[Bioc-devel] Error building the vignette

[Lluís Revilla]

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

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