Re: [Bioc-devel] Python package dependency loading problem on malbec1 builder

2020-01-28 Thread Pages, Herve 
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
>  
> 
> 
> 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 
> )
>  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  > 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$OS.type != "windows")
>         use_python(Sys.which("python3"), required=TRUE)
> 
> Then you can import the phate module:
> 
>     import("phate")
>     # Module(phate)
> 
> Successfully tested on malbec2, tokay2, and celaya2.
> 
> Hope this helps,
> H.
> 
> 
> On 12/26/19 17:49, William Chen wrote:
>  > Thanks for looking into this and confirming! Would appreciate any
>  > suggestions on how to correctly import the python module on malbec1.
>  >
>  > Best
>  > Will
>  > ᐧ
>  >
>  > On Mon, Dec 23, 2019 at 8:41 PM Pages, Herve
> mailto:hpa...@fredhutch.org>
>  > >> wrote:
>  >
>  >     Hi William,
>  >
>  >     I can confirm that the phate module is installed for Python 3 on
>  >     malbec1:
>  >
>  >     biocbuild@malbec1:~$ 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@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 "", line 1, in 
>  >     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

Re: [Bioc-devel] Python package dependency loading problem on malbec1 builder

2019-12-28 Thread Pages, Herve 
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  > wrote:
> 
> Hi William,
> 
> I can confirm that the phate module is installed for Python 3 on
> malbec1:
> 
> biocbuild@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@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 "", line 1, in 
> 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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg=0mydgs8zLKpjMbGeLEhBkhh8phXWfQi2pXPF431wR10=
>  >
>  > Thanks!
>  > Will
>  >
>  > ᐧ
>  >
>  >       [[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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg=ZoAsmfsXMbKVd97M8Gy9hqBAIKWHz07tGe4YkCtmlE8=
>  >
> 
> -- 
> 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
> 

-- 
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

Re: [Bioc-devel] Python package dependency loading problem on malbec1 builder

2019-12-23 Thread Pages, Herve 
Hi William,

I can confirm that the phate module is installed for Python 3 on malbec1:

biocbuild@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@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 "", line 1, in 
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_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg=0mydgs8zLKpjMbGeLEhBkhh8phXWfQi2pXPF431wR10=
> 
> Thanks!
> Will
> 
> ᐧ
> 
>   [[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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=F3I6u7a5ehHjXSCdocoJZt6QyxonF1Mr9yERW8nrkJg=ZoAsmfsXMbKVd97M8Gy9hqBAIKWHz07tGe4YkCtmlE8=
> 

-- 
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
___
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[Bioc-devel] Python package dependency loading problem on malbec1 builder

2019-12-22 Thread William Chen 
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://master.bioconductor.org/checkResults/3.10/bioc-LATEST/phemd/

Thanks!
Will

ᐧ

[[alternative HTML version deleted]]

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