[Bioc-devel] Python package dependency loading problem on malbec1 builder
Pages, Herve
hp@ge@ @end|ng |rom |redhutch@org
Wed Jan 29 04:32:12 CET 2020
Hi Will,
Let's keep this on the mailing list.
On 1/13/20 16:00, William Chen wrote:
> Hi Herve,
>
> Thanks for this reply. I have been looking into the R CMD CHECK error
> that has been thrown by the tokay1 builder and am still unsure how to
> potentially mitigate the error message given.
>
> https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/phemd/tokay1-checksrc.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.10_bioc-2DLATEST_phemd_tokay1-2Dchecksrc.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WY6C8M_ZPX4_9k2G8rpbW1W7rTpVAeAuAK5jtt7Yjn4&s=N0w5SeDu3ULL4uGmFV3VWl7AMv8ARVJ8CXT-CiRy0Wc&e=>
>
> There are no issues with the Mac OS X builder merida1 (which gives the
> same log as my local machine which is also a Mac), but the tokay1
> builder seems to give the following error which (per
> http://r-pkgs.had.co.nz/check.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__r-2Dpkgs.had.co.nz_check.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WY6C8M_ZPX4_9k2G8rpbW1W7rTpVAeAuAK5jtt7Yjn4&s=HHY_jUrizS6gw2CbuEXYS1uLN5v6gA9gRLFjLW6jUP0&e=>) I
> am interpreting as an error with the library(phemd) call made by R CMD
> CHECK, and per the log this seems to be in the setting of "loading
> checks for arch 'x64'"
>
> Do you have any specific ideas on how I might modify the my DESCRIPTION
> and/or NAMESPACE files to address this issue on the tokay1 builder?
Unfortunately we cannot install the phate module on tokay1 at the moment
(the Windows builder for BioC 3.10). We still have Python 2.7 on this
machine and phate requires Python >= 3.5.
Please mark **the RELEASE_3_10 branch** of your package as unsupported
on Windows by adding a .BBSoptions file in its top level folder with the
following line in it:
UnsupportedPlatforms: win
Sorry for the inconvenience.
Regards,
H.
>
> I believe this does not affect the core functionality of the package as
> I believe users are still able to install and load my package, but would
> ideally address this error message if possible.
>
> Thanks so much for your help!
>
> Best,
> Will
>
> PS It makes sense to me that the malbec1 linux builder would give that
> error since the phate Python module cannot be installed on python2
> (which is the version of Python used by malbec1) but as Kayla pointed
> out, it seems this error should not be occurring on the tokay1 builder.
>
>
>
>
> ᐧ
>
> On Sat, Dec 28, 2019 at 1:26 PM Pages, Herve <hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>> wrote:
>
> By default the reticulate package uses the python command that is in
> the
> PATH. On our Linux and Mac builders the python command found in the
> PATH
> points to Python 2. On our Windows builder it points to Python 3.
>
> So on a non-Windows system, you need to tell reticulate to use the
> python3 command:
>
> library(reticulate)
>
> if (.Platform$OS.type != "windows")
> use_python(Sys.which("python3"), required=TRUE)
>
> Then you can import the phate module:
>
> import("phate")
> # Module(phate)
>
> Successfully tested on malbec2, tokay2, and celaya2.
>
> Hope this helps,
> H.
>
>
> On 12/26/19 17:49, William Chen wrote:
> > Thanks for looking into this and confirming! Would appreciate any
> > suggestions on how to correctly import the python module on malbec1.
> >
> > Best
> > Will
> > ᐧ
> >
> > On Mon, Dec 23, 2019 at 8:41 PM Pages, Herve
> <hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> > <mailto:hpages using fredhutch.org <mailto:hpages using fredhutch.org>>> wrote:
> >
> > Hi William,
> >
> > I can confirm that the phate module is installed for Python 3 on
> > malbec1:
> >
> > biocbuild using malbec1:~$ python3
> > Python 3.6.9 (default, Nov 7 2019, 10:44:02)
> > [GCC 8.3.0] on linux
> > Type "help", "copyright", "credits" or "license" for more
> information.
> > >>> import phate
> > >>> phate.__version__
> > '0.4.5'
> >
> > However please note that it is NOT installed for Python 2:
> >
> > biocbuild using malbec1:~$ python
> > Python 2.7.17 (default, Nov 7 2019, 10:07:09)
> > [GCC 7.4.0] on linux2
> > Type "help", "copyright", "credits" or "license" for more
> information.
> > >>> import phate
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > ImportError: No module named phate
> >
> > So make sure you invoke Python 3.
> >
> > Best,
> > H.
> >
> >
> > On 12/22/19 22:51, William Chen wrote:
> > > Hi all,
> > >
> > > A package I maintain on Bioconductor ('phemd') has failed
> R CMD
> > check on
> > > two of three of the Bioconductor builders (tokay1 and malbec1)
> > with the
> > > following error message:
> > >
> > > Error in py_module_import(module, convert = convert) :
> > >
> > > ImportError: No module named phate
> > >
> > >
> > > It looks like this package (or one of its dependent
> packages) has an
> > >
> > > unstated dependence on a standard package. All
> dependencies must be
> > >
> > > declared in DESCRIPTION.
> > >
> > > See section ‘The DESCRIPTION file’ in the ‘Writing R
> Extensions’
> > >
> > > manual.
> > >
> > > * checking whether the package can be unloaded cleanly ...
> WARNING
> > >
> > > ---- unloading
> > >
> > > * checking whether the namespace can be loaded with stated
> > dependencies ...
> > > WARNING
> > >
> > > Error in py_module_import(module, convert = convert) :
> > >
> > > ImportError: No module named phate
> > >
> > >
> > > A namespace must be able to be loaded with just the base
> namespace
> > >
> > > loaded: otherwise if the namespace gets loaded by a saved
> object, the
> > >
> > > session will be unable to start.
> > >
> > > I have been told that the 'phate' python module is unable
> to be
> > installed
> > > on tokay1 which uses Python2 (phate requires Python3) but
> that it
> > has been
> > > installed on the malbec1 builder such that the error
> should not
> > be occuring
> > > on that build. I have tried without avail to fix this /
> search for a
> > > solution online (including the 'Writing R Extensions'
> manual). Any
> > > recommendations on how to address this issue?
> > >
> > > Link to build:
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.10_bioc-2DLATEST_phemd_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg&s=0mydgs8zLKpjMbGeLEhBkhh8phXWfQi2pXPF431wR10&e=
> > >
> > > Thanks!
> > > Will
> > >
> > > ᐧ
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
> <mailto:Bioc-devel using r-project.org <mailto:Bioc-devel using 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=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg&s=ZoAsmfsXMbKVd97M8Gy9hqBAIKWHz07tGe4YkCtmlE8&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: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> <mailto:hpages using fredhutch.org <mailto:hpages using fredhutch.org>>
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> >
>
> --
> 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: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
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: hpages using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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