atankka
commented
8 months ago Never mind, i figured out the issue, I fixed the issue by adding in a 'Downloads' folder inside the path listed in the above warnings and was able to pull the firebrowse data
Thank you for providing this useful tool to the community. I am using your package in a conda environment at the command line and am unable to download files using
data <- loadFirebrowseData(folder=folder, cohort="BRCA", data=c("clinical","junction_quantification","RSEM_genes"), date="2016-01-28")and I see these warnings:
There were 20 warnings (use warnings() to see them) warnings() Warning messages: 1: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz', reason 'No such file or directory' 2: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 3: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz.md5: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz.md5', reason 'No such file or directory' 4: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 5: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz', reason 'No such file or directory' 6: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 7: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz.md5: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz.md5', reason 'No such file or directory' 8: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 9: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz', reason 'No such file or directory' 10: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 11: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz.md5: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz.md5', reason 'No such file or directory' 12: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 13: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz', reason 'No such file or directory' 14: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 15: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz.md5: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz.md5', reason 'No such file or directory' 16: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 17: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz', reason 'No such file or directory' 18: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit status 19: In download.file(f, destfile = file.path(folder, basename(f))) : URL http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz.md5: cannot open destfile '/tscc/nfs/home/atankka/Downloads//gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz.md5', reason 'No such file or directory' 20: In download.file(f, destfile = file.path(folder, basename(f))) : download had nonzero exit statusI do not have a downloads folder such as the one listed in the paths and don't know where these files might be found. Could you please advise?
Thank you for the help!