioc-devel on behalf of Vincent Carey" <bioc-devel-bounces using r-project.org on behalf of stvjc using channing.harvard.edu> wrote:

    Here's what happened when I tried to build your package as instructed in
    the report page:

    stvjc using stvjc-XPS-13-9300:~/BIOC_SOURCES$ R_ENVIRON_USER=~/.Renviron.bioc
    Rdev CMD build multiGSEA
    1/9 packages newly attached/loaded, see sessionInfo() for details.
    * checking for file ‘multiGSEA/DESCRIPTION’ ... OK
    * preparing ‘multiGSEA’:
    * checking DESCRIPTION meta-information ... OK
    * installing the package to build vignettes
    * creating vignettes ... ERROR
    --- re-building ‘multiGSEA.rmd’ using rmarkdown
    Loading required package: AnnotationDbi
    Loading required package: stats4
    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':

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

    Loading required package: Biobase
    Welcome to Bioconductor

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

    Loading required package: IRanges
    Loading required package: S4Vectors

    Attaching package: 'S4Vectors'

    The following object is masked from 'package:base':


    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:many mapping between keys and columns
    'select()' returned 1:many mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns

    this goes on for pages.   then:

    select()' returned 1:many mapping between keys and columns
    'select()' returned 1:many mapping between keys and columns
    'select()' returned 1:many mapping between keys and columns
    Quitting from lines 259-267 (multiGSEA.rmd)
    Error: processing vignette 'multiGSEA.rmd' failed with diagnostics:
    The necessary package metabolieIDmapping is not installed.
    --- failed re-building ‘multiGSEA.rmd’

    SUMMARY: processing the following file failed:

    Error: Vignette re-building failed.
    Execution halted

    Now is "metabolieIDmapping" a spelling error?


    > library(multiGSEA)
    1/70 packages newly attached/loaded, see sessionInfo() for details.
    > sessionInfo()
    R Under development (unstable) (2020-10-29 r79387)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 20.04 LTS (fossa-melisa X20)

    Matrix products: default
    BLAS:   /home/stvjc/R-dev-dist/lib/R/lib/libRblas.so
    LAPACK: /home/stvjc/R-dev-dist/lib/R/lib/libRlapack.so

     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
     [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
     [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
     [9] LC_ADDRESS=C               LC_TELEPHONE=C

    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base

    other attached packages:
    [1] multiGSEA_1.1.0 rmarkdown_2.5

    loaded via a namespace (and not attached):
     [1] Biobase_2.51.0       httr_1.4.2           bit64_4.0.5
     [4] splines_4.1.0        tmvnsim_1.0-2        sn_1.6-2
     [7] Rdpack_2.0           stats4_4.1.0         blob_1.2.1
    [10] TFisher_0.2.0        numDeriv_2016.8-1.1  pillar_1.4.6
    [13] RSQLite_2.2.1        backports_1.1.10     lattice_0.20-41
    [16] glue_1.4.2           digest_0.6.27        rbibutils_1.3
    [19] checkmate_2.0.0      colorspace_1.4-1     sandwich_3.0-0
    [22] htmltools_0.5.0      Matrix_1.2-18        pkgconfig_2.0.3
    [25] purrr_0.3.4          mvtnorm_1.1-1        scales_1.1.1
    [28] BiocParallel_1.25.0  tibble_3.0.4         generics_0.0.2
    [31] IRanges_2.25.0       ggplot2_3.3.2        ellipsis_0.3.1
    [34] TH.data_1.0-10       BiocGenerics_0.37.0  mnormt_2.0.2
    [37] survival_3.2-7       magrittr_1.5         crayon_1.3.4
    [40] memoise_1.1.0        evaluate_0.14        MASS_7.3-53
    [43] xml2_1.3.2           graph_1.69.0         tools_4.1.0
    [46] data.table_1.13.2    gbRd_0.4-11          lifecycle_0.2.0
    [49] multcomp_1.4-14      mutoss_0.1-12        S4Vectors_0.29.0
    [52] munsell_0.5.0        plotrix_3.7-8        AnnotationDbi_1.53.0
    [55] compiler_4.1.0       rlang_0.4.8          grid_4.1.0
    [58] rappdirs_0.3.1       startup_0.15.0       multtest_2.47.0
    [61] gtable_0.3.0         codetools_0.2-16     DBI_1.1.0
    [64] R6_2.5.0             gridExtra_2.3        zoo_1.8-8
    [67] knitr_1.30           dplyr_1.0.2          graphite_1.37.0
    [70] bit_4.0.4            mathjaxr_1.0-1       fastmatch_1.1-0
    [73] fgsea_1.17.0         metap_1.4            parallel_4.1.0
    [76] Rcpp_1.0.5           vctrs_0.3.4          tidyselect_1.1.0
    [79] xfun_0.18

    On Wed, Nov 4, 2020 at 5:29 AM Sebastian Canzler <sebastian.canzler using ufz.de>

    > Dear BioC-Developers,
    > after the Release of Bioconductor 3.12 I encountered a building error of
    > the multiGSEA package in the devel branch (building the vignette causes
    > the error, see:
    > http://bioconductor.org/checkResults/devel/bioc-LATEST/multiGSEA/machv2-buildsrc.html
    > ).
    > Until now, I am not able to reproduce this error locally. Within my
    > local testing environment with R 4.1 and BioC 3.13 everything runs
    > smoothly.
    > R CMD build finishes without errors and the vignette caused no problems
    > at al.
    > Furthermore, I didn't change anything in the package or vignette and it
    > builds without error in the 3.12 version.
    > Any advice on this issue is much appreciated.
    > Thanks,
    > Sebastian
    > --
    > Dr. Sebastian Canzler
    > Young Investigators Group Bioinformatics & Transcriptomics
    > Department of Molecular Systems Biology
    > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
    > Helmholtz Centre for Environmental Research GmbH - UFZ
    > Permoserstraße 15, 04318 Leipzig, Germany
    > Phone +49 341 235 1353
    > sebastian.canzler using ufz.de
    > www.ufz.de
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