[Advent bug squashing] Bug#1001349: marked as done (python-anndata: autopkgtest fail with pandas 1.3: missing openpyxl)
That was an easy one Package: python3-anndata Version: 0.7.5+ds-3 Severity: serious Tags: patch pandas.read_excel() now defaults to using openpyxl only, not openpyxl-or-xlrd: https://pandas.pydata.org/pandas-docs/version/1.3.4/whatsnew/v1.2.0.html Please update your build and test dependencies. -- http://fam-tille.de
[Advent bug squashing] Bug#1001020: marked as done (python-anndata: FTBFS with sklearn 1.0.1-1: ModuleNotFoundError: No module named 'sklearn.utils.testing')
This seems to be fixed Date: Fri, 03 Dec 2021 00:55:42 +0530 From: Nilesh Patra To: Debian Bug Tracking System Subject: python-anndata: FTBFS with sklearn 1.0.1-1: ModuleNotFoundError: No module named 'sklearn.utils.testing' Source: python-anndata Version: 0.7.5+ds-3 Severity: serious Dear Maintainer, python-anndata FTBFS, it probably needs changes with new sklearn. Log pasted below. -- http://fam-tille.de
Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with
Am Fri, Dec 10, 2021 at 11:57:49AM +0100 schrieb Steffen Möller: > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001436 > > for r-bioc-txdb.hsapiens.ucsc.hg19.knowngene and when I wanted to inject > it found that it is already existing at > > https://salsa.debian.org/r-pkg-team/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene > > in a "debian folder only" stage and 4 years old. > > You do not mind if I somehow adopt that? I don't mind at all. I remember that I used debian/ dir only due to the size of the source which might have been an issue at the time of creation. Technically I wonder whether it makes sense to remove the repository first and create it from scratch via prepare_missing_cran_package. It could perfectly be the case that it is the more straight approach to get a sensible package - but I'll leave this decision to you. Kind regards Andreas. -- http://fam-tille.de
Re: Any help to get pydicom build welcome
On Fri, Dec 10, 2021 at 2:40 PM Andreas Tille wrote: > > Hi Mathieu, > > Am Fri, Dec 10, 2021 at 02:31:20PM +0100 schrieb Mathieu Malaterre: > > On Fri, Dec 10, 2021 at 12:22 PM Étienne Mollier > > wrote: > > [...] > > > My impression by looking at it to unroll is that something seems > > > caught in a recursive loop. > > > > The bug is upstream. One cannot do: > > > > image = gdcm.Image() > > > > This will not work with the simple shared pointer implementation in > > upstream gdcm. > > I'f volunteer to open an upstream issue about this - but could you > give some more verbose information what will work instead? You can copy/paste the following [...] GDCM is a C++ project, that is wrapped to python using swig. It use a simple reference counting mechanism (c++98 style), where application programmer are required to write: gdcm::SmartPointer im = new gdcm::Image; Since SmartPointer is a class template it is not accessible from python. A predefined set of class have been explicitly wrapped to python using something like: %template(SmartPtrScan) gdcm::SmartPointer; this is not the case for gdcm.Image as of release 3.0.10. --- A potential solution would be to use an image instance from an ImageReader/ImageWriter . writer = gdcm.ImageWriter() proper_image_ref_count = writer.GetImage() [...] > > I would just remove the gdcm test suite from pydicom. > > I'll do so - but it would be great to get this working in the next > release. Agreed. Thanks
Re: Any help to get pydicom build welcome
Hi Mathieu, Am Fri, Dec 10, 2021 at 02:31:20PM +0100 schrieb Mathieu Malaterre: > On Fri, Dec 10, 2021 at 12:22 PM Étienne Mollier > wrote: > [...] > > My impression by looking at it to unroll is that something seems > > caught in a recursive loop. > > The bug is upstream. One cannot do: > > image = gdcm.Image() > > This will not work with the simple shared pointer implementation in > upstream gdcm. I'f volunteer to open an upstream issue about this - but could you give some more verbose information what will work instead? > I would just remove the gdcm test suite from pydicom. I'll do so - but it would be great to get this working in the next release. Thanks a lot for your help Andreas. -- http://fam-tille.de
Re: Any help to get pydicom build welcome
On Fri, Dec 10, 2021 at 12:22 PM Étienne Mollier wrote: [...] > My impression by looking at it to unroll is that something seems > caught in a recursive loop. The bug is upstream. One cannot do: image = gdcm.Image() This will not work with the simple shared pointer implementation in upstream gdcm. I would just remove the gdcm test suite from pydicom. -M
Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with
On 10.12.21 07:15, Andreas Tille wrote: Am Fri, Dec 10, 2021 at 03:07:51AM +0530 schrieb Nilesh Patra: On Thu, Dec 09, 2021 at 08:32:46PM +0100, Steffen Möller wrote: Hello this goes out to Andreas in particular, I hope you do not mind me taking over (have a few spare cycles) I definitely encourage everybody to take over anything that was addressed to me in particular! ;-) Same here :) And I have another one . I just prepared this ITP https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001436 for r-bioc-txdb.hsapiens.ucsc.hg19.knowngene and when I wanted to inject it found that it is already existing at https://salsa.debian.org/r-pkg-team/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene in a "debian folder only" stage and 4 years old. You do not mind if I somehow adopt that? Best, Steffen Uploaded after a few changes. Thanks a lot Andreas.
