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.
?
On Sat, Dec 28, 2019 at 1:26 PM Pages, Herve <hpages at fredhutch.org
<mailto:hpages at 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$OS.type != "windows")
? ? ? ?use_python(Sys.which("python3"), required=TRUE)
Then you can import the phate module:
? ?import("phate")
? ?# Module(phate)
Successfully tested on malbec2, tokay2, and celaya2.
Hope this helps,
H.
On 12/26/19 17:49, William Chen wrote:
> Thanks for looking into this and confirming! Would appreciate any
> suggestions on how to correctly import the python module on malbec1.
>
> Best
> Will
> ?
>
> On Mon, Dec 23, 2019 at 8:41 PM Pages, Herve
<hpages at fredhutch.org <mailto:hpages at fredhutch.org>
> <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>> wrote:
>
>? ? ?Hi William,
>
>? ? ?I can confirm that the phate module is installed for Python 3 on
>? ? ?malbec1:
>
>? ? ?biocbuild at malbec1:~$ 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 at 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
>? ? ? >
>? ? ? > ?
>? ? ? >
>? ? ? >? ? ? ?[[alternative HTML version deleted]]
>? ? ? >
>? ? ? > _______________________________________________
>? ? ? > Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at 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=
>? ? ? >
>
>? ? ?--
>? ? ?Herv? Pag?s
>
>? ? ?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 at fredhutch.org <mailto:hpages at fredhutch.org>
<mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
>? ? ?Phone:? (206) 667-5791
>? ? ?Fax:? ? (206) 667-1319
>
--
Herv? Pag?s
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 at fredhutch.org <mailto:hpages at fredhutch.org>
Phone:? (206) 667-5791
Fax:? ? (206) 667-1319
Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319