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Hi, I'm trying to use PureCN and I consistently get this error message:
Possible Ensembl SSL connectivity problems detected.
Please see the 'Connection Troubleshooting' section of the biomaRt vignette
vignette('accessing_ensembl', package = 'biomaRt')Error in curl::curl_fetch_memory(url, handle = handle) :
Peer certificate cannot be authenticated with given CA certificates: [uswest.ensembl.org] SSL certificate problem: certificate has expired
I've tried changing the mirror by adding these lines to the PureCN source code:
ensembl <- useEnsembl(biomart = "ensembl",
dataset = "hsapiens_gene_ensembl",
mirror = "www")
this doesn't work, it doesn't remove the warning message and all it does is it just keeps trying all mirrors and around half the time it returns this error and stops:
Error in bmRequest(request = request, verbose = verbose) :
Not Found (HTTP 404).
Calls: useEnsembl ... listMarts -> .listMarts -> bmRequest -> stop_for_status
Execution halted
It's a gamble if it works, I usually have 15 bam files I want to loop through and I keep having to redo about half of them. Is there a way to resolve this?
my session info:
Session info
version R version 4.0.2 (2020-06-22)
os Ubuntu 18.04.6 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz Europe/Budapest
date 2024-08-30
rstudio 1.3.959 Middlemist Red (server)
pandoc NA
Packages
package * version date (UTC) lib source
AnnotationDbi 1.52.0 2020-10-27 [1] Bioconductor
askpass 1.2.0 2023-09-03 [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 * 0.36.1 2021-04-16 [1] Bioconductor
BiocManager * 1.30.25 2024-08-28 [1] CRAN (R 4.0.2)
BiocParallel * 1.24.1 2020-11-06 [1] Bioconductor
biomaRt * 2.46.3 2024-08-26 [1] Bioconductor
Biostrings * 2.58.0 2020-10-27 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.0.2)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2)
bitops 1.0-8 2024-07-29 [1] CRAN (R 4.0.2)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.0.2)
BSgenome 1.58.0 2020-10-27 [1] Bioconductor
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.0.2)
Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.0.2)
circlize * 0.4.16 2024-02-20 [1] CRAN (R 4.0.2)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.0.2)
clue 0.3-65 2023-09-23 [1] CRAN (R 4.0.2)
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.0.2)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.0.2)
ComplexHeatmap * 2.6.2 2020-11-12 [1] Bioconductor
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.0.2)
curl * 5.2.2 2024-08-26 [1] CRAN (R 4.0.2)
data.table 1.16.0 2024-08-27 [1] CRAN (R 4.0.2)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.0.2)
dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.0.2)
DelayedArray 0.16.3 2021-03-24 [1] Bioconductor
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.0.2)
digest 0.6.37 2024-08-19 [1] CRAN (R 4.0.2)
DNAcopy * 1.64.0 2020-10-27 [1] Bioconductor
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.0.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.2)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.0.2)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.0.2)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.0.2)
formatR 1.14 2023-01-17 [1] CRAN (R 4.0.2)
fs * 1.6.4 2024-04-25 [1] CRAN (R 4.0.2)
futile.logger * 1.4.3 2016-07-10 [1] CRAN (R 4.0.2)
futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.0.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.0.2)
GenomeInfoDb * 1.26.7 2021-04-08 [1] Bioconductor
GenomeInfoDbData 1.2.4 2024-06-25 [1] Bioconductor
GenomicAlignments 1.26.0 2020-10-27 [1] Bioconductor
GenomicFeatures 1.42.3 2021-04-01 [1] Bioconductor
GenomicRanges * 1.42.0 2020-10-27 [1] Bioconductor
getopt 1.20.4 2023-10-01 [1] CRAN (R 4.0.2)
GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.0.2)
ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.0.2)
GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.0.2)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.0.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
gtable 0.3.5 2024-04-22 [1] CRAN (R 4.0.2)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.0.2)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.0.2)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.0.2)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.0.2)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.0.2)
IRanges * 2.24.1 2020-12-12 [1] Bioconductor
lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.0.2)
later 1.3.2 2023-12-06 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.0.2)
lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.0.2)
maftools * 2.6.05 2021-02-04 [1] Bioconductor
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.2)
MatrixGenerics * 1.2.1 2021-01-30 [1] Bioconductor
matrixStats * 1.3.0 2024-04-11 [1] CRAN (R 4.0.2)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2)
mime 0.12 2021-09-28 [1] CRAN (R 4.0.2)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.0.2)
openssl 2.2.1 2024-08-16 [1] CRAN (R 4.0.2)
optparse * 1.7.5 2024-04-16 [1] CRAN (R 4.0.2)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.0.2)
plyr 1.8.9 2023-10-02 [1] CRAN (R 4.0.2)
png 0.1-8 2022-11-29 [1] CRAN (R 4.0.2)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.0.2)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.0.2)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.0.2)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.0.2)
PureCN * 1.20.0 2020-10-27 [1] Bioconductor
purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.0.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.0.2)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.0.2)
RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.0.2)
Rcpp 1.0.13 2024-07-17 [1] CRAN (R 4.0.2)
RCurl 1.98-1.16 2024-07-11 [1] CRAN (R 4.0.2)
readr * 2.1.5 2024-01-10 [1] CRAN (R 4.0.2)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.0.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.2)
rhdf5 2.34.0 2020-10-27 [1] Bioconductor
rhdf5filters 1.2.1 2021-05-03 [1] Bioconductor
Rhdf5lib 1.12.1 2021-01-26 [1] Bioconductor
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.0.2)
rlang 1.1.4 2024-06-04 [1] CRAN (R 4.0.2)
Rsamtools * 2.6.0 2020-10-27 [1] Bioconductor
RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.0.2)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.0.2)
rtracklayer 1.50.0 2020-10-27 [1] Bioconductor
S4Vectors * 0.28.1 2020-12-09 [1] Bioconductor
scales 1.3.0 2023-11-28 [1] CRAN (R 4.0.2)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.0.2)
shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.0.2)
shiny 1.9.1 2024-08-01 [1] CRAN (R 4.0.2)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.0.2)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.0.2)
SummarizedExperiment * 1.20.0 2020-10-27 [1] Bioconductor
survival 3.1-12 2020-04-10 [2] CRAN (R 4.0.2)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.0.2)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.0.2)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.0.2)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.0.2)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.0.2)
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.0.2)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.0.2)
usethis * 3.0.0 2024-07-29 [1] CRAN (R 4.0.2)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.0.2)
VariantAnnotation * 1.36.0 2020-10-27 [1] Bioconductor
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.0.2)
VGAM 1.1-11 2024-05-15 [1] CRAN (R 4.0.2)
vroom * 1.6.5 2023-12-05 [1] CRAN (R 4.0.2)
withr 3.0.1 2024-07-31 [1] CRAN (R 4.0.2)
XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.0.2)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.0.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2)
XVector * 0.30.0 2020-10-27 [1] Bioconductor
zlibbioc 1.36.0 2020-10-27 [1] Bioconductor
Hi Mike, Thank you for the response. Updating the versions would be quite difficult as I'm working on a local server where I'm not the sole user of the programs, but it starts to seem it would be the only viable solution at this point.
I have tried all available mirrors, none of them seemed to work for some reason.