Hi Tiago, On 9/16/19 06:35, Tiago Lubiana Alves wrote: > Hello Mike, > > Thank you for the detailed explanation. > > You are right, for the vignette, I can download it from the ExperimentHub > subset the pbmc3k dataset in the first few lines. The main point of having > a new dataset was to use it in the examples of functions. The full dataset > is too big and the examples would take too long otherwise. > > Still, if someone knows how to "transform from an HDF5 back > SingleCellExperiment to using the data in memory", it would be of great > help.
Just to clarify, it's not that you have to choose between using the full on-disk dataset or using a small in-memory subset in your vignette. A 3rd option is to start your vignette with the full on-disk dataset and to immediately subset it. Like what Pete is doing in his 3-line snippet but without the last line (replacement of on-disk assay with in-memory assay). H. > Best, > Tiago > > > Tiago Lubiana > Mestrando em Bioinformática, FCF/USP > *Computational Systems Biology Laboratory (CSBL)* > Telefone (laboratório): +55 (11) 2648-0240 > Telefone (pessoal): +55 (11) 954258000 > > > On Mon, Sep 16, 2019 at 5:39 AM Mike Smith <grimbo...@gmail.com> wrote: > >> Hi Tiago, >> >> I suspect what has happened here is that when create the mini_pbmc3k >> object, you're doing this by subsetting the PBMC, 3k scRNA-seq data from >> ExperimenHub. The assay data for that are are actually stored in an HDF5 >> file which will be downloaded and stored in your ExperimentHub cache on >> your local machine. When you take the subset for your new object it still >> points to the same HDF5 file, and when you save mini_pbmc3k all it actually >> saves is the location of the HDF5 rather than putting the data in the >> object. This works locally, but naturally the BioC build server doesn't >> have the original HDF5 in exactly the same location, and so it fails. >> >> Is there a reason you don't want to use the whole dataset and make the >> first section of the vignette demonstrate how to download it via >> ExperimentHub? Alternatively there is a way to transform from an HDF5 back >> SingleCellExperiment to using the data in memory, but I can't remember it >> right now - hopefully someone else will be along shortly. >> >> This also seems like the perfect opportunity to point out that our next >> BioC Developers' Forum ( >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2019-2DSeptember_015499.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s7A_Q0fNE8fpu3Ob4M_wxwPfLdlY2QkGSbNwInWB2mo&s=TDo6rxwdtAE-kwlyPoYbbHn9JI69Wdw3scAgxje60ck&e= >> ) will >> have a discussion on object serilaisation which should cover exactly this >> type of issue. >> >> Best, >> Mike >> >> >> >> On Sat, 14 Sep 2019 at 23:26, Tiago Lubiana Alves < >> tiago.lubiana.al...@usp.br> wrote: >> >>> Hello, >>> >>> I am having a problem with a package submission build. >>> >>> This is the package issue: >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1241&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s7A_Q0fNE8fpu3Ob4M_wxwPfLdlY2QkGSbNwInWB2mo&s=HRcbdQHP2-fSp-0NnFZw8H0NrGgT8IerVORN96IaUrs&e= >>> And this is the ERROR: >>> >>> HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0: >>> #000: C:/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/src/H5F.c line 509 >>> in H5Fopen(): unable to open file >>> major: File accessibilty >>> minor: Unable to open file >>> #001: C:/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/src/H5Fint.c line >>> 1498 in H5F_open(): unable to open file: time = Fri Sep 13 15:05:35 >>> 2019 >>> , name = '/home/lubianat/.cache/ExperimentHub/5486ffbe0e3_1605', >>> tent_flags = 0 >>> (...) >>> >>> Quitting from lines 46-51 (fcoex.Rmd) >>> Error: processing vignette 'fcoex.Rmd' failed with diagnostics: >>> failed to open file '/home/lubianat/.cache/ExperimentHub/5486ffbe0e3_1605' >>> --- failed re-building 'fcoex.Rmd' >>> >>> >>> It looks like something is pointing in the wrong direction, but I have not >>> been able to figure out exactly what. I've tried re-saving the data file >>> ("mini_pbmc3k"), which is loaded in the vignette chunk of the error, but >>> that did not help. >>> >>> Does anyone have a suggestion of what might be happening? >>> >>> Thank you very much for your time, >>> Best, >>> Tiago >>> >>> Tiago Lubiana >>> Mestrando em Bioinformática, FCF/USP >>> *Computational Systems Biology Laboratory (CSBL)* >>> Telefone (laboratório): +55 (11) 2648-0240 >>> Telefone (pessoal): +55 (11) 954258000 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s7A_Q0fNE8fpu3Ob4M_wxwPfLdlY2QkGSbNwInWB2mo&s=b1C-benewoBq9gx9nDOXMGDReO7x4cpbfzQWEzUSRhc&e= >>> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s7A_Q0fNE8fpu3Ob4M_wxwPfLdlY2QkGSbNwInWB2mo&s=b1C-benewoBq9gx9nDOXMGDReO7x4cpbfzQWEzUSRhc&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel