Error: Repository must be specified for Bioconductor package source
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bloosnail g
Sep 23, 2016, 6:51:58 PM9/23/16
to shinyapps.io Users
Hi all,
We are trying to upload our app using ShinyApps but there is an error, "Error: Unhandled Exception: Child Task 255007750 error: Unhandled Exception: Repository must be specified for Bioconductor package source". Out of the packages we used there is one, cellrangerRkit, that uses Bioconductor, we have tried updating it along with all versions of R and Bioconductor but there is still error. If anyone has ideas on how to fix this it would be greatly appreciated, thanks.
Daniel
Joshua Spiewak
Sep 26, 2016, 9:08:13 AM9/26/16
to shinyapps.io Users
What is the output of rsconnect::appDependencies() and devtools::session_info()?
Tiago Chedraoui Silva
Oct 19, 2016, 6:26:13 PM10/19/16
to shinyapps.io Users
Please, I have the same problem. Were you able to identify the solution?
Best regards,
Tiago
> deployApp()
Preparing to deploy application...DONE
Uploading bundle for application: 132669...DONE
Deploying bundle: 591277 for application: 132669 ...
Waiting for task: 275172923
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 275172924 error: Unhandled Exception: Repository must be specified for Bioconductor package source
In addition: Warning messages:
1: invalid uid value replaced by that for user 'nobody'
2: invalid gid value replaced by that for user 'nobody'
> rsconnect::appDependencies()
package version source
1 ALL 1.15.0 Bioconductor
2 AnnotationDbi 1.36.0 Bioconductor
3 BH 1.60.0-2 CRAN
4 Biobase 2.34.0 Bioconductor
5 BiocGenerics 0.20.0 Bioconductor
6 BiocInstaller 1.24.0 Bioconductor
7 BiocParallel 1.8.0 Bioconductor
8 Biostrings 2.42.0 Bioconductor
9 ComplexHeatmap 1.12.0 Bioconductor
10 ConsensusClusterPlus 1.38.0 Bioconductor
11 DBI 0.5-1 CRAN
12 DESeq 1.26.0 Bioconductor
13 DEoptimR 1.0-6 CRAN
14 DO.db 2.9 Bioconductor
15 DOSE 3.0.0 Bioconductor
16 EDASeq 2.8.0 Bioconductor
17 ELMER 1.4.2 Bioconductor
18 ELMER.data 1.3.2 Bioconductor
19 GEOquery 2.40.0 Bioconductor
20 GGally 1.2.0 CRAN
21 GO.db 3.4.0 Bioconductor
22 GOSemSim 2.0.0 Bioconductor
23 GenomeInfoDb 1.10.0 Bioconductor
24 GenomicAlignments 1.10.0 Bioconductor
25 GenomicFeatures 1.26.0 Bioconductor
26 GenomicRanges 1.26.0 Bioconductor
27 GetoptLong 0.1.5 CRAN
28 GlobalOptions 0.0.10 CRAN
29 Homo.sapiens 1.3.1 Bioconductor
30 IRanges 2.8.0 Bioconductor
31 IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0 Bioconductor
32 KEGGREST 1.14.0 Bioconductor
33 KEGGgraph 1.32.0 Bioconductor
34 KernSmooth 2.23-15 CRAN
35 MASS 7.3-45 CRAN
36 Matrix 1.2-7.1 CRAN
37 NMF 0.20.6 CRAN
38 OrganismDbi 1.16.0 Bioconductor
39 R.methodsS3 1.7.1 CRAN
40 R.oo 1.20.0 CRAN
41 R.utils 2.4.0 CRAN
42 R6 2.2.0 CRAN
43 RBGL 1.50.0 Bioconductor
44 RColorBrewer 1.1-2 CRAN
45 RCurl 1.95-4.8 CRAN
46 RSQLite 1.0.0 CRAN
47 Rcpp 0.12.7 CRAN
48 Rgraphviz 2.18.0 Bioconductor
49 Rsamtools 1.26.0 Bioconductor
50 S4Vectors 0.12.0 Bioconductor
51 ShortRead 1.32.0 Bioconductor
52 SummarizedExperiment 1.4.0 Bioconductor
53 TCGAbiolinks 2.3.1 github
54 TH.data 1.0-7 CRAN
55 TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Bioconductor
56 XML 3.98-1.4 CRAN
57 XVector 0.14.0 Bioconductor
58 affy 1.52.0 Bioconductor
59 affyio 1.44.0 Bioconductor
60 animation 2.4 CRAN
61 annotate 1.52.0 Bioconductor
62 ape 3.5 CRAN
63 aroma.light 3.4.0 Bioconductor
64 assertthat 0.1 CRAN
65 base64 2.0 CRAN
66 beanplot 1.2 CRAN
67 biomaRt 2.30.0 Bioconductor
68 bitops 1.0-6 CRAN
69 bumphunter 1.14.0 Bioconductor
70 caTools 1.17.1 CRAN
71 chron 2.3-47 CRAN
72 circlize 0.3.9 CRAN
73 class 7.3-14 CRAN
74 cluster 2.0.5 CRAN
75 clusterProfiler 3.2.0 Bioconductor
76 codetools 0.2-15 CRAN
77 coin 1.1-2 CRAN
78 colorspace 1.2-7 CRAN
79 colourpicker 0.2 CRAN
80 curl 2.1 CRAN
81 data.table 1.9.6 CRAN
82 dendextend 1.3.0 CRAN
83 dichromat 2.0-0 CRAN
84 digest 0.6.10 CRAN
85 diptest 0.75-7 CRAN
86 dnet 1.0.9 Bioconductor
87 doParallel 1.0.10 CRAN
88 doRNG 1.6 CRAN
89 downloader 0.4 CRAN
90 dplyr 0.5.0 CRAN
91 edgeR 3.16.0 Bioconductor
92 evaluate 0.10 CRAN
93 fastmatch 1.0-4 CRAN
94 fgsea 1.0.0 Bioconductor
95 flexmix 2.3-13 CRAN
96 foreach 1.4.3 CRAN
97 formatR 1.4 CRAN
98 fpc 2.1-10 CRAN
99 futile.logger 1.4.3 CRAN
100 futile.options 1.0.0 CRAN
101 gdata 2.17.0 CRAN
102 genefilter 1.56.0 Bioconductor
103 geneplotter 1.52.0 Bioconductor
104 ggplot2 2.1.0 CRAN
105 ggrepel 0.5 CRAN
106 ggthemes 3.2.0 CRAN
107 googleVis 0.6.1 CRAN
108 gplots 3.0.1 CRAN
109 graph 1.52.0 Bioconductor
110 gridBase 0.4-7 CRAN
111 gridExtra 2.2.1 CRAN
112 gtable 0.2.0 CRAN
113 gtools 3.5.0 CRAN
114 hexbin 1.27.1 CRAN
115 highr 0.6 CRAN
116 hms 0.2 CRAN
117 htmltools 0.3.5 CRAN
118 htmlwidgets 0.7 CRAN
119 httpuv 1.3.3 CRAN
120 httr 1.2.1 CRAN
121 hwriter 1.3.2 CRAN
122 igraph 1.0.1 CRAN
123 illuminaio 0.16.0 Bioconductor
124 irlba 2.1.2 CRAN
125 iterators 1.0.8 CRAN
126 jsonlite 1.1 CRAN
127 kernlab 0.9-25 CRAN
128 knitr 1.14 CRAN
129 labeling 0.3 CRAN
130 lambda.r 1.1.9 CRAN
131 lattice 0.20-34 CRAN
132 latticeExtra 0.6-28 CRAN
133 lazyeval 0.2.0 CRAN
134 limma 3.30.0 Bioconductor
135 locfit 1.5-9.1 CRAN
136 magrittr 1.5 CRAN
137 markdown 0.7.7 CRAN
138 matlab 1.0.2 CRAN
139 matrixStats 0.51.0 CRAN
140 mclust 5.2 CRAN
141 mime 0.5 CRAN
142 minfi 1.20.0 Bioconductor
143 miniUI 0.1.1 CRAN
144 modeltools 0.2-21 CRAN
145 multcomp 1.4-6 CRAN
146 multtest 2.30.0 Bioconductor
147 munsell 0.4.3 CRAN
148 mvtnorm 1.0-5 CRAN
149 nlme 3.1-128 CRAN
150 nnet 7.3-12 CRAN
151 nor1mix 1.2-2 CRAN
152 openssl 0.9.4 CRAN
153 org.Hs.eg.db 3.4.0 Bioconductor
154 packrat 0.4.8-1 CRAN
155 parmigene 1.0.2 CRAN
156 pathview 1.14.0 Bioconductor
157 pkgmaker 0.22 CRAN
158 plyr 1.8.4 CRAN
159 png 0.1-7 CRAN
160 prabclus 2.2-6 CRAN
161 preprocessCore 1.36.0 Bioconductor
162 quadprog 1.5-5 CRAN
163 qvalue 2.6.0 Bioconductor
164 readr 1.0.0 CRAN
165 registry 0.3 CRAN
166 reshape 0.8.5 CRAN
167 reshape2 1.4.1 CRAN
168 rjson 0.2.15 CRAN
169 rngtools 1.2.4 CRAN
170 robustbase 0.92-6 CRAN
171 rtracklayer 1.34.0 Bioconductor
172 rvest 0.3.2 CRAN
173 sandwich 2.3-4 CRAN
174 scales 0.4.0 CRAN
175 selectr 0.3-0 CRAN
176 shape 1.4.2 CRAN
177 shiny 0.14.1 CRAN
178 shinyBS 0.62 github
179 shinyFiles 0.6.2 github
180 shinyjs 0.7 github
181 siggenes 1.48.0 Bioconductor
182 snow 0.4-2 CRAN
183 sourcetools 0.1.5 CRAN
184 stringi 1.1.2 CRAN
185 stringr 1.1.0 CRAN
186 supraHex 1.12.0 Bioconductor
187 survival 2.39-5 CRAN
188 tibble 1.2 CRAN
189 tidyr 0.6.0 CRAN
190 trimcluster 0.1-2 CRAN
191 whisker 0.3-2 CRAN
192 xml2 1.0.0 CRAN
193 xtable 1.8-2 CRAN
194 yaml 2.1.13 CRAN
195 zlibbioc 1.20.0 Bioconductor
196 zoo 1.7-13 CRAN
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.1 (2016-06-21)
system x86_64, darwin13.4.0
ui RStudio (0.99.903)
language (EN)
collate en_US.UTF-8
tz US/Pacific
date 2016-10-19
Packages ---------------------------------------------------------------------------------------------------------------------------------------------------------
package * version date source
affy 1.52.0 2016-10-18 Bioconductor
affyio 1.44.0 2016-10-18 Bioconductor
annotate 1.52.0 2016-10-18 Bioconductor
AnnotationDbi 1.36.0 2016-10-18 Bioconductor
ape 3.5 2016-05-24 CRAN (R 3.3.0)
aroma.light 3.4.0 2016-10-18 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
base64 2.0 2016-05-10 CRAN (R 3.3.0)
beanplot 1.2 2014-09-19 CRAN (R 3.3.0)
Biobase 2.34.0 2016-10-18 Bioconductor
BiocGenerics 0.20.0 2016-10-18 Bioconductor
BiocInstaller 1.24.0 2016-10-18 Bioconductor
BiocParallel 1.8.0 2016-10-18 Bioconductor
biomaRt 2.30.0 2016-10-18 Bioconductor
Biostrings 2.42.0 2016-10-18 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
bumphunter 1.14.0 2016-10-18 Bioconductor
caTools 1.17.1 2014-09-10 CRAN (R 3.3.0)
chron 2.3-47 2015-06-24 CRAN (R 3.3.0)
circlize 0.3.9 2016-09-26 CRAN (R 3.3.1)
class 7.3-14 2015-08-30 CRAN (R 3.3.1)
cluster 2.0.5 2016-10-08 CRAN (R 3.3.0)
clusterProfiler 3.2.0 2016-10-18 Bioconductor
codetools 0.2-15 2016-10-05 CRAN (R 3.3.0)
coin 1.1-2 2015-11-16 CRAN (R 3.3.0)
colorspace 1.2-7 2016-10-11 CRAN (R 3.3.0)
colourpicker 0.2 2016-09-07 CRAN (R 3.3.0)
ComplexHeatmap 1.12.0 2016-10-14 Bioconductor (R 3.3.1)
ConsensusClusterPlus 1.38.0 2016-10-18 Bioconductor
data.table 1.9.6 2015-09-19 CRAN (R 3.3.0)
DBI 0.5-1 2016-09-10 CRAN (R 3.3.0)
dendextend 1.3.0 2016-08-27 CRAN (R 3.3.0)
DEoptimR 1.0-6 2016-07-06 CRAN (R 3.3.0)
DESeq 1.26.0 2016-10-18 Bioconductor
devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
digest 0.6.10 2016-08-02 CRAN (R 3.3.0)
diptest 0.75-7 2015-06-08 CRAN (R 3.3.0)
dnet 1.0.9 2016-05-31 CRAN (R 3.3.0)
DO.db 2.9 2016-09-23 Bioconductor
doParallel 1.0.10 2015-10-14 CRAN (R 3.3.0)
doRNG 1.6 2014-03-07 CRAN (R 3.3.0)
DOSE 3.0.0 2016-10-18 Bioconductor
downloader 0.4 2015-07-09 CRAN (R 3.3.0)
dplyr 0.5.0 2016-06-24 CRAN (R 3.3.0)
EDASeq 2.8.0 2016-10-18 Bioconductor
edgeR 3.16.0 2016-10-18 Bioconductor
ELMER 1.4.2 2016-05-16 Bioconductor
fastmatch 1.0-4 2012-01-21 CRAN (R 3.3.0)
fgsea 1.0.0 2016-10-18 Bioconductor
flexmix 2.3-13 2015-01-17 CRAN (R 3.3.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.0)
fpc 2.1-10 2015-08-14 CRAN (R 3.3.0)
gdata 2.17.0 2015-07-04 CRAN (R 3.3.0)
genefilter 1.56.0 2016-10-18 Bioconductor
geneplotter 1.52.0 2016-10-18 Bioconductor
GenomeInfoDb 1.10.0 2016-10-18 Bioconductor
GenomicAlignments 1.10.0 2016-10-18 Bioconductor
GenomicFeatures 1.26.0 2016-10-18 Bioconductor
GenomicRanges 1.26.0 2016-10-18 Bioconductor
GEOquery 2.40.0 2016-10-18 Bioconductor
GetoptLong 0.1.5 2016-09-26 CRAN (R 3.3.1)
GGally 1.2.0 2016-07-01 CRAN (R 3.3.0)
ggplot2 2.1.0 2016-03-01 CRAN (R 3.3.0)
ggrepel 0.5 2016-02-08 CRAN (R 3.3.0)
ggthemes 3.2.0 2016-07-11 CRAN (R 3.3.0)
GlobalOptions 0.0.10 2016-04-17 CRAN (R 3.3.0)
GO.db 3.4.0 2016-10-18 Bioconductor
googleVis 0.6.1 2016-09-01 CRAN (R 3.3.0)
GOSemSim 2.0.0 2016-10-18 Bioconductor
gplots 3.0.1 2016-03-30 CRAN (R 3.3.0)
graph 1.52.0 2016-10-18 Bioconductor
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
gtools 3.5.0 2015-05-29 CRAN (R 3.3.0)
hexbin 1.27.1 2015-08-19 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
htmlwidgets 0.7 2016-08-02 CRAN (R 3.3.0)
httpuv 1.3.3 2015-08-04 CRAN (R 3.3.0)
httr 1.2.1 2016-07-03 CRAN (R 3.3.0)
hwriter 1.3.2 2014-09-10 CRAN (R 3.3.0)
igraph 1.0.1 2015-06-26 CRAN (R 3.3.0)
illuminaio 0.16.0 2016-10-18 Bioconductor
IRanges 2.8.0 2016-10-18 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.0)
jsonlite 1.1 2016-09-14 CRAN (R 3.3.0)
KEGGgraph 1.32.0 2016-10-18 Bioconductor
KEGGREST 1.14.0 2016-10-18 Bioconductor
kernlab 0.9-25 2016-10-03 CRAN (R 3.3.0)
KernSmooth 2.23-15 2015-06-29 CRAN (R 3.3.1)
knitr 1.14 2016-08-13 CRAN (R 3.3.0)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.0)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
limma 3.30.0 2016-10-18 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
MASS 7.3-45 2016-04-21 CRAN (R 3.3.0)
matlab 1.0.2 2014-06-24 CRAN (R 3.3.0)
Matrix 1.2-7.1 2016-09-01 CRAN (R 3.3.0)
matrixStats 0.51.0 2016-10-09 CRAN (R 3.3.0)
mclust 5.2 2016-03-31 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
mime 0.5 2016-07-07 CRAN (R 3.3.0)
minfi 1.20.0 2016-10-18 Bioconductor
miniUI 0.1.1 2016-01-15 cran (@0.1.1)
modeltools 0.2-21 2013-09-02 CRAN (R 3.3.0)
multcomp 1.4-6 2016-07-14 CRAN (R 3.3.0)
multtest 2.30.0 2016-10-18 Bioconductor
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
mvtnorm 1.0-5 2016-02-02 CRAN (R 3.3.0)
nlme 3.1-128 2016-05-10 CRAN (R 3.3.1)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.1)
nor1mix 1.2-2 2016-08-25 CRAN (R 3.3.0)
openssl 0.9.4 2016-05-25 CRAN (R 3.3.0)
OrganismDbi 1.16.0 2016-10-18 Bioconductor
packrat 0.4.8-1 2016-09-07 CRAN (R 3.3.0)
parmigene 1.0.2 2012-07-23 CRAN (R 3.3.0)
pathview 1.14.0 2016-10-18 Bioconductor
pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
png 0.1-7 2013-12-03 CRAN (R 3.3.0)
prabclus 2.2-6 2015-01-14 CRAN (R 3.3.0)
preprocessCore 1.36.0 2016-10-18 Bioconductor
quadprog 1.5-5 2013-04-17 CRAN (R 3.3.0)
qvalue 2.6.0 2016-10-18 Bioconductor
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.3.0)
R.oo 1.20.0 2016-02-17 CRAN (R 3.3.0)
R.utils 2.4.0 2016-09-14 CRAN (R 3.3.0)
R6 2.2.0 2016-10-05 cran (@2.2.0)
RBGL 1.50.0 2016-10-18 Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.7 2016-09-05 CRAN (R 3.3.0)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
readr 1.0.0 2016-08-03 CRAN (R 3.3.0)
registry 0.3 2015-07-08 CRAN (R 3.3.0)
reshape 0.8.5 2014-04-23 CRAN (R 3.3.0)
reshape2 1.4.1 2014-12-06 CRAN (R 3.3.0)
Rgraphviz 2.18.0 2016-10-18 Bioconductor
rjson 0.2.15 2014-11-03 CRAN (R 3.3.0)
RJSONIO 1.3-0 2014-07-28 cran (@1.3-0)
rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0)
robustbase 0.92-6 2016-05-31 CRAN (R 3.3.0)
roxygen2 5.0.1 2015-11-11 CRAN (R 3.3.0)
Rsamtools 1.26.0 2016-10-18 Bioconductor
rsconnect * 0.5 2016-10-19 Github (rstudio/rsconnect@48420f3)
RSQLite 1.0.0 2014-10-25 CRAN (R 3.3.0)
rtracklayer 1.34.0 2016-10-18 Bioconductor
rvest 0.3.2 2016-06-17 CRAN (R 3.3.0)
S4Vectors 0.12.0 2016-10-18 Bioconductor
sandwich 2.3-4 2015-09-24 CRAN (R 3.3.0)
scales 0.4.0 2016-02-26 CRAN (R 3.3.0)
shape 1.4.2 2014-11-05 CRAN (R 3.3.0)
shiny 0.14.1 2016-10-05 cran (@0.14.1)
shinyBS 0.62 2016-09-23 Github (ebailey78/shinyBS@c329f8c)
shinydashboard * 0.5.3 2016-09-20 CRAN (R 3.3.0)
shinyFiles 0.6.2 2016-10-03 Github (zeehio/shinyFiles@a11a785)
shinyjs 0.7 2016-09-23 Github (daattali/shinyjs@009256d)
ShortRead 1.32.0 2016-10-18 Bioconductor
siggenes 1.48.0 2016-10-18 Bioconductor
stringi 1.1.2 2016-10-01 CRAN (R 3.3.0)
stringr 1.1.0 2016-08-19 CRAN (R 3.3.0)
SummarizedExperiment 1.4.0 2016-10-18 Bioconductor
supraHex 1.12.0 2016-10-18 Bioconductor
survival 2.39-5 2016-06-26 CRAN (R 3.3.0)
TCGAbiolinks 2.3.1 2016-10-18 Github (BioinformaticsFMRP/TCGAbiolinks@899820e)
TCGAbiolinksGUI * 0.99.0 <NA> Bioconductor
TH.data 1.0-7 2016-01-28 CRAN (R 3.3.0)
tibble 1.2 2016-08-26 CRAN (R 3.3.0)
tidyr 0.6.0 2016-08-12 CRAN (R 3.3.0)
trimcluster 0.1-2 2012-10-29 CRAN (R 3.3.0)
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 2016-09-22 Bioconductor
whisker 0.3-2 2013-04-28 CRAN (R 3.3.0)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
xml2 1.0.0 2016-06-24 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.14.0 2016-10-18 Bioconductor
zlibbioc 1.20.0 2016-10-18 Bioconductor
zoo 1.7-13 2016-05-03 CRAN (R 3.3.0)
Joshua Spiewak
Oct 21, 2016, 4:44:24 PM10/21/16
to shinyapps.io Users
I looked at the manifest uploaded for your application and it appears the "dnet" package is not specifying its repository. Perhaps reinstall it?
"dnet" : {
"Source" : "Bioconductor",
"Repository" : null,
"GithubRepo" : null,
"GithubUsername" : null,
"GithubRef" : null,
"GithubSha1" : null,
"description" : {
"Package" : "dnet",
"Type" : "Package",
"Title" : "Integrative Analysis of Omics Data in Terms of Network,\nEvolution and Ontology",
"Version" : "1.0.9",
"Date" : "2016-5-31",
"Author" : "Hai Fang and Julian Gough",
"Maintainer" : "Hai Fang <hf...@well.ox.ac.uk>",
"Depends" : "R (>= 3.1.0), igraph, supraHex",
"Imports" : "graph, Rgraphviz, Matrix, Biobase",
"Suggests" : "limma, survival, foreach, doMC",
"Description" : "The focus of the dnet is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.",
"URL" : "http://supfam.org/dnet, http://cran.r-project.org/package=dnet,\nhttp://dnet.r-forge.r-project.org,\nhttps://github.com/hfang-bristol/dnet",
"Collate" : "'dGSEA.r' 'dGSEAview.r' 'dGSEAwrite.r' 'visGSEA.r'\n'dPvalAggregate.r' 'dNetInduce.r' 'dBUMfit.r' 'dBUMscore.r'\n'dNetFind.r' 'dNetPipeline.r' 'dNetConfidence.r' 'visNet.r'\n'visNetMul.r' 'visNetAnimate.r' 'visNetReorder.r'\n'dNetReorder.r' 'visNetArc.r' 'visNetCircle.r' 'dRWR.r'\n'dRWRcontact.r' 'dRWRpipeline.r' 'dContrast.r' 'dCommSignif.r'\n'dSVDsignif.r' 'dFDRscore.r' 'dDAGinduce.r' 'dDAGreverse.r'\n'dDAGroot.r' 'dDAGtip.r' 'dDAGlevel.r' 'dDAGannotate.r'\n'dDAGancestor.r' 'dDAGtermSim.r' 'dDAGgeneSim.r' 'visDAG.r'\n'dEnricher.r' 'dEnricherView.r' 'visBoxplotAdv.r'\n'dRDataLoader.r' 'dCheckParallel.r' 'dFunArgs.r'",
"License" : "GPL-2",
"biocViews" : "Bioinformatics",
"NeedsCompilation" : "no",
"Packaged" : "2016-05-31 09:01:09 UTC; hfang",
"Repository" : "CRAN",
"Date/Publication" : "2016-05-31 17:43:49",
"Built" : "R 3.3.0; ; 2016-06-01 10:17:27 UTC; unix"
}
},
Tiago Chedraoui Silva
Oct 27, 2016, 2:48:36 PM10/27/16
to shinyapps.io Users
The problem is that dnet is from CRAN, why is it mapping to Bioconductor?
Tiago Chedraoui Silva
Oct 27, 2016, 2:56:46 PM10/27/16
to shinyapps.io Users
I installed the package from Github, now it worked. Thanks!
Anastassiya Zidkova
Nov 18, 2016, 5:01:52 AM11/18/16
to shinyapps.io Users
IHi,
Anastassiya
I have similar problem with matrixStats, which looked like Bioconductor package, but was in CRAN.
Removing package and reinstalling it with following command helped:
devtools::install_github("HenrikBengtsson/matri...@0.50.2")
Anastassiya
bloosnail g
Feb 1, 2017, 2:53:57 PM2/1/17
to shinyapps.io Users
I am very sorry, I do not think I was getting updates on this post and I missed your original correspondence. We are still having trouble uploading the app to the web, we would be thankful for any help.
This is the output of rsconnect::appDependencies():
This is the output of rsconnect::appDependencies():
> rsconnect::appDependencies()
package version source
1 Biobase 2.32.0 Bioconductor
2 BiocGenerics 0.18.0 Bioconductor
3 MASS 7.3-45 CRAN
4 Matrix 1.2-8 CRAN
5 R6 2.1.3 CRAN
6 RColorBrewer 1.1-2 CRAN
7 RJSONIO 1.3-0 CRAN
8 Rcpp 0.12.7 CRAN
9 Rmisc 1.5 CRAN
10 Rtsne 0.11 CRAN
11 assertthat 0.1 CRAN
12 bit 1.1-12 CRAN
13 bit64 0.9-5 CRAN
14 cellrangerRkit 1.1.0 Bioconductor
15 colorspace 1.2-6 CRAN
16 data.table 1.10.2 CRAN
17 dichromat 2.0-0 CRAN
18 digest 0.6.10 CRAN
19 ggplot2 2.2.1 CRAN
20 gtable 0.2.0 CRAN
21 htmltools 0.3.5 CRAN
22 httpuv 1.3.3 CRAN
23 irlba 2.1.2 CRAN
24 jsonlite 1.1 CRAN
25 labeling 0.3 CRAN
26 lattice 0.20-34 CRAN
27 lazyeval 0.2.0 CRAN
28 magrittr 1.5 CRAN
29 markdown 0.7.7 CRAN
30 mime 0.5 CRAN
31 munsell 0.4.3 CRAN
32 packrat 0.4.8-1 CRAN
33 pheatmap 1.0.8 CRAN
34 plyr 1.8.4 CRAN
35 reshape2 1.4.1 CRAN
36 rhdf5 2.16.0 Bioconductor
37 scales 0.4.1 CRAN
38 shiny 0.14 CRAN
39 shinysky 0.1.2 github
40 sourcetools 0.1.5 CRAN
41 stringi 1.1.1 CRAN
42 stringr 1.1.0 CRAN
43 tibble 1.2 CRAN
44 xtable 1.8-2 CRAN
45 zlibbioc 1.18.0 Bioconductor
This is the output from devtools::session_info():
> devtools::session_info()
Session info -------------------------------------------------------------------
setting value
version R version 3.3.1 (2016-06-21)
system x86_64, linux-gnu
ui X11
language en_US
collate en_US.UTF-8
tz <NA>
date 2017-02-01
Packages -----------------------------------------------------------------------
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.3.1)
Biobase * 2.32.0 2016-09-29 Bioconductor
BiocGenerics * 0.18.0 2016-09-29 Bioconductor
BiocInstaller * 1.22.3 2016-08-21 Bioconductor
bit * 1.1-12 2014-04-09 CRAN (R 3.3.1)
bit64 * 0.9-5 2015-07-05 CRAN (R 3.3.1)
bitops 1.0-6 2013-08-17 CRAN (R 3.3.1)
cellrangerRkit * 1.1.0 2017-02-01 Bioconductor
colorspace 1.2-6 2015-03-11 CRAN (R 3.3.1)
data.table 1.10.2 2017-01-31 CRAN (R 3.3.1)
devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
digest 0.6.10 2016-08-02 CRAN (R 3.3.1)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.1)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.1)
httpuv 1.3.3 2015-08-04 CRAN (R 3.3.1)
irlba 2.1.2 2016-09-21 CRAN (R 3.3.1)
jsonlite 1.1 2016-09-14 CRAN (R 3.3.1)
labeling 0.3 2014-08-23 CRAN (R 3.3.1)
lattice * 0.20-34 2016-09-06 CRAN (R 3.3.1)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.1)
markdown * 0.7.7 2015-04-22 CRAN (R 3.3.1)
Matrix * 1.2-8 2017-01-20 CRAN (R 3.3.1)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.1)
mime 0.5 2016-07-07 CRAN (R 3.3.1)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.1)
packrat 0.4.8-1 2016-09-07 CRAN (R 3.3.1)
pheatmap 1.0.8 2015-12-11 CRAN (R 3.3.1)
plyr * 1.8.4 2016-06-08 cran (@1.8.4)
R6 2.1.3 2016-08-19 CRAN (R 3.3.1)
RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.3.1)
Rcpp 0.12.7 2016-09-05 CRAN (R 3.3.1)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.1)
rhdf5 2.16.0 2017-02-01 Bioconductor
RJSONIO * 1.3-0 2014-07-28 CRAN (R 3.3.1)
Rmisc * 1.5 2013-10-22 CRAN (R 3.3.1)
rsconnect * 0.4.3 2016-05-02 CRAN (R 3.3.1)
rstudioapi 0.6 2016-06-27 CRAN (R 3.3.1)
Rtsne 0.11 2016-06-30 CRAN (R 3.3.1)
scales 0.4.1 2016-11-09 CRAN (R 3.3.1)
shiny * 0.14 2016-09-10 CRAN (R 3.3.1)
shinysky * 0.1.2 2016-08-24 Github (AnalytixWare/ShinySky@15c29be)
tibble 1.2 2016-08-26 CRAN (R 3.3.1)
withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.1)
zlibbioc 1.18.0 2016-09-29 Bioconductor
Daniel
Joshua Spiewak
Feb 2, 2017, 10:20:16 AM2/2/17
to shinyapps.io Users
The manifest in the bundle that is uploaded is missing the repository information for the cellrangerRkit package.
Searching for that package, it appears to be nominally available only as a download. We currently support installing packages from CRAN, Bioconductor, and GitHub. It appears some folks have created their own GitHub repositories with the package contents, but I could not comment about whether that is acceptable use.
Message has been deleted
bloosnail g
Feb 2, 2017, 7:11:23 PM2/2/17
to shinyapps.io Users
Thank you very much Joshua! I tried it and it is now deploying successfully. However, there now seems to be a problem where after loading the page it will say "Disconnected from the server." and the screen will go grey. The instance size in settings is at the max of 1 GB, and there is only 149 MB of data. I tried increasing the Instance Idle Timeout to 10 minutes from 5, but it still crashes -- I looked at the log and it seems to crash after exactly 8 seconds. I tried two different computers.
Would you happen to know what the problem is? Here is the link to the app: https://dah124.shinyapps.io/singleCell/
Daniel
Joshua Spiewak
Feb 3, 2017, 8:44:49 AM2/3/17
to shinyapps.io Users
149 MB of data on disk may load into memory less efficiently.
It does appear your application is running out of memory and the R process is being killed.
If you run the application locally, you can monitor the R process and see how much it consumes, and then try on shinyapps.io with a larger instance type that has at least that much memory.
bloosnail g
Feb 3, 2017, 12:23:09 PM2/3/17
to shinyapps.io Users
Ah I see, I guess we will have to refactor the code or get more space. Thank you very much though, we are very glad that we are able to have the app on the web now, the issue had been on the back of our minds for several months. You have been very helpful and thorough and it is greatly appreciated!
Daniel
Joshua Spiewak
Feb 3, 2017, 12:24:03 PM2/3/17
to shinyapps.io Users
You are most welcome.
Nadine Schrode
Aug 30, 2017, 10:07:02 AM8/30/17
to shinyapps.io Users
I have the same issue and I tried figuring out how you identified the packages that were the problem... but couldn't. It all looks the same to me.
So here is my info. Could you do your magic?
rsconnect::appDependencies()
package version source
1 AnnotationDbi 1.36.2 Bioconductor
2 AnnotationHub 2.6.5 Bioconductor
3 BH 1.62.0-1 CRAN
4 BSgenome 1.42.0 Bioconductor
5 Biobase 2.34.0 Bioconductor
6 BiocGenerics 0.20.0 Bioconductor
7 BiocInstaller 1.12.1 Bioconductor
8 BiocParallel 1.8.2 Bioconductor
9 BiocStyle 2.2.1 Bioconductor
10 Biostrings 2.42.1 Bioconductor
11 DBI 0.7 CRAN
12 DESeq2 1.14.1 Bioconductor
13 Formula 1.2-2 CRAN
14 GenomeInfoDb 1.10.3 Bioconductor
15 GenomicAlignments 1.10.1 Bioconductor
16 GenomicFeatures 1.26.4 Bioconductor
17 GenomicRanges 1.26.4 Bioconductor
18 Gviz 1.18.2 Bioconductor
19 Hmisc 4.0-3 CRAN
20 IRanges 2.8.2 Bioconductor
21 MASS 7.3-47 CRAN
22 Matrix 1.2-11 CRAN
23 PoiClaClu 1.0.2 CRAN
24 R6 2.2.2 CRAN
25 RColorBrewer 1.1-2 CRAN
26 RCurl 1.95-4.8 CRAN
27 RSQLite 2.0 CRAN
28 Rcpp 0.12.12 CRAN
29 RcppArmadillo 0.7.960.1.1 CRAN
30 Rsamtools 1.26.2 Bioconductor
31 S4Vectors 0.12.2 Bioconductor
32 SummarizedExperiment 1.4.0 Bioconductor
33 VariantAnnotation 1.20.3 Bioconductor
34 XML 3.98-1.9 CRAN
35 XVector 0.14.1 Bioconductor
36 acepack 1.4.1 CRAN
37 affy 1.52.0 Bioconductor
38 affyio 1.44.0 Bioconductor
39 airway 0.108.0 Bioconductor
40 annotate 1.52.1 Bioconductor
41 assertthat 0.2.0 CRAN
42 backports 1.1.0 CRAN
43 base64enc 0.1-3 CRAN
44 beeswarm 0.2.3 CRAN
45 bindr 0.1 CRAN
46 bindrcpp 0.2 CRAN
47 biomaRt 2.30.0 Bioconductor
48 biovizBase 1.22.0 Bioconductor
49 bit 1.1-12 CRAN
50 bit64 0.9-7 CRAN
51 bitops 1.0-6 CRAN
52 blob 1.1.0 CRAN
53 caTools 1.17.1 CRAN
54 checkmate 1.8.3 CRAN
55 cluster 2.0.6 CRAN
56 colorspace 1.3-2 CRAN
57 curl 2.8.1 CRAN
58 data.table 1.10.4 CRAN
59 dichromat 2.0-0 CRAN
60 digest 0.6.12 CRAN
61 dplyr 0.7.2 CRAN
62 ensembldb 1.6.2 Bioconductor
63 evaluate 0.10.1 CRAN
64 fission 0.108.0 Bioconductor
65 foreign 0.8-69 CRAN
66 futile.logger 1.4.3 CRAN
67 futile.options 1.0.0 CRAN
68 genefilter 1.56.0 Bioconductor
69 geneplotter 1.52.0 Bioconductor
70 ggbeeswarm 0.6.0 CRAN
71 ggplot2 2.2.1 CRAN
72 glue 1.1.1 CRAN
73 gridExtra 2.2.1 CRAN
74 gtable 0.2.0 CRAN
75 highr 0.6 CRAN
76 htmlTable 1.9 CRAN
77 htmltools 0.3.6 CRAN
78 htmlwidgets 0.9 CRAN
79 httpuv 1.3.5 CRAN
80 httr 1.3.1 CRAN
81 interactiveDisplayBase 1.12.0 Bioconductor
82 jsonlite 1.5 CRAN
83 knitr 1.17 CRAN
84 labeling 0.3 CRAN
85 lambda.r 1.1.9 CRAN
86 lattice 0.20-35 CRAN
87 latticeExtra 0.6-28 CRAN
88 lazyeval 0.2.0 CRAN
89 limma 3.30.13 Bioconductor
90 locfit 1.5-9.1 CRAN
91 magrittr 1.5 CRAN
92 markdown 0.8 CRAN
93 matrixStats 0.52.2 CRAN
94 memoise 1.1.0 CRAN
95 mgcv 1.8-18 CRAN
96 mime 0.5 CRAN
97 munsell 0.4.3 CRAN
98 nlme 3.1-131 CRAN
99 nnet 7.3-12 CRAN
100 openssl 0.9.6 CRAN
101 org.Hs.eg.db 3.4.0 Bioconductor
102 packrat 0.4.8-1 CRAN
103 pheatmap 1.0.8 CRAN
104 pkgconfig 2.0.1 CRAN
105 plogr 0.1-1 CRAN
106 plyr 1.8.4 CRAN
107 preprocessCore 1.36.0 Bioconductor
108 reshape2 1.4.2 CRAN
109 rlang 0.1.2 CRAN
110 rmarkdown 1.6 CRAN
111 rnaseqGene 0.99.128030 Bioconductor
112 rpart 4.1-11 CRAN
113 rprojroot 1.2 CRAN
114 rtracklayer 1.34.2 Bioconductor
115 scales 0.4.1 CRAN
116 shiny 1.0.4 CRAN
117 snow 0.4-2 CRAN
118 sourcetools 0.1.6 CRAN
119 stringi 1.1.5 CRAN
120 stringr 1.2.0 CRAN
121 survival 2.41-3 CRAN
122 sva 3.22.0 Bioconductor
123 tibble 1.3.4 CRAN
124 vipor 0.4.5 CRAN
125 viridis 0.4.0 CRAN
126 viridisLite 0.2.0 CRAN
127 vsn 3.30.0 Bioconductor
128 xtable 1.8-2 CRAN
129 yaml 2.1.14 CRAN
130 zlibbioc 1.20.0 Bioconductor
> devtools::session_info()
Session info ---------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.3 (2017-03-06)
system x86_64, darwin13.4.0
ui RStudio (1.0.136)
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2017-08-30
Packages -------------------------------------------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.0)
annotate 1.52.1 2017-08-21 Bioconductor
AnnotationDbi * 1.36.2 2017-08-21 Bioconductor
backports 1.1.0 2017-05-22 CRAN (R 3.3.3)
base * 3.3.3 2017-03-07 local
base64enc 0.1-3 2015-07-28 CRAN (R 3.3.3)
Biobase * 2.34.0 2017-08-21 Bioconductor
BiocGenerics * 0.20.0 2017-08-21 Bioconductor
BiocInstaller 1.12.1 2017-08-22 Bioconductor
BiocParallel 1.8.2 2017-08-21 Bioconductor
bit 1.1-12 2014-04-09 CRAN (R 3.3.3)
bit64 0.9-7 2017-05-08 CRAN (R 3.3.3)
bitops 1.0-6 2013-08-17 CRAN (R 3.3.3)
blob 1.1.0 2017-06-17 CRAN (R 3.3.3)
checkmate 1.8.3 2017-07-03 CRAN (R 3.3.3)
cluster 2.0.6 2017-03-16 CRAN (R 3.3.2)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.3)
data.table 1.10.4 2017-02-01 CRAN (R 3.3.3)
datasets * 3.3.3 2017-03-07 local
DBI 0.7 2017-06-18 CRAN (R 3.3.3)
DESeq2 * 1.14.1 2016-12-01 Bioconductor
devtools 1.13.3 2017-08-02 CRAN (R 3.3.2)
digest 0.6.12 2017-01-27 CRAN (R 3.3.3)
evaluate 0.10.1 2017-06-24 CRAN (R 3.3.3)
foreign 0.8-69 2017-06-21 CRAN (R 3.3.3)
Formula 1.2-2 2017-07-10 CRAN (R 3.3.3)
genefilter 1.56.0 2016-10-18 Bioconductor
geneplotter 1.52.0 2017-08-21 Bioconductor
GenomeInfoDb * 1.10.3 2017-08-21 Bioconductor
GenomicRanges * 1.26.4 2017-08-21 Bioconductor
ggplot2 2.2.1 2016-12-30 CRAN (R 3.3.3)
graphics * 3.3.3 2017-03-07 local
grDevices * 3.3.3 2017-03-07 local
grid 3.3.3 2017-03-07 local
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.3)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.3)
Hmisc 4.0-3 2017-05-02 CRAN (R 3.3.2)
htmlTable 1.9 2017-01-26 CRAN (R 3.3.3)
htmltools 0.3.6 2017-04-28 CRAN (R 3.3.3)
htmlwidgets 0.9 2017-07-10 CRAN (R 3.3.3)
httpuv 1.3.5 2017-07-04 CRAN (R 3.3.3)
IRanges * 2.8.2 2017-08-21 Bioconductor
jsonlite 1.5 2017-06-01 CRAN (R 3.3.3)
knitr 1.17 2017-08-10 CRAN (R 3.3.3)
lattice 0.20-35 2017-03-25 CRAN (R 3.3.3)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.3)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.3)
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.3)
magrittr 1.5 2014-11-22 CRAN (R 3.3.3)
Matrix 1.2-11 2017-08-16 CRAN (R 3.3.2)
memoise 1.1.0 2017-04-21 CRAN (R 3.3.3)
methods * 3.3.3 2017-03-07 local
mime 0.5 2016-07-07 CRAN (R 3.3.3)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.3)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.3)
org.Hs.eg.db * 3.4.0 2017-08-21 Bioconductor
packrat 0.4.8-1 2016-09-07 CRAN (R 3.3.0)
parallel * 3.3.3 2017-03-07 local
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.3.3)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.3)
R6 2.2.2 2017-06-17 CRAN (R 3.3.3)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.3)
Rcpp 0.12.12 2017-07-15 CRAN (R 3.3.3)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.3)
RJSONIO 1.3-0 2014-07-28 CRAN (R 3.3.0)
rlang 0.1.2 2017-08-09 CRAN (R 3.3.3)
rmarkdown 1.6 2017-06-15 CRAN (R 3.3.3)
rpart 4.1-11 2017-04-21 CRAN (R 3.3.3)
rprojroot 1.2 2017-01-16 CRAN (R 3.3.3)
rsconnect * 0.8.5 2017-08-23 CRAN (R 3.3.2)
RSQLite 2.0 2017-06-19 CRAN (R 3.3.3)
S4Vectors * 0.12.2 2017-08-21 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.3)
shiny * 1.0.4 2017-08-14 CRAN (R 3.3.3)
splines 3.3.3 2017-03-07 local
stats * 3.3.3 2017-03-07 local
stats4 * 3.3.3 2017-03-07 local
stringi 1.1.5 2017-04-07 CRAN (R 3.3.3)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.3)
SummarizedExperiment * 1.4.0 2017-08-21 Bioconductor
survival 2.41-3 2017-04-04 CRAN (R 3.3.3)
tibble 1.3.4 2017-08-22 CRAN (R 3.3.3)
tools 3.3.3 2017-03-07 local
utils * 3.3.3 2017-03-07 local
withr 2.0.0 2017-07-28 CRAN (R 3.3.2)
XML 3.98-1.9 2017-06-19 CRAN (R 3.3.3)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.3)
XVector 0.14.1 2017-08-21 Bioconductor
zlibbioc 1.20.0 2017-08-21 Bioconductor
Tareef Kawaf
Aug 30, 2017, 11:50:22 AM8/30/17
to Nadine Schrode, shinyapps.io Users
Hello Nadine,
When you say you are having the same issue, can you describe a little bit more of what you are seeing?
Are you seeing a grey screen? If so, have you had a chance to read over this section in the user guide?
If you are having issues debugging your application, please take a look at the logs and see what errors you see. Here is the section on troubleshooting which could be helpful.
Best,
Tareef
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Nadine Schrode
Aug 30, 2017, 11:57:54 AM8/30/17
to Tareef Kawaf, shinyapps.io Users
When I try to deploy my app, I get this:
Preparing to deploy application...DONE
Uploading bundle for application: 208647...DONE
Deploying bundle: 959554 for application: 208647 ...
Waiting for task: 483202195
building: Processing bundle: 959554
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 483202203 error: Unhandled Exception: Repository must be specified for Bioconductor package source
Execution halted
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Tareef Kawaf
Aug 30, 2017, 5:12:32 PM8/30/17
to Nadine Schrode, shinyapps.io Users
Hi Nadine,
I think you need to re-install the following packages and then try deploying again.
GenomeInfoDb
GenomicAlignments
S4Vectors
SummarizedExperiment
airway
ensembledb
fission
interactiveDisplayBase
rnaseqGene
Hope this helps
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Audrey Lemacon
Mar 14, 2018, 12:04:12 AM3/14/18
to shinyapps.io Users
Dear all,
I'm struggling with the sadly famous "Unhandled Exception: Repository must be specified for Bioconductor package source" error.
As the deployment fails I have no logs to help the debugging process.
Here is the complete error message :
Uploading bundle for application: 298940...DONE
Deploying bundle: 1267596 for application: 298940 ...
Waiting for task: 513697657
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Erreur : Unhandled Exception: Child Task 513697658 error: Unhandled Exception: Repository must be specified for Bioconductor package source
De plus : Warning message:
In data.frame(..., check.names = FALSE) :
row names were found from a short variable and have been discarded
I get the same warning message when calling appDependencies()
Here is the ordered out of appDepencies() :
package version source
43 acepack 1.4.1 CRAN
1 AnnotationDbi 1.40.0 Bioconductor
2 AnnotationFilter 1.2.0 Bioconductor
3 AnnotationHub 2.10.1 Bioconductor
44 assertthat 0.2.0 CRAN
45 backports 1.1.2 CRAN
46 base64enc 0.1-3 CRAN
4 BH 1.66.0-1 CRAN
47 bindr 0.1.1 CRAN
48 bindrcpp 0.2 CRAN
6 Biobase 2.38.0 Bioconductor
7 BiocGenerics 0.24.0 Bioconductor
8 BiocInstaller 1.28.0 Bioconductor
9 BiocParallel 1.12.0 Bioconductor
49 biomaRt 2.34.2 Bioconductor
10 Biostrings 2.46.0 Bioconductor
50 biovizBase 1.26.0 Bioconductor
51 bit 1.1-12 CRAN
52 bit64 0.9-7 CRAN
53 bitops 1.0-6 CRAN
54 blob 1.1.0 CRAN
5 BSgenome 1.46.0 Bioconductor
55 checkmate 1.8.5 CRAN
56 chopsticks 1.42.0 Bioconductor
57 class 7.3-14 CRAN
58 cli 1.0.0 CRAN
59 cluster 2.0.6 CRAN
60 colorspace 1.3-2 CRAN
61 combinat 0.0-8 CRAN
62 crayon 1.3.4 CRAN
63 crosstalk 1.0.0 CRAN
64 curl 3.1 CRAN
65 d3heatmap 0.6.1.2 CRAN
66 data.table 1.10.4-3 CRAN
11 DBI 0.8 CRAN
14 DelayedArray 0.4.1 Bioconductor
67 dendextend 1.7.0 CRAN
12 DEoptimR 1.0-8 CRAN
68 dichromat 2.0-0 CRAN
69 digest 0.6.15 CRAN
70 diptest 0.75-7 CRAN
71 dplyr 0.7.4 CRAN
13 DT 0.4 CRAN
72 ensembldb 2.2.2 Bioconductor
73 evaluate 0.10.1 CRAN
74 flexmix 2.3-14 CRAN
75 foreign 0.8-69 CRAN
15 Formula 1.2-2 CRAN
76 fpc 2.1-11 CRAN
77 futile.logger 1.4.3 CRAN
78 futile.options 1.0.0 CRAN
79 gdata 2.18.0 CRAN
80 genetics 1.3.8.1 Bioconductor
17 GenomeInfoDb 1.14.0 Bioconductor
18 GenomeInfoDbData 1.0.0 Bioconductor
19 GenomicAlignments 1.14.1 Bioconductor
20 GenomicFeatures 1.30.3 Bioconductor
21 GenomicRanges 1.30.3 Bioconductor
16 GGally 1.3.2 CRAN
81 ggbio 1.26.1 Bioconductor
82 ggplot2 2.2.1 CRAN
83 ggrepel 0.7.0 CRAN
84 glue 1.2.0 CRAN
85 graph 1.56.0 Bioconductor
86 gridExtra 2.3 CRAN
87 gtable 0.2.0 CRAN
88 gtools 3.5.0 CRAN
89 highr 0.6 CRAN
22 Hmisc 4.1-1 CRAN
90 htmlTable 1.11.2 CRAN
91 htmltools 0.3.6 CRAN
92 htmlwidgets 1.0 CRAN
93 httpuv 1.3.6.2 CRAN
94 httr 1.3.1 CRAN
95 interactiveDisplayBase 1.16.0 Bioconductor
23 IRanges 2.12.0 Bioconductor
96 jsonlite 1.5 CRAN
97 kernlab 0.9-25 CRAN
98 knitr 1.20 CRAN
99 labeling 0.3 CRAN
100 lambda.r 1.2 CRAN
101 lattice 0.20-35 CRAN
102 latticeExtra 0.6-28 CRAN
103 lazyeval 0.2.1 CRAN
24 LDheatmap 0.99-4 CRAN
104 magrittr 1.5 CRAN
105 markdown 0.8 CRAN
25 MASS 7.3-49 CRAN
26 Matrix 1.2-12 CRAN
106 matrixStats 0.53.1 CRAN
107 mclust 5.4 CRAN
108 memoise 1.1.0 CRAN
109 mime 0.5 CRAN
110 modeltools 0.2-21 CRAN
111 munsell 0.4.3 CRAN
112 mvtnorm 1.0-7 CRAN
113 nnet 7.3-12 CRAN
114 openssl 1.0.1 CRAN
115 org.Hs.eg.db 3.5.0 Bioconductor
27 OrganismDbi 1.20.0 Bioconductor
116 packrat 0.4.9-1 CRAN
117 pillar 1.2.1 CRAN
118 pkgconfig 2.0.1 CRAN
119 plogr 0.1-1 CRAN
120 plyr 1.8.4 CRAN
121 png 0.1-7 CRAN
122 prabclus 2.2-6 CRAN
123 prettyunits 1.0.2 CRAN
124 progress 1.1.2 CRAN
28 ProtGenerics 1.10.0 Bioconductor
29 R6 2.2.2 CRAN
30 RBGL 1.54.0 Bioconductor
31 RColorBrewer 1.1-2 CRAN
35 Rcpp 0.12.16 CRAN
32 RCurl 1.95-4.10 CRAN
125 reshape 0.8.7 CRAN
126 reshape2 1.4.3 CRAN
127 rlang 0.2.0 CRAN
33 RMySQL 0.10.14 CRAN
128 robustbase 0.92-8 CRAN
129 rpart 4.1-13 CRAN
36 Rsamtools 1.30.0 Bioconductor
34 RSQLite 2.0 CRAN
130 rstudioapi 0.7 CRAN
131 rtracklayer 1.38.3 Bioconductor
37 S4Vectors 0.16.0 Bioconductor
132 scales 0.5.0 CRAN
133 shiny 1.0.5 CRAN
134 shinyBS 0.61 CRAN
135 shinydashboard 0.6.1 CRAN
136 shinyjs 1.0 CRAN
137 snow 0.4-2 CRAN
138 snpStats 1.28.0 Bioconductor
139 sourcetools 0.1.6 CRAN
140 stringi 1.1.7 CRAN
141 stringr 1.3.0 CRAN
38 SummarizedExperiment 1.8.1 Bioconductor
142 survival 2.41-3 CRAN
143 tibble 1.4.2 CRAN
144 trimcluster 0.1-2 CRAN
39 TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Bioconductor
145 utf8 1.1.3 CRAN
40 VariantAnnotation 1.24.5 Bioconductor
146 viridis 0.5.0 CRAN
147 viridisLite 0.3.0 CRAN
148 whisker 0.3-2 CRAN
41 XML 3.98-1.10 CRAN
149 xtable 1.8-2 CRAN
42 XVector 0.18.0 Bioconductor
150 yaml 2.1.18 CRAN
151 zlibbioc 1.24.0 Bioconductor
Here is the output of devtools::session_info() :
Session info --------------------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.3 (2017-11-30)
system x86_64, darwin15.6.0
ui RStudio (1.2.140)
language (EN)
collate fr_CA.UTF-8
tz America/Montreal
date 2018-03-13
Packages ------------------------------------------------------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.4.0)
AnnotationDbi * 1.40.0 2017-10-31 Bioconductor
AnnotationFilter 1.2.0 2017-10-31 Bioconductor
AnnotationHub 2.10.1 2017-11-08 Bioconductor
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
backports 1.1.2 2017-12-13 CRAN (R 3.4.3)
base * 3.4.3 2017-12-07 local
base64enc 0.1-3 2015-07-28 CRAN (R 3.4.0)
bindr 0.1.1 2018-03-13 CRAN (R 3.4.3)
bindrcpp 0.2 2017-06-17 CRAN (R 3.4.0)
Biobase * 2.38.0 2017-10-31 Bioconductor
BiocGenerics * 0.24.0 2017-10-31 Bioconductor
BiocInstaller * 1.28.0 2017-10-31 Bioconductor
BiocParallel 1.12.0 2017-10-31 Bioconductor
biomaRt 2.34.2 2018-01-20 Bioconductor
Biostrings 2.46.0 2017-10-31 Bioconductor
biovizBase * 1.26.0 2017-10-31 Bioconductor
bit 1.1-12 2014-04-09 CRAN (R 3.4.0)
bit64 0.9-7 2017-05-08 CRAN (R 3.4.0)
bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
blob 1.1.0 2017-06-17 CRAN (R 3.4.0)
BSgenome 1.46.0 2017-10-31 Bioconductor
checkmate 1.8.5 2017-10-24 CRAN (R 3.4.2)
chopsticks * 1.42.0 2017-10-31 Bioconductor
cluster 2.0.6 2017-03-10 CRAN (R 3.4.3)
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
combinat * 0.0-8 2012-10-29 CRAN (R 3.4.0)
compiler 3.4.3 2017-12-07 local
crosstalk 1.0.0 2016-12-21 CRAN (R 3.4.0)
curl 3.1 2017-12-12 CRAN (R 3.4.3)
d3heatmap * 0.6.1.2 2018-02-01 CRAN (R 3.4.3)
data.table 1.10.4-3 2017-10-27 CRAN (R 3.4.2)
datasets * 3.4.3 2017-12-07 local
DBI 0.8 2018-03-02 CRAN (R 3.4.3)
DelayedArray 0.4.1 2017-11-07 Bioconductor
devtools 1.13.5 2018-02-18 CRAN (R 3.4.3)
dichromat 2.0-0 2013-01-24 CRAN (R 3.4.0)
digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
dplyr * 0.7.4 2017-09-28 CRAN (R 3.4.2)
DT * 0.4 2018-01-30 CRAN (R 3.4.3)
ensembldb 2.2.2 2018-02-15 Bioconductor
foreign 0.8-69 2017-06-22 CRAN (R 3.4.3)
Formula 1.2-2 2017-07-10 CRAN (R 3.4.1)
gdata * 2.18.0 2017-06-06 CRAN (R 3.4.0)
genetics * 1.3.8.1 2013-09-03 CRAN (R 3.4.0)
GenomeInfoDb * 1.14.0 2017-10-31 Bioconductor
GenomeInfoDbData 1.0.0 2018-03-13 Bioconductor
GenomicAlignments 1.14.1 2017-11-18 Bioconductor
GenomicFeatures * 1.30.3 2018-02-02 Bioconductor
GenomicRanges * 1.30.3 2018-02-26 Bioconductor
GGally 1.3.2 2017-08-02 CRAN (R 3.4.1)
ggbio * 1.26.1 2018-03-09 Bioconductor
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.0)
ggrepel * 0.7.0 2017-09-29 CRAN (R 3.4.2)
glue 1.2.0 2017-10-29 CRAN (R 3.4.2)
graph 1.56.0 2017-10-31 Bioconductor
graphics * 3.4.3 2017-12-07 local
grDevices * 3.4.3 2017-12-07 local
grid 3.4.3 2017-12-07 local
gridExtra 2.3 2017-09-09 CRAN (R 3.4.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
gtools * 3.5.0 2015-05-29 CRAN (R 3.4.0)
Hmisc 4.1-1 2018-01-03 CRAN (R 3.4.3)
htmlTable 1.11.2 2018-01-20 CRAN (R 3.4.3)
htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0)
htmlwidgets * 1.0 2018-01-20 CRAN (R 3.4.3)
httpuv 1.3.6.2 2018-03-02 CRAN (R 3.4.3)
httr * 1.3.1 2017-08-20 CRAN (R 3.4.1)
interactiveDisplayBase 1.16.0 2017-10-31 Bioconductor
IRanges * 2.12.0 2017-10-31 Bioconductor
jsonlite * 1.5 2017-06-01 CRAN (R 3.4.0)
knitr 1.20 2018-02-20 CRAN (R 3.4.3)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.4.0)
lazyeval * 0.2.1 2017-10-29 CRAN (R 3.4.2)
LDheatmap * 0.99-4 2018-03-12 CRAN (R 3.4.3)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
MASS * 7.3-49 2018-02-23 CRAN (R 3.4.3)
Matrix 1.2-12 2017-11-20 CRAN (R 3.4.3)
matrixStats 0.53.1 2018-02-11 CRAN (R 3.4.3)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.3 2017-12-07 local
mime 0.5 2016-07-07 CRAN (R 3.4.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
mvtnorm * 1.0-7 2018-01-25 CRAN (R 3.4.3)
nnet 7.3-12 2016-02-02 CRAN (R 3.4.3)
org.Hs.eg.db * 3.5.0 2018-03-13 Bioconductor
OrganismDbi 1.20.0 2017-10-31 Bioconductor
packrat 0.4.9-1 2018-03-12 CRAN (R 3.4.3)
parallel * 3.4.3 2017-12-07 local
pillar 1.2.1 2018-02-27 CRAN (R 3.4.3)
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
plyr * 1.8.4 2016-06-08 CRAN (R 3.4.0)
png 0.1-7 2013-12-03 CRAN (R 3.4.0)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.0)
progress 1.1.2 2016-12-14 CRAN (R 3.4.0)
ProtGenerics 1.10.0 2017-10-31 Bioconductor
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
RBGL 1.54.0 2017-10-31 Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.0)
Rcpp 0.12.16 2018-03-13 CRAN (R 3.4.3)
RCurl 1.95-4.10 2018-01-04 CRAN (R 3.4.3)
reshape 0.8.7 2017-08-06 CRAN (R 3.4.1)
reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)
rlang 0.2.0 2018-02-20 CRAN (R 3.4.3)
RMySQL 0.10.14 2018-02-26 CRAN (R 3.4.3)
rpart 4.1-13 2018-02-23 CRAN (R 3.4.3)
Rsamtools 1.30.0 2017-10-31 Bioconductor
rsconnect 0.8.8 2018-03-09 CRAN (R 3.4.4)
RSQLite * 2.0 2017-06-19 CRAN (R 3.4.1)
rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)
rtracklayer * 1.38.3 2018-01-23 Bioconductor
S4Vectors * 0.16.0 2017-10-31 Bioconductor
scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
shiny * 1.0.5 2017-08-23 CRAN (R 3.4.1)
shinyBS * 0.61 2015-03-31 CRAN (R 3.4.0)
shinydashboard * 0.6.1 2017-06-14 CRAN (R 3.4.0)
shinyjs * 1.0 2018-01-08 CRAN (R 3.4.3)
splines 3.4.3 2017-12-07 local
stats * 3.4.3 2017-12-07 local
stats4 * 3.4.3 2017-12-07 local
stringi 1.1.7 2018-03-12 CRAN (R 3.4.3)
stringr 1.3.0 2018-02-19 CRAN (R 3.4.3)
SummarizedExperiment 1.8.1 2017-12-19 Bioconductor
survival * 2.41-3 2017-04-04 CRAN (R 3.4.3)
tibble 1.4.2 2018-01-22 CRAN (R 3.4.3)
tools 3.4.3 2017-12-07 local
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2018-03-13 Bioconductor
utils * 3.4.3 2017-12-07 local
VariantAnnotation 1.24.5 2018-01-06 Bioconductor
withr 2.1.1 2017-12-19 CRAN (R 3.4.3)
XML 3.98-1.10 2018-02-19 CRAN (R 3.4.3)
xtable 1.8-2 2016-02-05 CRAN (R 3.4.0)
XVector 0.18.0 2017-10-31 Bioconductor
yaml * 2.1.18 2018-03-08 CRAN (R 3.4.4)
zlibbioc 1.24.0 2017-10-31 Bioconductor
Any help would be most appreciated.
Thank you very much
Audrey
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Andy Kipp
Mar 14, 2018, 11:13:31 AM3/14/18
to Audrey Lemacon, shinyapps.io Users
You seem to have many Bioconductor packages, but no Bioconductor repository configured.
What does your repository configuration look like?To unsubscribe from this group and stop receiving emails from it, send an email to shinyapps-users+unsubscribe@googlegroups.com.
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Audrey Lemacon
Mar 14, 2018, 2:49:25 PM3/14/18
to shinyapps.io Users
Hi Andy,
And I have re-run rsconnect::deployApp()
Thank you for your help,
Here is my repository configuration :
....
I have tried to update repos with the following command :
I have tried to update repos with the following command :
options(repos = BiocInstaller::biocinstallRepos())
getOption("repos")
BioCsoft BioCann BioCexp
"https://bioconductor.org/packages/3.6/bioc" "https://bioconductor.org/packages/3.6/data/annotation" "https://bioconductor.org/packages/3.6/data/experiment"
CRAN
And I have re-run rsconnect::deployApp()
DONE
Uploading bundle for application: 298940...DONE
Deploying bundle: 1268718 for application: 298940 ...
Waiting for task: 513805210
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Erreur : Unhandled Exception: Child Task 513805211 error: Unhandled Exception: Repository must be specified for Bioconductor package source
....Thanks again
Audrey
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