[Bioc-devel] Vignette building error in multiGSEA

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Wed Nov 4 14:01:33 CET 2020

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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> Prof. Dr. Georg Teutsch
> Administrative Geschäftsführerin/Administrative Managing Director:
> Dr. Sabine König
> _______________________________________________
> Bioc-devel using r-project.org mailing list
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