Not really helpful but this could be simplified a bit by removing the redirect from experiment hub, and the layer from httr to curl, so
url = "https://functionalgenomics.upf.edu/experimenthub/gdnainrnaseqdata/LiYu22subsetBAMfiles/s32gDNA0.bam"; curl::curl_fetch_disk(url, tempfile()) Error in curl::curl_fetch_disk("https://functionalgenomics.upf.edu/experimenthub/gdnainrnaseqdata/LiYu22subsetBAMfiles/s32gDNA0.bam";, : Failed writing received data to disk/application I notice the index file (extension .bai) works; do other BAM files work, too? Martin From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Robert Castelo <robert.cast...@upf.edu> Date: Wednesday, March 29, 2023 at 1:18 PM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] httr::GET() problem downloading a ExperimentHub resource hi, we recently added a few new ExperimentHub resources, consisting of BAM files and their corresponding BAI files and hosted in my own server. while it seems that they are accessible, they cannot be downloaded through the ExperimentHub API. the minimum example reproducing the problem is this one (using Bioc devel): library(ExperimentHub) httr::GET("https://experimenthub.bioconductor.org/fetch/8129";) Error in curl::curl_fetch_memory(url, handle = handle) : Failed writing received data to disk/application while there's apparently no problem to "manually" download the resource using 'download.file()' and loading it with 'GenomicAlignments::readGAlignments()': download.file("https://experimenthub.bioconductor.org/fetch/8129";, "file.bam") trying URL 'https://experimenthub.bioconductor.org/fetch/8129' Content type 'application/octet-stream' length 13296358 bytes (12.7 MB) ================================================== downloaded 12.7 MB gal <- GenomicAlignments::readGAlignments("file.bam") gal[1:3] GAlignments object with 3 alignments and 0 metadata columns: seqnames strand cigar qwidth start end width <Rle> <Rle> <character> <integer> <integer> <integer> <integer> [1] chr1 + 49M1S 50 16208 16256 49 [2] chr1 + 3S47M 50 16976 17022 47 [3] chr1 - 10M177N40M 50 17046 17272 227 njunc <integer> [1] 0 [2] 0 [3] 1 ------- seqinfo: 2580 sequences from an unspecified genome any hint why 'httr::GET()' fails, while 'download.file()' doesn't? thanks!! robert. ps: just to clarify, the 'httr::GET()' example is behind the following problem: eh <- ExperimentHub() z <- eh[["EH8079"]] see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation downloading 2 resources retrieving 2 resources |======================================================================| 100% Error: failed to load resource name: EH8079 title: RNA-seq data BAM file subset of HRR589632 contaminated with 0% gDNA reason: 1 resources failed to download In addition: Warning messages: 1: download failed web resource path: �https://experimenthub.bioconductor.org/fetch/8129� <https://secure-web.cisco.com/1G9U1udOgqvil7BzSrk1HB2QvPNNeRPXidZLvh_epNXLPv1TrhUqn08C9P35HGdtTOb7o618WNCTyiVyN33-XUDlHCBdrEge6kXsqOKgSLtQvTHIAy-lStrk-VCkYpHvBPBmBnsfje9oWlLBS3j_GHaZhn97VjWPhVuy-Dmaf2COELmWHmMNGFKsbPFgrf9c1uASwhF8epk0meG_S_IDryWy2EhVlyNGlVjBrkp6aeXox1IKgdVUV4h_1Q3moBEJ7FXMDzCUtfHd7zJDkhSL7Bf81pLeAlTWkC0lVAVXTKS6egI4Q-0-6mFXz7ui7zJM6/https%3A%2F%2Fexperimenthub.bioconductor.org%2Ffetch%2F8129%E2%80%99> local file path: �/home/rcastelo/.cache/R/ExperimentHub/12ba1aa03_8129� reason: Failed writing received data to disk/application 2: bfcadd() failed; resource removed rid: BFC3 fpath: �https://experimenthub.bioconductor.org/fetch/8129� <https://secure-web.cisco.com/1G9U1udOgqvil7BzSrk1HB2QvPNNeRPXidZLvh_epNXLPv1TrhUqn08C9P35HGdtTOb7o618WNCTyiVyN33-XUDlHCBdrEge6kXsqOKgSLtQvTHIAy-lStrk-VCkYpHvBPBmBnsfje9oWlLBS3j_GHaZhn97VjWPhVuy-Dmaf2COELmWHmMNGFKsbPFgrf9c1uASwhF8epk0meG_S_IDryWy2EhVlyNGlVjBrkp6aeXox1IKgdVUV4h_1Q3moBEJ7FXMDzCUtfHd7zJDkhSL7Bf81pLeAlTWkC0lVAVXTKS6egI4Q-0-6mFXz7ui7zJM6/https%3A%2F%2Fexperimenthub.bioconductor.org%2Ffetch%2F8129%E2%80%99> reason: download failed 3: download failed hub path: �https://experimenthub.bioconductor.org/fetch/8129� <https://secure-web.cisco.com/1G9U1udOgqvil7BzSrk1HB2QvPNNeRPXidZLvh_epNXLPv1TrhUqn08C9P35HGdtTOb7o618WNCTyiVyN33-XUDlHCBdrEge6kXsqOKgSLtQvTHIAy-lStrk-VCkYpHvBPBmBnsfje9oWlLBS3j_GHaZhn97VjWPhVuy-Dmaf2COELmWHmMNGFKsbPFgrf9c1uASwhF8epk0meG_S_IDryWy2EhVlyNGlVjBrkp6aeXox1IKgdVUV4h_1Q3moBEJ7FXMDzCUtfHd7zJDkhSL7Bf81pLeAlTWkC0lVAVXTKS6egI4Q-0-6mFXz7ui7zJM6/https%3A%2F%2Fexperimenthub.bioconductor.org%2Ffetch%2F8129%E2%80%99> cache resource: �EH8079 : 8129� reason: bfcadd() failed; see warnings() [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]]
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