Error building the package

[llrs]

Error (on build of 2018-10-21 21:45:59 -0400 (Sun, 21 Oct 2018)) related to $ operator, but for building an image. It doesn't seem related to my package' code

MacOS

* creating vignettes ... ERROR
sh: line 1: 30774 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: 31077 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: 31136 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
Execution halted

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
Execution halted

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
Execution halted

[llrs]

restfulS, metagene, do have the same error messages

[llrs]

Still on erro on (2018-10-23 10:39:46 -0400 (Tue, 23 Oct 2018)).

Today restfulSE builds correctly but metagene still don't.

[llrs]

Marin Morgan reported that the error raises from the new GO.db.
Download and install it the new version (as well as GOSemSim) and then update the code ( remove the $geneSim) at the end of this line:

BioCor/vignettes/BioCor_1_basics.Rmd

Lines 271 to 272 in 8b39582

	goSemSim <- GOSemSim::geneSim("241", "251", semData = hsGO,
	measure = "Wang", combine="BMA")$geneSim

The code surrounding the vignette might need to change too.

I should take note: to use/update the GO.db to check the packages I depend when it fails!!

[llrs]

Perhaps the geneSim should be consistent and provide the same structure regardless of what is the geneSim outcome?