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rnabioco / raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments
https://rnabioco.github.io/raer/
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Cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt' #121

Closed shmmuzhangh closed 3 months ago

shmmuzhangh commented 3 months ago

When I tried the “seqlevelsStyle(alus) <- "NCBI" script for “4.4 Examine overall editing activites using the Alu Editing Index” The issue was said to be “error in download.file(url, destfile, quiet = TRUE): cannot open URL'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt'”， which I can easily Access throught both the Internet explorer and Chrome browser.

R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20 BSgenome_1.72.0
[3] rtracklayer_1.64.0 BiocIO_1.14.0
[5] Biostrings_2.72.1 XVector_0.44.0
[7] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[9] IRanges_2.38.1 S4Vectors_0.42.1
[11] raer_1.2.0 AnnotationHub_3.12.0
[13] BiocFileCache_2.12.0 dbplyr_2.5.0
[15] BiocGenerics_0.50.0

loaded via a namespace (and not attached): [1] tidyselect_1.2.1 dplyr_1.1.4 blob_1.2.4
[4] filelock_1.0.3 bitops_1.0-7 fastmap_1.2.0
[7] SingleCellExperiment_1.26.0 RCurl_1.98-1.14 GenomicAlignments_1.40.0
[10] XML_3.99-0.17 lifecycle_1.0.4 KEGGREST_1.44.1
[13] RSQLite_2.3.7 magrittr_2.0.3 compiler_4.4.1
[16] rlang_1.1.4 tools_4.4.1 utf8_1.2.4
[19] yaml_2.3.9 S4Arrays_1.4.1 bit_4.0.5
[22] curl_5.2.1 DelayedArray_0.30.1 abind_1.4-5
[25] BiocParallel_1.38.0 grid_4.4.1 fansi_1.0.6
[28] colorspace_2.1-0 ggplot2_3.5.1 scales_1.3.0
[31] SummarizedExperiment_1.34.0 cli_3.6.3 crayon_1.5.3
[34] generics_0.1.3 httr_1.4.7 rjson_0.2.21
[37] DBI_1.2.3 cachem_1.1.0 zlibbioc_1.50.0
[40] parallel_4.4.1 AnnotationDbi_1.66.0 BiocManager_1.30.23
[43] restfulr_0.0.15 matrixStats_1.3.0 vctrs_0.6.5
[46] Matrix_1.7-0 jsonlite_1.8.8 bit64_4.0.5
[49] GenomicFeatures_1.56.0 locfit_1.5-9.10 glue_1.7.0
[52] codetools_0.2-20 gtable_0.3.5 BiocVersion_3.19.1
[55] UCSC.utils_1.0.0 munsell_0.5.1 tibble_3.2.1
[58] pillar_1.9.0 rappdirs_0.3.3 GenomeInfoDbData_1.2.12
[61] R6_2.5.1 lattice_0.22-6 Biobase_2.64.0
[64] png_0.1-8 Rsamtools_2.20.0 memoise_2.0.1
[67] Rcpp_1.0.12 SparseArray_1.4.8 DESeq2_1.44.0
[70] MatrixGenerics_1.16.0 pkgconfig_2.0.3

kriemo commented 3 months ago

I suspect this is related to the same underlying internet connection issue from #120 . How did you solve that issue?

It's possible that you need to specify a different configuration for downloading files using download.file(). Could you try the different options (e.g. auto, libcurl, wget, curl, wininet) for the method parameter?

e.g.

url <- "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt"
tf <- tempfile()
download.file(url, tf, method = "auto")

If a particular option works without error then you can set it as a global option (e.g. options("download.file.method" = "curl")) , which will be used by the seqlevelsStyle(alus) <- "NCBI" command.

shmmuzhangh commented 3 months ago

I suspect this is related to the same underlying internet connection issue from #120 . How did you solve that issue?

It's possible that you need to specify a different configuration for downloading files using download.file(). Could you try the different options (e.g. auto, libcurl, wget, curl, wininet) for the method parameter?

e.g.

url <- "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt"
tf <- tempfile()
download.file(url, tf, method = "auto")

If a particular option works without error then you can set it as a global option (e.g. options("download.file.method" = "curl")) , which will be used by the seqlevelsStyle(alus) <- "NCBI" command.

Many thanks for the helpful comment. According to your suggestions, I successfully downloaded the files using the winnet method. Best regards.

shmmuzhangh commented 3 months ago

I suspect this is related to the same underlying internet connection issue from #120 . How did you solve that issue?

It's possible that you need to specify a different configuration for downloading files using download.file(). Could you try the different options (e.g. auto, libcurl, wget, curl, wininet) for the method parameter?

e.g.

url <- "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt"
tf <- tempfile()
download.file(url, tf, method = "auto")

If a particular option works without error then you can set it as a global option (e.g. options("download.file.method" = "curl")) , which will be used by the seqlevelsStyle(alus) <- "NCBI" command.

For this, I confirm it as an interner acess issue. I tried several times, and sometimes it works. Thank you.