[Bioc-devel] "access forbidden" trying to add new data to experiment package

Martin Morgan martin.morgan at roswellpark.org
Fri Dec 9 22:00:57 CET 2016 

On 12/09/2016 03:20 PM, Michael Love wrote:
> hi,
>
> After checking out the data_store version, I get an svn error "access
> forbidden". Can you remind me the proper steps (I tried to following
> variations on the Source Code instructions for experiment packages)?

Hi Mike - please try again; there seems to have been a permissions 
problem. Martin

>
> love:test/ $ svn co
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/tximportData
> A    tximportData/inst
> A    tximportData/inst/extdata
> A    tximportData/inst/extdata/cufflinks
> A    tximportData/inst/extdata/cufflinks/isoforms.count_table
> A    tximportData/inst/extdata/cufflinks/isoforms.attr_table
> A    tximportData/inst/extdata/cufflinks/isoforms.fpkm_table
> A    tximportData/inst/extdata/rsem
> A    tximportData/inst/extdata/rsem/ERR188329
> A    tximportData/inst/extdata/rsem/ERR188329/ERR188329.genes.results
> A    tximportData/inst/extdata/rsem/ERR188356
> A    tximportData/inst/extdata/rsem/ERR188356/ERR188356.genes.results
> A    tximportData/inst/extdata/rsem/ERR188088
> A    tximportData/inst/extdata/rsem/ERR188088/ERR188088.genes.results
> A    tximportData/inst/extdata/rsem/ERR188288
> A    tximportData/inst/extdata/rsem/ERR188288/ERR188288.genes.results
> A    tximportData/inst/extdata/rsem/ERR188297
> A    tximportData/inst/extdata/rsem/ERR188297/ERR188297.genes.results
> A    tximportData/inst/extdata/rsem/ERR188021
> A    tximportData/inst/extdata/rsem/ERR188021/ERR188021.genes.results
> A    tximportData/inst/extdata/tx2gene.csv
> A    tximportData/inst/extdata/salmon
> A    tximportData/inst/extdata/salmon/ERR188329
> A    tximportData/inst/extdata/salmon/ERR188329/cmd_info.json
> A    tximportData/inst/extdata/salmon/ERR188329/quant.sf
> A    tximportData/inst/extdata/salmon/ERR188356
> A    tximportData/inst/extdata/salmon/ERR188356/quant.sf
> A    tximportData/inst/extdata/salmon/ERR188356/cmd_info.json
> A    tximportData/inst/extdata/salmon/ERR188088
> A    tximportData/inst/extdata/salmon/ERR188088/quant.sf
> A    tximportData/inst/extdata/salmon/ERR188088/cmd_info.json
> A    tximportData/inst/extdata/salmon/ERR188288
> A    tximportData/inst/extdata/salmon/ERR188288/quant.sf
> A    tximportData/inst/extdata/salmon/ERR188288/cmd_info.json
> A    tximportData/inst/extdata/salmon/ERR188297
> A    tximportData/inst/extdata/salmon/ERR188297/cmd_info.json
> A    tximportData/inst/extdata/salmon/ERR188297/quant.sf
> A    tximportData/inst/extdata/salmon/ERR188021
> A    tximportData/inst/extdata/salmon/ERR188021/cmd_info.json
> A    tximportData/inst/extdata/salmon/ERR188021/quant.sf
> A    tximportData/inst/extdata/kallisto
> A    tximportData/inst/extdata/kallisto/ERR188329
> A    tximportData/inst/extdata/kallisto/ERR188329/run_info.json
> A    tximportData/inst/extdata/kallisto/ERR188329/abundance.tsv
> A    tximportData/inst/extdata/kallisto/ERR188356
> A    tximportData/inst/extdata/kallisto/ERR188356/run_info.json
> A    tximportData/inst/extdata/kallisto/ERR188356/abundance.tsv
> A    tximportData/inst/extdata/kallisto/ERR188088
> A    tximportData/inst/extdata/kallisto/ERR188088/run_info.json
> A    tximportData/inst/extdata/kallisto/ERR188088/abundance.tsv
> A    tximportData/inst/extdata/kallisto/ERR188288
> A    tximportData/inst/extdata/kallisto/ERR188288/abundance.tsv
> A    tximportData/inst/extdata/kallisto/ERR188288/run_info.json
> A    tximportData/inst/extdata/kallisto/ERR188297
> A    tximportData/inst/extdata/kallisto/ERR188297/run_info.json
> A    tximportData/inst/extdata/kallisto/ERR188297/abundance.tsv
> A    tximportData/inst/extdata/kallisto/ERR188021
> A    tximportData/inst/extdata/kallisto/ERR188021/run_info.json
> A    tximportData/inst/extdata/kallisto/ERR188021/abundance.tsv
> A    tximportData/inst/extdata/sailfish
> A    tximportData/inst/extdata/sailfish/ERR188329
> A    tximportData/inst/extdata/sailfish/ERR188329/cmd_info.json
> A    tximportData/inst/extdata/sailfish/ERR188329/quant.sf
> A    tximportData/inst/extdata/sailfish/ERR188356
> A    tximportData/inst/extdata/sailfish/ERR188356/quant.sf
> A    tximportData/inst/extdata/sailfish/ERR188356/cmd_info.json
> A    tximportData/inst/extdata/sailfish/ERR188088
> A    tximportData/inst/extdata/sailfish/ERR188088/cmd_info.json
> A    tximportData/inst/extdata/sailfish/ERR188088/quant.sf
> A    tximportData/inst/extdata/sailfish/ERR188288
> A    tximportData/inst/extdata/sailfish/ERR188288/quant.sf
> A    tximportData/inst/extdata/sailfish/ERR188288/cmd_info.json
> A    tximportData/inst/extdata/sailfish/ERR188297
> A    tximportData/inst/extdata/sailfish/ERR188297/quant.sf
> A    tximportData/inst/extdata/sailfish/ERR188297/cmd_info.json
> A    tximportData/inst/extdata/sailfish/ERR188021
> A    tximportData/inst/extdata/sailfish/ERR188021/quant.sf
> A    tximportData/inst/extdata/sailfish/ERR188021/cmd_info.json
> A    tximportData/inst/extdata/samples.txt
> A    tximportData/inst/extdata/samples_extended.txt
> Checked out revision 4006.
>
> love:tximportData/ $ cd inst/extdata
>     [15:06:02]
>
>
> Then I add new files:
>
>
> love:extdata/ $ svn add kallisto_h5
>     [15:06:19]
> A         kallisto_h5
> A         kallisto_h5/ERR188329
> A         kallisto_h5/ERR188329/run_info.json
> A  (bin)  kallisto_h5/ERR188329/abundance.h5
> A         kallisto_h5/ERR188356
> A         kallisto_h5/ERR188356/run_info.json
> A  (bin)  kallisto_h5/ERR188356/abundance.h5
> A         kallisto_h5/ERR188088
> A         kallisto_h5/ERR188088/run_info.json
> A  (bin)  kallisto_h5/ERR188088/abundance.h5
> A         kallisto_h5/ERR188288
> A         kallisto_h5/ERR188288/run_info.json
> A  (bin)  kallisto_h5/ERR188288/abundance.h5
> A         kallisto_h5/ERR188297
> A  (bin)  kallisto_h5/ERR188297/abundance.h5
> A         kallisto_h5/ERR188297/run_info.json
> A         kallisto_h5/ERR188021
> A         kallisto_h5/ERR188021/run_info.json
> A  (bin)  kallisto_h5/ERR188021/abundance.h5
>
> love:extdata/ $ svn commit -m "add kallisto HDF5 files"
>     [15:06:27]
> Adding         kallisto_h5
> svn: E195023: Commit failed (details follow):
> svn: E195023: Changing directory
> '/Users/love/bioc/test/tximportData/inst/extdata/kallisto_h5' is
> forbidden by the server
> svn: E175013: Access to
> '/bioc-data/!svn/txr/4006-1/trunk/experiment/data_store/tximportData/inst/extdata/kallisto_h5'
> forbidden
>
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