[Bioc-devel] Error building the vignette

[Martin Morgan]

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-bounces using r-project.org on behalf of lluis.revilla using 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]]
    
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