[Bioc-devel] rtracklayer::import.bed(genome = Seqinfo)

2019-10-22 Thread Bhagwat, Aditya 
Dear Michael,

Sorry for my incomplete email - the send button got hit too fast. Better this 
time.

rtracklayer::import.bed mentions the argument "genome" to be either a genome 
identifier (like 'mm10') or a Seqinfo object.

I notice that the second option does not work on my BED file (in attach).

# This works
rtracklayer::import.bed('SRF.bed', genome = 'mm10') # this works

# But this doesn't
seqinfo1<- 
GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
rtracklayer::import.bed('SRF.bed', genome = seqinfo1)

So I am requesting feedback.
I thought to use this channel

Aditya
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[Bioc-devel] (no subject)

2019-10-22 Thread Bhagwat, Aditya 
Dear Michael,

# This works
rtracklayer::import.bed('SRF.bed', genome = 'mm10') # this works

# But this doesn't
seqinfo1<- 
GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
rtracklayer::import.bed('SRF.bed', genome = seqinfo1)

# Neither does
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[Bioc-devel] HDF5Array/DelayedArray matrix operations fail on windows

2019-10-22 Thread Kevin Wang 
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 
(http://bioconductor.org/checkResults/3.10/bioc-LATEST/scMerge/). Upon closer 
inspection, the failures seem to come a test for compatibility of HDF5Array
(the script can be viewed here 
https://github.com/SydneyBioX/scMerge/blob/master/tests/testthat/test-hdf5array.R).
 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://github.com/SydneyBioX/scMerge/blob/master/tests/testthat/test-sparsematrix.R)
 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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