Re: [Bioc-devel] HDF5Array/DelayedArray matrix operations fail on windows

2019-10-26 Thread Kevin Wang 
Dear Herve,

Thank you for your help. I did not manage the replicate the error on my Windows 
VM. However, I did comment out the only offending line of code which used 
parallelisation and manually set the BiocParallel backend to SerialParam during 
testthat and the error was gone. Thanks a lot for your help!

Best Wishes
Kevin
The University of Sydney

On 24 Oct 2019, at 4:28 am, Pages, Herve 
mailto:hpa...@fredhutch.org>> wrote:

Hi Kevin,

Running this particular code (e.g. the code in the test-sparsematrix.R
file) also works for me on our Windows builders. However, trying to run
the **full suite** of tests does trigger the error. So it seems to be a
situation where some code in some other tests is altering the state of
the session in a way that breaks the `scMerge()` calls in
test-hdf5array.R and test-sparsematrix.R.

I see that you use parallelization a lot. Could it be that some code at
some point alters the state of the current parallelization backend? All
these socketConnection() warnings makes me suspect that. This would also
explain why we only see the problem on Windows. Parallelization problems
are very platform specific and tend to occur more often on Windows where
backends like MulticoreParam are not supported.

Best,
H.


On 10/21/19 23:32, Kevin Wang wrote:
Hi, I am trying to make my package scMerge to be compatible with HDF5Array. 
While all the checks passed on Linux and Mac, it errored on Windows 
(https://protect-au.mimecast.com/s/-9LqC81Zj6tK3KPLtnsVJT?domain=urldefense.proofpoint.com
 ). Upon closer inspection, the failures seem to come a test for compatibility 
of HDF5Array
(the script can be viewed here 
https://protect-au.mimecast.com/s/VjnLC91ZkQtpnpN9FEm10J?domain=urldefense.proofpoint.com
 ). The error message was "non-numeric argument to binary operator” and calls 
to DelayedArray. I have tried to run this specific line on a Windows machine 
with Rtools35 installed and there was no error. A similar scenario occurred for 
sparse matrix 
(https://protect-au.mimecast.com/s/Z1HxC0YZWVFLvLgZh2bUev?domain=urldefense.proofpoint.com
 ) where the error was "'a' must be a numeric matrix”.

Any help is greatly appreciated.

Thank you
Best Wishes
Kevin
The University of Sydney

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--
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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Re: [Bioc-devel] HDF5Array/DelayedArray matrix operations fail on windows

2019-10-23 Thread Pages, Herve 
Hi Kevin,

Running this particular code (e.g. the code in the test-sparsematrix.R 
file) also works for me on our Windows builders. However, trying to run 
the **full suite** of tests does trigger the error. So it seems to be a 
situation where some code in some other tests is altering the state of 
the session in a way that breaks the `scMerge()` calls in 
test-hdf5array.R and test-sparsematrix.R.

I see that you use parallelization a lot. Could it be that some code at 
some point alters the state of the current parallelization backend? All 
these socketConnection() warnings makes me suspect that. This would also 
explain why we only see the problem on Windows. Parallelization problems 
are very platform specific and tend to occur more often on Windows where 
backends like MulticoreParam are not supported.

Best,
H.


On 10/21/19 23:32, Kevin Wang wrote:
> Hi, I am trying to make my package scMerge to be compatible with HDF5Array. 
> While all the checks passed on Linux and Mac, it errored on Windows 
> (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_scMerge_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=wQziv6_QxHSybX-rtoi3C555HFUVEY19GZ44tKr3knA=
>  ). Upon closer inspection, the failures seem to come a test for 
> compatibility of HDF5Array
> (the script can be viewed here 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SydneyBioX_scMerge_blob_master_tests_testthat_test-2Dhdf5array.R=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=MWdFZy6IM1p7JLqe93W5_OG0D4kf79BIJm12U2BDS78=
>  ). The error message was "non-numeric argument to binary operator” and calls 
> to DelayedArray. I have tried to run this specific line on a Windows machine 
> with Rtools35 installed and there was no error. A similar scenario occurred 
> for sparse matrix 
> (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SydneyBioX_scMerge_blob_master_tests_testthat_test-2Dsparsematrix.R=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=ACuxhvv3ZHIB1CXLN0gvFo7LDQmOnaeipbdnstyDdZo=
>  ) where the error was "'a' must be a numeric matrix”.
> 
> Any help is greatly appreciated.
> 
> Thank you
> Best Wishes
> Kevin
> The University of Sydney
> 
>   [[alternative HTML version deleted]]
> 
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> 

-- 
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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