Thank you so much--Number 1 was indeed the issue. I truly appreciate your
quick response.
Best,
KMS
On Monday, December 18, 2017 at 10:49:06 PM UTC-6, Henrik Bengtsson wrote:
>
> 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
>
> On Mon, Dec 18, 2017 at 3:25 PM, Karyn Meltz Steinberg
> <karyn.s...@gmail.com <javascript:>> wrote:
> > 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
> >
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