Here's what happened when I tried to build your package as instructed in the report page:
stvjc@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': expand.grid '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: ‘multiGSEA.rmd’ Error: Vignette re-building failed. Execution halted Now is "metabolieIDmapping" a spelling error? sessionInfo: > 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 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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.canz...@ufz.de> wrote: > 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.canz...@ufz.de > www.ufz.de > > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzende des Aufsichtsrats/Chairwoman of the Supervisory Board: > MinDirig'in Oda Keppler > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Georg Teutsch > Administrative Geschäftsführerin/Administrative Managing Director: > Dr. Sabine König > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel