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Error when trying to connect to RegulonDB #33
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Hi @rioualen, Thanks for the report! I see that the Dropbox link to the data had changed. This is now fixed on version 1.2.1 and 1.3.1 which correspond to Bioconductor 3.12 (release) and 3.13 (devel). It'll take about 2 days for the updated @jemilianosf @CarBarJon @josschavezf we should also finalize the data submission to Best, |
Thanks @lcolladotor! I've reinstalled regutools but I'm still having an issue, is there something more I need to do? I'm running on Bioconductor 3.12, should I switch to 3.13?
|
Hi Claire, I think that you need to use a fresh R session. Maybe you had already loaded Best, > library("regutools")
> library("sessioninfo")
> if (!exists("regulondb_conn")) regulondb_conn <- connect_database()
snapshotDate(): 2020-10-27
> options(width = 120)
> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.3 (2020-10-10)
os macOS Catalina 10.15.7
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-11-25
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
AnnotationDbi 1.52.0 2020-10-27 [1] Bioconductor
AnnotationFilter 1.14.0 2020-10-27 [1] Bioconductor
AnnotationHub 2.22.0 2020-10-27 [1] Bioconductor
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)
backports 1.2.0 2020-11-02 [1] CRAN (R 4.0.3)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.2)
Biobase 2.50.0 2020-10-27 [1] Bioconductor
BiocFileCache 1.14.0 2020-10-27 [1] Bioconductor
BiocGenerics 0.36.0 2020-10-27 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.2)
BiocParallel 1.24.1 2020-11-06 [1] Bioconductor
BiocVersion 3.12.0 2020-05-14 [1] Bioconductor
biomaRt 2.46.0 2020-10-27 [1] Bioconductor
Biostrings 2.58.0 2020-10-27 [1] Bioconductor
biovizBase 1.38.0 2020-10-27 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.2)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.2)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2)
BSgenome 1.58.0 2020-10-27 [1] Bioconductor
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)
cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.3)
colorout 1.2-2 2020-11-03 [1] Github (jalvesaq/colorout@726d681)
colorspace 2.0-0 2020-11-11 [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 4.0.1)
data.table 1.13.2 2020-10-19 [1] CRAN (R 4.0.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2)
dbplyr 2.0.0 2020-11-03 [1] CRAN (R 4.0.3)
DelayedArray 0.16.0 2020-10-27 [1] Bioconductor
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)
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
ensembldb 2.14.0 2020-10-27 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2)
foreign 0.8-80 2020-05-24 [1] CRAN (R 4.0.3)
Formula 1.2-4 2020-10-16 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.2)
GenomeInfoDb 1.26.1 2020-11-18 [1] Bioconductor
GenomeInfoDbData 1.2.4 2020-11-03 [1] Bioconductor
GenomicAlignments 1.26.0 2020-10-27 [1] Bioconductor
GenomicFeatures 1.42.1 2020-11-11 [1] Bioconductor
GenomicRanges 1.42.0 2020-10-27 [1] Bioconductor
ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
graph 1.68.0 2020-10-27 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
Gviz 1.34.0 2020-10-27 [1] Bioconductor
Hmisc 4.4-1 2020-08-10 [1] CRAN (R 4.0.2)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2)
htmlTable 2.1.0 2020-09-16 [1] CRAN (R 4.0.2)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
htmlwidgets 1.5.2 2020-10-03 [1] CRAN (R 4.0.2)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
igraph 1.2.6 2020-10-06 [1] CRAN (R 4.0.2)
interactiveDisplayBase 1.28.0 2020-10-27 [1] Bioconductor
IRanges 2.24.0 2020-10-27 [1] Bioconductor
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.2)
knitr 1.30 2020-09-22 [1] CRAN (R 4.0.2)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.3)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
lubridate 1.7.9.2 2020-11-13 [1] CRAN (R 4.0.2)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.3)
MatrixGenerics 1.2.0 2020-10-27 [1] Bioconductor
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
nnet 7.3-14 2020-04-26 [1] CRAN (R 4.0.3)
openssl 1.4.3 2020-09-18 [1] CRAN (R 4.0.2)
pillar 1.4.7 2020-11-20 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.2)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
ProtGenerics 1.22.0 2020-10-27 [1] Bioconductor
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.0.2)
R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.0.2)
R.utils 2.10.1 2020-08-26 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.2)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.2)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.2)
RCy3 2.10.2 2020-11-19 [1] Bioconductor
regutools * 1.3.1 2020-11-25 [1] Github (ComunidadBioinfo/regutools@5330c34)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
RJSONIO 1.3-1.4 2020-01-15 [1] CRAN (R 4.0.2)
rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.2)
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.3)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
Rsamtools 2.6.0 2020-10-27 [1] Bioconductor
RSQLite 2.2.1 2020-09-30 [1] CRAN (R 4.0.2)
rsthemes 0.1.0 2020-11-03 [1] Github (gadenbuie/rsthemes@6391fe5)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
rtracklayer 1.50.0 2020-10-27 [1] Bioconductor
S4Vectors 0.28.0 2020-10-27 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
SummarizedExperiment 1.20.0 2020-10-27 [1] Bioconductor
suncalc 0.5.0 2019-04-03 [1] CRAN (R 4.0.2)
survival 3.2-7 2020-09-28 [1] CRAN (R 4.0.3)
testthat * 3.0.0 2020-10-31 [1] CRAN (R 4.0.2)
tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
usethis * 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
VariantAnnotation 1.36.0 2020-10-28 [1] Bioconductor
vctrs 0.3.5 2020-11-17 [1] CRAN (R 4.0.2)
withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
xfun 0.19 2020-10-30 [1] CRAN (R 4.0.2)
XML 3.99-0.5 2020-07-23 [1] CRAN (R 4.0.2)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2)
XVector 0.30.0 2020-10-28 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
zlibbioc 1.36.0 2020-10-28 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library |
Hi @rioualen , I think was my fault, sorry. I have been re-organizing my Dropbox and accidentally moved the file to a new location, but is back to its place. I think it should work now. Please let me know if it's working. |
It's working just fine now, thank you guys for answering so fast! |
Hola!
I'm trying out Regutools for the first time and I stumbled upon an error when trying to connect to RegulonDB, using the code provided in the Regutools main page. I tried both the released version and the dev one. Here's what I get, any idea about what's going on?
The text was updated successfully, but these errors were encountered: