Entering edit mode
21 months ago
Ondina
▴
100
Hello everyone,
I want to use GEO Query but I'm getting an error and I'm stuck. This is the code:
gse <- getGEO("GSE21653", GSEMatrix = T)
And instead of loading the data, I get this instead:
Found 1 file(s)
GSE21653_series_matrix.txt.gz
Using locally cached version: C:\Users\AppData\Local\Temp\RtmpYRotrS/GSE21653_series_matrix.txt.gz
Error in app$vspace(new_style$`margin-top` %||% 0) :
attempt to apply non-function
Does anyone knows what is going on and how to fix this?
Here's my session info:
- Session info ---------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 4.1.0 (2021-05-18)
os Windows 10 x64 (build 19043)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz Europe/Paris
date 2022-07-11
rstudio 1.4.1717 Juliet Rose (desktop)
pandoc 2.11.4 @ C:/Program Files/RStudio/bin/pandoc/ (via rmarkdown)
- Packages -------------------------------------------------------------------------------------------------------------------------------------------------
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.1)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2)
Biobase * 2.54.0 2021-10-26 [1] Bioconductor
BiocGenerics * 0.40.0 2021-10-26 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.1)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.1)
broom 1.0.0 2022-07-01 [1] CRAN (R 4.1.3)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.1)
cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.3)
colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.1)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.1)
crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.3)
curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.1)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.3)
dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.1.3)
devtools * 2.4.3 2021-11-30 [1] CRAN (R 4.1.2)
digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.1)
dplyr * 1.0.9 2022-04-28 [1] CRAN (R 4.1.3)
DT 0.23 2022-05-10 [1] CRAN (R 4.1.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.1)
evaluate 0.15 2022-02-18 [1] CRAN (R 4.1.2)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.1)
forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.1.1)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.0)
GEOquery * 2.60.0 2021-05-20 [1] Bioconductor
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.1.0)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.1)
haven 2.5.0 2022-04-15 [1] CRAN (R 4.1.3)
hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.1)
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.1)
httr 1.4.3 2022-05-04 [1] CRAN (R 4.1.0)
jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.1.3)
knitr 1.39 2022-04-26 [1] CRAN (R 4.1.3)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1)
limma 3.48.3 2021-08-10 [1] Bioconductor
lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.1.1)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.2)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.1.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.1)
patchwork 1.1.1 2020-12-17 [1] CRAN (R 4.1.1)
pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.0)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.1)
pkgload 1.3.0 2022-06-27 [1] CRAN (R 4.1.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.1)
processx 3.6.1 2022-06-17 [1] CRAN (R 4.1.3)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.1.3)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.1.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
readr * 2.1.2 2022-01-30 [1] CRAN (R 4.1.2)
readxl 1.4.0 2022-03-28 [1] CRAN (R 4.1.3)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.3)
reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.1)
rlang 1.0.3 2022-06-27 [1] CRAN (R 4.1.3)
rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.3)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
rvest 1.0.2 2021-10-16 [1] CRAN (R 4.1.1)
scales 1.2.0 2022-04-13 [1] CRAN (R 4.1.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2)
stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
tibble * 3.1.5 2021-09-30 [1] CRAN (R 4.1.1)
tidyr * 1.2.0 2022-02-01 [1] CRAN (R 4.1.2)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.1.1)
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.1.3)
usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.1.3)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.3)
vroom 1.5.7 2021-11-30 [1] CRAN (R 4.1.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
xfun 0.29 2021-12-14 [1] CRAN (R 4.1.2)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.2)
yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.3)`
Yeah, actually it is an error with the cli package, with the latest version (3.3.0), when I remove cli, I can import tables and GEOQuery works fine too ... But I need cli for other steps of the analysis, I'm searching for another solution, maybe downgrading the cli version to an older one ...