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mksamur / RTCGAToolbox

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getFirehoseData error: Error in file(name, "wb") #22

Closed cqneosun closed 4 years ago

cqneosun commented 7 years ago

@mksamur luscData = getFirehoseData (dataset="LUSC", runDate="20160128",gistic2_Date = "20160128",

gdac.broadinstitute.org_LUSC.Merge_snpgenome_wide_snp_6broad_mit_eduLevel_3segmented_scna_minus_germline_cnv_hg19seg.Level_3.2016012800.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUSC/20160128/gdac.broadinstitute.org_LUSC.Merge_snp__genome_wide_snp_6broad_mit_eduLevel_3__segmented_scna_minus_germline_cnv_hg19seg.Level_3.2016012800.0.0.tar.gz' Content type 'application/x-gzip' length 2298041 bytes (2.2 MB) downloaded 2.2 MB

Error in file(name, "wb") : cannot open the connection In addition: Warning message: In file(name, "wb") : cannot open file 'gdac.broadinstitute.org_LUSC.Merge_snpgenome_wide_snp_6broad_mit_eduLevel_3segmented_scna_minus_germline_cnv_hg19seg.Level_3.2016012800.0.0/LUSC.snp__genome_wide_snp_6broad_mit_eduLevel_3__segmented_scna_minus_germline_cnv_hg19seg.seg.txt': No such file or directory

cqneosun commented 7 years ago

gdac.broadinstitute.org_LUSC.Merge_methylationhumanmethylation27jhu_usc_eduLevel_3within_bioassay_data_set_functiondata.Level_3.2016012800.0.0.tar.gzgdac.broadinstitute.org_LUSC.Merge_methylationhumanmethylation450jhu_usc_eduLevel_3within_bioassay_data_set_functiondata.Level_3.2016012800.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUSC/20160128/gdac.broadinstitute.org_LUSC.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz' Content type 'application/x-gzip' length 41288333 bytes (39.4 MB) downloaded 8.0 MB

Error in untar2(tarfile, files, list, exdir) : incomplete block on file In addition: Warning message: In download.file(url = fileLink, destfile = tcgafile, method = "auto", : downloaded length 8413184 != reported length 41288333

cqneosun commented 7 years ago

gdac.broadinstitute.org_LUSC.Merge_transcriptomeagilentg4502a_07_3unc_eduLevel_3unc_lowess_normalization_gene_leveldata.Level_3.2016012800.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata2016_01_28/data/LUSC/20160128/gdac.broadinstitute.org_LUSC.Merge_transcriptomeagilentg4502a_07_3unc_edu__Level_3unc_lowess_normalization_gene_leveldata.Level_3.2016012800.0.0.tar.gz' Content type 'application/x-gzip' length 10429884 bytes (9.9 MB) downloaded 9.9 MB

Error in dirname(name) : path too long

cqneosun commented 7 years ago

How to deal with these error?

LiNk-NY commented 7 years ago

There are errors with long file names on the Windows platform. We hope to find a fix for this soon. Thank you for reporting these issues. Best regards, Marcel

gy80 commented 5 years ago

Hi I am wondering if you guys have solutions now to fix this issue! Thanks a lot!

LiNk-NY commented 4 years ago

See #19 Closing this one