Are you using the correct version of R and up-to-date Bioconductor 'devel' packages? I installed your package from git.bioconductor.org then started R, tangled the vignette, and sourced the result
> setwd("BioCor/vignettes") > knitr::purl("BioCor_1_basics.Rmd") > source("BioCor_1_basics.R", max=Inf, echo=TRUE) And eventually came to > goSemSim <- GOSemSim::geneSim("241", "251", semData = hsGO, + measure = "Wang", combine="BMA")$geneSim Error in GOSemSim::geneSim("241", "251", semData = hsGO, measure = "Wang", (from BioCor_1_basics.R#130) : $ operator is invalid for atomic vectors In addition: Warning message: In mgeneSim(genes, genesReact) : Some genes are not in the list provided. Looking just a little more I see > GOSemSim::geneSim("241", "251", semData = hsGO, > measure = "Wang", combine="BMA") [1] NA I didn't look further; it could have to do with recently updated GO.db? > sessionInfo() R version 3.5.1 Patched (2018-10-05 r75405) Platform: x86_64-apple-darwin17.7.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /Users/ma38727/bin/R-3-5-branch/lib/libRblas.dylib LAPACK: /Users/ma38727/bin/R-3-5-branch/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 stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GOSemSim_2.7.1 reactome.db_1.64.0 org.Hs.eg.db_3.7.0 [4] AnnotationDbi_1.43.1 IRanges_2.15.18 S4Vectors_0.19.23 [7] Biobase_2.41.2 BiocGenerics_0.27.1 BioCor_1.5.5 [10] BiocStyle_2.9.6 BiocManager_1.30.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.19 compiler_3.5.1 bitops_1.0-6 [4] tools_3.5.1 digest_0.6.18 bit_1.1-14 [7] lattice_0.20-35 annotate_1.59.1 evaluate_0.12 [10] RSQLite_2.1.1 memoise_1.1.0 pkgconfig_2.0.2 [13] Matrix_1.2-14 graph_1.59.2 DBI_1.0.0 [16] yaml_2.2.0 stringr_1.3.1 knitr_1.20 [19] rprojroot_1.3-2 bit64_0.9-7 grid_3.5.1 [22] GSEABase_1.43.1 XML_3.98-1.16 BiocParallel_1.15.15 [25] rmarkdown_1.10 GO.db_3.7.0 blob_1.1.1 [28] magrittr_1.5 backports_1.1.2 htmltools_0.3.6 [31] xtable_1.8-3 stringi_1.2.4 RCurl_1.95-4.11 On 10/25/18, 4:24 AM, "Bioc-devel on behalf of Lluís Revilla" <bioc-devel-boun...@r-project.org on behalf of lluis.revi...@gmail.com> wrote: Dear Bioconductor team and list, I found that my package on devel (BioCor) fails to build on all the OS. The error message is related to creating figures of the vignette (see below). I haven't touched the vignettes in a while. and building the package on my machine passes all the checks. In addition, I found the same type of error happens to other packages (metagene, and yesterday to restfulSE). I don't know where to look at to solve this problem. Do you have any recommendation? Many thanks, Lluís PS: Errors on the devel branch: Linux: * creating vignettes ... ERROR Quitting from lines 271-282 (BioCor_1_basics.Rmd) Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors Windows: * creating vignettes ... ERROR Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BioCor_1_basics_files/figure-html/hclust1-1.png" -trim "BioCor_1_basics_files/figure-html/hclust1-1.png"' execution failed with error code 4 Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BioCor_1_basics_files/figure-html/hclust3-1.png" -trim "BioCor_1_basics_files/figure-html/hclust3-1.png"' execution failed with error code 4 Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BioCor_1_basics_files/figure-html/hclust3b-1.png" -trim "BioCor_1_basics_files/figure-html/hclust3b-1.png"' execution failed with error code 4 Quitting from lines 271-282 (BioCor_1_basics.Rmd) Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors MacOS * creating vignettes ... ERROR sh: line 1: 8065 Abort trap: 6 'convert' 'BioCor_1_basics_files/figure-html/hclust1-1.png' -trim 'BioCor_1_basics_files/figure-html/hclust1-1.png' > /dev/null sh: line 1: 8098 Abort trap: 6 'convert' 'BioCor_1_basics_files/figure-html/hclust3-1.png' -trim 'BioCor_1_basics_files/figure-html/hclust3-1.png' > /dev/null sh: line 1: 8163 Abort trap: 6 'convert' 'BioCor_1_basics_files/figure-html/hclust3b-1.png' -trim 'BioCor_1_basics_files/figure-html/hclust3b-1.png' > /dev/null Quitting from lines 271-282 (BioCor_1_basics.Rmd) Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel