Using Bioconductor packages on shinyapps.io

shiny
1

I've written a simple R Shiny app that I can't get deployed to shinyapps.io. The problem seems to be that my local version of two Bioconductor packages (ggtree and treeio) are more recent than what gets pulled from CRAN. I've tried downgrading my local packages, but downgrading ggtree breaks my code. I've also tried forcing shinyapps.io to use BiocManager to install the versions of treeio and ggtree I'm using, but I haven't found the right incantation to chant. I am currently including the following in my code:

library(BiocManager)
install()

I'd appreciate any pointers on how to fix this. I've got repositories set to look at Bioconductor. Here's the error message:

Error: Unhandled Exception: Child Task 575591382 failed: Error building image: Error fetching treeio (1.6.1) source. Error downloading package source. Please update your BioConductor packages to the latest version and try again: <BioconductorPackageSource repo='
Execution halted
2

What is the value of your repos option?
What is the output of rsconnect::appDependencies()?

3 
$repos
                                                   CRAN 
                            "https://cran.rstudio.com/" 
                                               BioCsoft 
           "https://bioconductor.org/packages/3.7/bioc" 
                                                BioCann 
"https://bioconductor.org/packages/3.7/data/annotation" 
                                                BioCexp 
"https://bioconductor.org/packages/3.7/data/experiment" 
                                              CRANextra 
                  "https://www.stats.ox.ac.uk/pub/RWin" 
> rsconnect::appDependencies()
         package     version       source
1             BH    1.66.0-1         CRAN
2     KernSmooth     2.23-15         CRAN
3           MASS    7.3-51.1         CRAN
4         Matrix      1.2-15         CRAN
5             R6       2.3.0         CRAN
6   RColorBrewer       1.1-2         CRAN
7           Rcpp       1.0.0         CRAN
8  RcppArmadillo 0.9.200.5.0         CRAN
9            ape         5.2         CRAN
10    assertthat       0.2.0         CRAN
11         bindr       0.1.1         CRAN
12      bindrcpp       0.2.2         CRAN
13        bitops       1.0-6         CRAN
14       caTools    1.17.1.1         CRAN
15           cli       1.0.1         CRAN
16         coala       0.5.2         CRAN
17    colorspace       1.3-2         CRAN
18       cowplot       0.9.3         CRAN
19        crayon       1.3.4         CRAN
20        digest      0.6.18         CRAN
21         dplyr       0.7.8         CRAN
22         fansi       0.4.0         CRAN
23         gdata      2.18.0         CRAN
24       ggplot2       3.1.0         CRAN
25        ggtree      1.14.4 Bioconductor
26          glue       1.3.0         CRAN
27        gplots       3.0.1         CRAN
28        gtable       0.2.0         CRAN
29        gtools       3.8.1         CRAN
30     htmltools       0.3.6         CRAN
31        httpuv     1.4.5.1         CRAN
32      jsonlite         1.6         CRAN
33      labeling         0.3         CRAN
34         later       0.7.5         CRAN
35       lattice     0.20-38         CRAN
36      lazyeval       0.2.1         CRAN
37      magrittr         1.5         CRAN
38          mgcv      1.8-26         CRAN
39          mime         0.6         CRAN
40       munsell       0.5.0         CRAN
41          nlme     3.1-137         CRAN
42        pillar       1.3.1         CRAN
43     pkgconfig       2.0.2         CRAN
44         plogr       0.2.0         CRAN
45          plyr       1.8.4         CRAN
46      promises       1.0.1         CRAN
47         purrr       0.2.5         CRAN
48          rehh       2.0.2         CRAN
49     rehh.data       1.0.0         CRAN
50      reshape2       1.4.3         CRAN
51         rlang     0.3.0.1         CRAN
52       rvcheck       0.1.3         CRAN
53        scales       1.0.0         CRAN
54          scrm     1.7.3-1         CRAN
55         shiny       1.2.0         CRAN
56   sourcetools       0.1.7         CRAN
57       stringi       1.2.4         CRAN
58       stringr       1.3.1         CRAN
59        tibble       1.4.2         CRAN
60         tidyr       0.8.2         CRAN
61    tidyselect       0.2.5         CRAN
62      tidytree       0.2.1         CRAN
63        treeio       1.6.1 Bioconductor
64          utf8       1.1.4         CRAN
65   viridisLite       0.3.0         CRAN
66         withr       2.1.2         CRAN
67        xtable       1.8-3         CRAN
>
1 Like
4

Can you try updating to BioConductor 3.8 and see if that helps?

5

I managed to fix it by explicitly setting my repository to point to 3.8. https://forum.posit.co/t/http-599-time-out-error-while-deployapp-with-package-mzr/20644/3

6

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