Shiny app error parsing manifest: unsupported package mzR

shiny shinyapps.io
1

Hello,
I am trying to deploy a shiny app to shinyapps.io and the deployment fails with the following message:

Preparing to deploy application...DONE
Uploading bundle for application: 2944544...DONE
Deploying bundle: 3703773 for application: 2944544 ...
Waiting for task: 801618928
building: Processing bundle: 3703773
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 801618933 failed: Error parsing manifest: Unsupported package found in manifest: mzR
Execution halted

I reinstalled the mzR package, but still get the same error.
Any suggestions?
Thanks in advance!

2

what version of BioConductor do you have ?

3

3.11. Reinstalled last week.

4

hmm. I don't know, possibly shinapps.io platform doesnt support it yet.
I saw that Josh was looking at something similar in March. Http 599 Time Out Error while deployApp() with package mzR

5

Hi all, I am having the same problem and i really don't know what to try else.

Preparing to deploy application...DONE
Uploading bundle for application: 3324816...DONE
Deploying bundle: 3923619 for application: 3324816 ...
Waiting for task: 832348543
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 832348547 failed: Error parsing manifest: Unsupported package found in manifest: mzR
Execution halted

rsconnect::appDependencies()
package version source
1 BH 1.72.0-3 CRAN
2 Biobase 2.50.0 Bioconductor
3 BiocGenerics 0.36.0 Bioconductor
4 BiocManager 1.30.10 CRAN
5 BiocParallel 1.24.1 Bioconductor
6 DBI 1.1.0 CRAN
7 IRanges 2.24.0 Bioconductor
8 MALDIquant 1.19.3 CRAN
9 MASS 7.3-53 CRAN
10 MSnbase 2.16.0 Bioconductor
11 Matrix 1.2-18 CRAN
12 ProtGenerics 1.22.0 Bioconductor
13 R6 2.5.0 CRAN
14 RColorBrewer 1.1-2 CRAN
15 Rcpp 1.0.5 CRAN
16 Rhdf5lib 1.12.0 Bioconductor
17 S4Vectors 0.28.0 Bioconductor
18 XML 3.99-0.5 CRAN
19 affy 1.68.0 Bioconductor
20 affyio 1.60.0 Bioconductor
21 askpass 1.1 CRAN
22 assertthat 0.2.1 CRAN
23 backports 1.2.0 CRAN
24 base64enc 0.1-3 CRAN
25 blob 1.2.1 CRAN
26 brio 1.1.0 CRAN
27 broom 0.7.2 CRAN
28 callr 3.5.1 CRAN
29 cellranger 1.1.0 CRAN
30 cli 2.2.0 CRAN
31 clipr 0.7.1 CRAN
32 codetools 0.2-18 CRAN
33 colorspace 2.0-0 CRAN
34 commonmark 1.7 CRAN
35 cpp11 0.2.4 CRAN
36 crayon 1.3.4 CRAN
37 curl 4.3 CRAN
38 dbplyr 2.0.0 CRAN
39 desc 1.2.0 CRAN
40 diffobj 0.3.2 CRAN
41 digest 0.6.27 CRAN
42 doParallel 1.0.16 CRAN
43 dplyr 1.0.2 CRAN
44 ellipsis 0.3.1 CRAN
45 evaluate 0.14 CRAN
46 fansi 0.4.1 CRAN
47 farver 2.0.3 CRAN
48 fastmap 1.0.1 CRAN
49 forcats 0.5.0 CRAN
50 foreach 1.5.1 CRAN
51 formatR 1.7 CRAN
52 fs 1.5.0 CRAN
53 futile.logger 1.4.3 CRAN
54 futile.options 1.0.1 CRAN
55 generics 0.1.0 CRAN
56 ggplot2 3.3.2 CRAN
57 glue 1.4.2 CRAN
58 gtable 0.3.0 CRAN
59 haven 2.3.1 CRAN
60 highr 0.8 CRAN
61 hms 0.5.3 CRAN
62 htmltools 0.5.0 CRAN
63 httpuv 1.5.4 CRAN
64 httr 1.4.2 CRAN
65 impute 1.64.0 Bioconductor
66 isoband 0.2.2 CRAN
67 iterators 1.0.13 CRAN
68 jsonlite 1.7.1 CRAN
69 knitr 1.30 CRAN
70 labeling 0.4.2 CRAN
71 lambda.r 1.2.4 CRAN
72 later 1.1.0.1 CRAN
73 lattice 0.20-41 CRAN
74 lifecycle 0.2.0 CRAN
75 limma 3.46.0 Bioconductor
76 lubridate 1.7.9.2 CRAN
77 magrittr 2.0.1 CRAN
78 markdown 1.1 CRAN
79 mgcv 1.8-33 CRAN
80 mime 0.9 CRAN
81 modelr 0.1.8 CRAN
82 munsell 0.5.0 CRAN
83 mzID 1.28.0 Bioconductor
84 mzR 2.24.1 Bioconductor
85 ncdf4 1.17 CRAN
86 nlme 3.1-150 CRAN
87 openssl 1.4.3 CRAN
88 openxlsx 4.2.3 CRAN
89 pcaMethods 1.82.0 Bioconductor
90 pillar 1.4.7 CRAN
91 pkgbuild 1.1.0 CRAN
92 pkgconfig 2.0.3 CRAN
93 pkgload 1.1.0 CRAN
94 plyr 1.8.6 CRAN
95 praise 1.0.0 CRAN
96 preprocessCore 1.52.0 Bioconductor
97 prettyunits 1.1.1 CRAN
98 processx 3.4.5 CRAN
99 progress 1.2.2 CRAN
100 promises 1.1.1 CRAN
101 ps 1.4.0 CRAN
102 purrr 0.3.4 CRAN
103 readr 1.4.0 CRAN
104 readxl 1.3.1 CRAN
105 rematch 1.0.1 CRAN
106 rematch2 2.1.2 CRAN
107 reprex 0.3.0 CRAN
108 rlang 0.4.9 CRAN
109 rmarkdown 2.5 CRAN
110 rprojroot 2.0.2 CRAN
111 rstudioapi 0.13 CRAN
112 rvest 0.3.6 CRAN
113 scales 1.1.1 CRAN
114 selectr 0.4-2 CRAN
115 shiny 1.5.0 CRAN
116 snow 0.4-3 CRAN
117 sourcetools 0.1.7 CRAN
118 stringi 1.5.3 CRAN
119 stringr 1.4.0 CRAN
120 sys 3.4 CRAN
121 testthat 3.0.0 CRAN
122 tibble 3.0.4 CRAN
123 tidyr 1.1.2 CRAN
124 tidyselect 1.1.0 CRAN
125 tidyverse 1.3.0 CRAN
126 tinytex 0.27 CRAN
127 utf8 1.1.4 CRAN
128 vctrs 0.3.5 CRAN
129 viridisLite 0.3.0 CRAN
130 vsn 3.58.0 Bioconductor
131 waldo 0.2.3 CRAN
132 whisker 0.4 CRAN
133 withr 2.3.0 CRAN
134 xfun 0.19 CRAN
135 xml2 1.3.2 CRAN
136 xtable 1.8-4 CRAN
137 yaml 2.2.1 CRAN
138 zip 2.1.1 CRAN
139 zlibbioc 1.36.0 Bioconductor

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS High Sierra 10.13.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/Madrid
date 2020-11-30

─ Packages ───────────────────────────────────────────────────────────────────────────────────
package * version date lib source
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.2)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
openssl 1.4.3 2020-09-18 [1] CRAN (R 4.0.2)
packrat 0.5.0 2018-11-14 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.2)
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
rlang 0.4.9 2020-11-26 [1] CRAN (R 4.0.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 4.0.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
testthat 3.0.0 2020-10-31 [1] CRAN (R 4.0.2)
usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

getOption("repos")
BioCsoft
"Bioconductor - 3.12 Software Packages"
BioCann
"Bioconductor - 3.12 AnnotationData Packages"
BioCexp
"Bioconductor - 3.12 ExperimentData Packages"
BioCworkflows
"Bioconductor - 3.12 Workflow Packages"
CRAN
"https://cran.rstudio.com/"

I've updated all the packages, but still unable to deploy. Any help/suggestion will be more than welcome!
thanks
Chiara