Error in BiocFileCache::bfcrpath(bfc, url)
SiyuanHuang1 opened this issue · 3 comments
SiyuanHuang1 commented
hello!
when I followed your vignette for getting Human DLPFC Visium dataset (https://bioconductor.org/packages/release/data/experiment/vignettes/spatialLIBD/inst/doc/spatialLIBD.html#downloading-the-data-with-spatiallibd), an error happened:
library(spatialLIBD)
ehub <- ExperimentHub::ExperimentHub()
sce <- fetch_data(type = "sce_example", eh = ehub)error messages like this:
adding rname 'https://www.dropbox.com/s/5ra9o8ku9iyyf70/sce_sub_for_vignette.Rdata?dl=1'
Error in BiocFileCache::bfcrpath(bfc, url) :
not all 'rnames' found or unique.
此外: Warning messages:
1: download failed
web resource path: ‘https://www.dropbox.com/s/5ra9o8ku9iyyf70/sce_sub_for_vignette.Rdata?dl=1’
local file path: ‘C:\Users\15927\AppData\Local/R/cache/R/BiocFileCache/1454412214226_sce_sub_for_vignette.Rdata%3Fdl%3D1’
reason: Failed to connect to www.dropbox.com port 443: Timed out
2: bfcadd() failed; resource removed
rid: BFC13
fpath: ‘https://www.dropbox.com/s/5ra9o8ku9iyyf70/sce_sub_for_vignette.Rdata?dl=1’
reason: download failed
3: In value[[3L]](cond) :
trying to add rname 'https://www.dropbox.com/s/5ra9o8ku9iyyf70/sce_sub_for_vignette.Rdata?dl=1' produced error:
bfcadd() failed; see warnings()Any suggestions?
Thank u so much!!!
this is my R session information
> options(width = 120)
> sessioninfo::session_info()
- Session info -------------------------------------------------------------------------------------------------------
setting value
version R version 4.1.2 (2021-11-01)
os Windows 10 x64 (build 19042)
system x86_64, mingw32
ui RStudio
language (EN)
collate Chinese (Simplified)_China.936
ctype Chinese (Simplified)_China.936
tz Asia/Taipei
date 2022-03-04
rstudio 1.3.1073 Giant Goldenrod (desktop)
pandoc 2.10 @ D:\\hsy\\software\\anaconda\\Scripts\\pandoc.exe
- Packages -----------------------------------------------------------------------------------------------------------
! package * version date (UTC) lib source
AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor
AnnotationHub 3.2.2 2022-03-01 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.2)
attempt 0.3.1 2020-05-03 [1] CRAN (R 4.1.2)
beachmat 2.10.0 2021-10-26 [1] Bioconductor
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.1.1)
benchmarkme 1.0.7 2021-03-21 [1] CRAN (R 4.1.2)
benchmarkmeData 1.0.4 2020-04-23 [1] CRAN (R 4.1.2)
Biobase * 2.54.0 2021-10-26 [1] Bioconductor
BiocFileCache 2.2.1 2022-01-23 [1] Bioconductor
BiocGenerics * 0.40.0 2021-10-26 [1] Bioconductor
BiocIO 1.4.0 2021-10-26 [1] Bioconductor
BiocManager 1.30.16 2021-06-15 [1] CRAN (R 4.1.2)
BiocNeighbors 1.12.0 2021-10-26 [1] Bioconductor
BiocParallel 1.28.3 2021-12-09 [1] Bioconductor
BiocSingular 1.10.0 2021-10-26 [1] Bioconductor
BiocVersion 3.14.0 2021-05-27 [1] Bioconductor
Biostrings 2.62.0 2021-10-26 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.2)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.2)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.1)
blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.2)
brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.2)
bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.2)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.2)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.2)
cli 3.2.0 2022-02-14 [1] CRAN (R 4.1.2)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.1.2)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
config 0.3.1 2020-12-17 [1] CRAN (R 4.1.2)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.2)
crayon 1.5.0 2022-02-14 [1] CRAN (R 4.1.2)
curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.2)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.2)
DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.2)
dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.1.2)
DelayedArray 0.20.0 2021-10-26 [1] Bioconductor
DelayedMatrixStats 1.16.0 2021-10-26 [1] Bioconductor
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.2)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2)
dockerfiler 0.1.4 2021-09-03 [1] CRAN (R 4.1.2)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.1.2)
dotCall64 1.0-1 2021-02-11 [1] CRAN (R 4.1.2)
dplyr 1.0.8 2022-02-08 [1] CRAN (R 4.1.2)
dqrng 0.3.0 2021-05-01 [1] CRAN (R 4.1.2)
DropletUtils 1.14.2 2022-01-09 [1] Bioconductor
DT 0.21 2022-02-26 [1] CRAN (R 4.1.2)
edgeR 3.36.0 2021-10-26 [1] Bioconductor
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2)
ExperimentHub 2.2.1 2022-01-23 [1] Bioconductor
fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2)
fields 13.3 2021-10-30 [1] CRAN (R 4.1.2)
filelock 1.0.2 2018-10-05 [1] CRAN (R 4.1.2)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.1.2)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2)
generics 0.1.2 2022-01-31 [1] CRAN (R 4.1.2)
GenomeInfoDb * 1.30.1 2022-01-30 [1] Bioconductor
GenomeInfoDbData 1.2.7 2022-03-03 [1] Bioconductor
GenomicAlignments 1.30.0 2021-10-26 [1] Bioconductor
GenomicRanges * 1.46.1 2021-11-18 [1] Bioconductor
ggbeeswarm 0.6.0 2017-08-07 [1] CRAN (R 4.1.2)
ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.2)
ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
golem 0.3.1 2021-04-17 [1] CRAN (R 4.1.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.2)
HDF5Array 1.22.1 2021-11-14 [1] Bioconductor
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.2)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.2)
httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.1.2)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.2)
interactiveDisplayBase 1.32.0 2021-10-26 [1] Bioconductor
IRanges * 2.28.0 2021-10-26 [1] Bioconductor
irlba 2.3.5 2021-12-06 [1] CRAN (R 4.1.2)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.1.2)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.2)
jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.1.2)
KEGGREST 1.34.0 2021-10-26 [1] Bioconductor
knitr 1.37 2021-12-16 [1] CRAN (R 4.1.2)
later 1.3.0 2021-08-18 [1] CRAN (R 4.1.2)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.2)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2)
limma 3.50.1 2022-02-17 [1] Bioconductor
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.2)
magick 2.7.3 2021-08-18 [1] CRAN (R 4.1.2)
magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2)
maps 3.4.0 2021-09-25 [1] CRAN (R 4.1.2)
Matrix 1.4-0 2021-12-08 [1] CRAN (R 4.1.2)
MatrixGenerics * 1.6.0 2021-10-26 [1] Bioconductor
matrixStats * 0.61.0 2021-09-17 [1] CRAN (R 4.1.2)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.2)
mime 0.12 2021-09-28 [1] CRAN (R 4.1.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2)
pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2)
pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.2)
plotly 4.10.0 2021-10-09 [1] CRAN (R 4.1.2)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.1)
Polychrome 1.3.1 2021-07-16 [1] CRAN (R 4.1.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.2)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.2)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.2)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.2)
R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.1)
R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.1)
R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.2)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.1)
Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2)
RCurl 1.98-1.6 2022-02-08 [1] CRAN (R 4.1.2)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.2)
restfulr 0.0.13 2017-08-06 [1] CRAN (R 4.1.2)
rhdf5 2.38.0 2021-10-26 [1] Bioconductor
D rhdf5filters 1.6.0 2021-10-26 [1] Bioconductor
Rhdf5lib 1.16.0 2021-10-26 [1] Bioconductor
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.1.2)
rlang 1.0.1 2022-02-03 [1] CRAN (R 4.1.2)
roxygen2 7.1.2 2021-09-08 [1] CRAN (R 4.1.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.2)
Rsamtools 2.10.0 2021-10-26 [1] Bioconductor
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rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.2)
rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.1.2)
rtracklayer 1.54.0 2021-10-26 [1] Bioconductor
S4Vectors * 0.32.3 2021-11-21 [1] Bioconductor
sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.2)
ScaledMatrix 1.2.0 2021-10-26 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.2)
scater 1.22.0 2021-10-27 [1] Bioconductor
scatterplot3d 0.3-41 2018-03-14 [1] CRAN (R 4.1.1)
scuttle 1.4.0 2021-10-26 [1] Bioconductor
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2)
shiny 1.7.1 2021-10-02 [1] CRAN (R 4.1.2)
shinyWidgets 0.6.4 2022-02-06 [1] CRAN (R 4.1.2)
SingleCellExperiment * 1.16.0 2021-10-26 [1] Bioconductor
spam 2.8-0 2022-01-06 [1] CRAN (R 4.1.2)
sparseMatrixStats 1.6.0 2021-10-26 [1] Bioconductor
SpatialExperiment * 1.4.0 2021-10-26 [1] Bioconductor
spatialLIBD * 1.6.5 2022-01-12 [1] Bioconductor
stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.2)
SummarizedExperiment * 1.24.0 2021-10-26 [1] Bioconductor
testthat 3.1.2 2022-01-20 [1] CRAN (R 4.1.2)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2)
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)
usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.2)
vipor 0.4.5 2017-03-22 [1] CRAN (R 4.1.2)
viridis 0.6.2 2021-10-13 [1] CRAN (R 4.1.2)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.2)
withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2)
xfun 0.30 2022-03-02 [1] CRAN (R 4.1.2)
XML 3.99-0.9 2022-02-24 [1] CRAN (R 4.1.2)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.2)
XVector 0.34.0 2021-10-26 [1] Bioconductor
yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.2)
zlibbioc 1.40.0 2021-10-26 [1] Bioconductor
[1] D:/hsy/software/R-4.1.2/library
D -- DLL MD5 mismatch, broken installation.
----------------------------------------------------------------------------------------------------------------------lcolladotor commented
Hi,
@SiyuanHuang1, thank you for your interest in spatialLIBD and for reporting this issue.
Hm... what happens when you click on https://www.dropbox.com/s/5ra9o8ku9iyyf70/sce_sub_for_vignette.Rdata?dl=1 on the browser? Can you download the data?
It might be an internet connection issue. This seems like a repeat of #30.
Best,
Leo
SiyuanHuang1 commented
Thank you so much for such a quick reply. I clicked on the link above and was able to download the data. That's great news.
lcolladotor commented
Ok! I'm glad to hear it worked =) I'll close this issue as it might have been a random connection issue. The exact code you provided works for me right now.
Best,
Leo