Error writing to connection

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Karyn Meltz Steinberg

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Dec 18, 2017, 6:25:50 PM12/18/17
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Hello,

I am running doCRMAv2 on 8 CytoScanHD .CEL files. I get the following error in the  CRMAv2/Export to technology-independent data files...
step:

Error in base_save(file = fh, object, compress = compress, ...) :
  error writing to connection
In addition: Warning message:
In readRDS(con) : error reading from connection
          Saving to file cache...done
         Getting (unit, group, cell) map...done
        Extracting (total, freqB)...done
       Reading data...done
      Exporting CnChipEffectFile as an AromaUnitTotalCnBinaryFile...done
     Exporting (total, fracB) data...done
    Array #1 ('GBD-035') of 8...done
   Exporting CnChipEffectSet as AromaUnitTotalCnBinarySet...done

I have enough space on the disk and the correct permissions. I am running version 3.1.0 on R3.4.0. Any advice would be greatly appreciated

Best,
Karyn

Henrik Bengtsson

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Dec 18, 2017, 11:49:06 PM12/18/17
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Hi. From your verbose output, I think two things can have happened:

1. This error happens when it tries to write to the file cache, which
is located under ~/.Rcache/. It could be that this cache is using up
your home drive/folder/account. Not sure what OS you're on, but to
find where `~` is use `normalizePath("~"). If that is indeed full,
and you're on Unix/macOS, the easiest is to simply point `~/.Rcache/`
to another drive via symbol links, e.g. `mkdir -p /scratch/$USER; mv
~/.Rcache /scratch/$USER/; ln -s /scratch/$USER/ ~/.Rcache`.

2. Alternatively, it could just be a hiccup on your system, which
means you can just rerun the script (it should quickly skip everything
already processed in previous runs).

I think (1) is the most likely reason, because the error is in
`base_save(file = fh, object, compress = compress, ...)` which happens
after two very similar calls to the same file which did _not_ fail,
cf. https://github.com/HenrikBengtsson/R.cache/blob/0.12.0/R/saveCache.R#L111.
(I'll see if I can add a more informative error message in a future
version of R.cache, e.g. including the problematic filename.)

Hope this helps

Henrik
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Karyn Meltz Steinberg

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Dec 19, 2017, 12:38:27 PM12/19/17
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Thank you so much--Number 1 was indeed the issue. I truly appreciate your quick response.

Best,
KMS
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