File handles are not closed for backend pwiz

[jorainer]

Apparently, the file handles are not closed for backend = "pwiz":

library(mzR)
library(msdata)
f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_Erwinia")
for (i in 1:1000) {
    msd <- mzR::openMSfile(f, backend = "pwiz")
    mzR::close(msd)
}

Throws the error:

Error: failed opening file: Too many open files: unspecified iostream_category error

[lgatto]

@thirdwing - could you check this, please.

[thirdwing]

I think I know how to fix this, but I am really busy this week.

On 08/25/2016 04:43 AM, Laurent Gatto wrote:

@thirdwing https://github.com/thirdwing - could you check this, please.

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[lgatto]

If you could share your thoughts, I could try to have a look. Otherwise, next week is no problem at all. Thanks.

[jorainer]

@thirdwing @lgatto : I think I fixed it! I've implemented the close method for mzRpwiz objects (that did just return TRUE without doing anything). In the C++ code I implemented the close method to release all resources; there does not seem to be an explicit close function to be implemented in the pwiz code, so I think that's all what we can do. @thirdwing can you please check if that's similar to what you had in mind?
It's in pull request #49

With this I don't get the error message with too many open connections.

[lgatto]

I see you implemented the same as for the Ramp backend. Looks good to me. @thirdwing, any comment?

[thirdwing]

The problem is in
https://github.com/sneumann/mzR/blob/master/R/methods-mzRpwiz.R#L142

I don't know why I just put a placeholder for pwiz. We need to
explicitly call destructor or a close() method like
https://github.com/sneumann/mzR/blob/master/R/methods-mzRramp.R#L66

On 08/25/2016 02:43 PM, Laurent Gatto wrote:

I see you implemented the same as for the |Ramp| backend. Looks good
to me. @thirdwing https://github.com/thirdwing, any comment?

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[lgatto]

@thirdwing - and that's exactly what @jotsetung has done in #49, as far as I can see.

[thirdwing]

@jotsetung Sorry I missed your email.

@lgatto I think it is just what I thought.

[lgatto]

Great, thanks.

[jorainer]

sorry to post to the closed issue... I was just wondering who will then push the changes also to the Bioconductor svn (and when).

[lgatto]

I will, today.

[lgatto]

Done

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r120458 | l.gatto | 2016-08-26 08:40:19 +0100 (Fri, 26 Aug 2016) | 1 line

upgrade pwiz and close connection for pwiz backend