Hi Henrik,
Thanks for the help. I fixed the issue by running the fileAccess patch
available at http://www.braju.com/R/patches/R.utils/20100905/fileAccess.R.
But then i came across a Disk quota exceeded, which i guess is upto
the sys admin to fix...
Thanks again..
Regards
Elsa
On Nov 10, 4:50 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi,
>
> the fileAccess() write-permission test actually tries to write a small
> file to the directory to assert you have write permission to it. It
> seems like it cannot create a file and write to it in that directory.
> That provides an additional test on top of what file.access() does.
> (The filename 'K' is randomly generated, hence
> probeData/tissues,coreR2,QN/K in that error message).
>
> Q1. Are you sure you're not out of disk space?
>
> Q2. If you start a new R session, does the following work?
>
> path <- "/home/elsa/probeData/tissues,coreR2,QN";
> pathname <- file.path(path, "dummy.txt");
> cat("Hello world!", file=pathname);
>
> str(file.info(pathname));
> print(readLines(pathname));
>
> /Henrik
>
> PS. Independent of the above, you probably want to use tag="*,coreR2"
> instead of tag="coreR2" in order for the tags to reflect what steps
> have been made.
>
>
>
> On Tue, Nov 9, 2010 at 9:10 PM, Elsa Chacko <elsa.cha...@gmail.com> wrote:
> > $byChipType(chipType)
> > print(cdf)
> > cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
> > print(cs)
> > bc <- RmaBackgroundCorrection(cs, tag="coreR2")
> > csBC <- process(bc,verbose=verbose)
> > qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> > print(qn)
> > csN <- process(qn, verbose=verbose)
>
> > I get stuck at this point. I keep gettng an error
> > [2010-11-10 09:16:33] Exception: No write permission for directory:
> > probeData/tissues,coreR2,QN
> > at throw(Exception(...))
> > at throw.default("No write permission for directory: ", path)
> > at throw("No write permission for directory: ", path)
> > at method(static, ...)
> > at Arguments$getWritablePathname(path)
> > at normalizeQuantile.AffymetrixCelFile(df, path = path,
> > subsetToUpdate = subse
> > at normalizeQuantile(df, path = path, subsetToUpdate =
> > subsetToUpdate, typesTo
> > at normalizeQuantile.AffymetrixCelSet(NA, path = "probeData/tissues,
> > at normalizeQuantile(NA, path = "probeData/tissues,coreR2,QN/HuEx-1_
> > at do.call("normalizeQuantile", args = args)
> > at process.QuantileNormalization(qn, verbose = verbose)
> > at process(qn, verbose = verbose)
> > In addition: Warning messages:
> > 1: In writeBin(con = con, rawAll) : problem writing to connection
> > 2: In writeBin(con = con, rawAll) : problem writing to connection
> > 3: In fileAccess.default(pathT, mode = 2) :
> > file.access(..., mode=2) and file(..., open="ab") gives different
> > results (0 != -1). Will use the file() results: probeData/
> > tissues,coreR2,QN/K
> > 20101110 09:17:22| Array #2...done
> > 20101110 09:17:22| Normalizing 30 arrays...done
> > 20101110 09:17:22| Normalizing data towards target distribution...done
> > 20101110 09:17:22|Quantile normalizing data set...done
>
> > I did get a similar error for csBC <- process(bc,verbose=verbose), but
> > i fixed it by giving universal write permission n the probeData
> > folder. But this didn't work for csN <- process(qn, verbose=verbose).
>
> >> sessionInfo()
> > R version 2.10.1 (2009-12-14)
> > x86_64-pc-linux-gnu
>
> > locale:
> > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
> > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
> > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
> > [9] LC_ADDRESS=C LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
>
> > other attached packages:
> > [1] Biobase_2.6.1 aroma.affymetrix_1.7.3 aroma.apd_0.1.7
> > [4] affxparser_1.18.0 R.huge_0.2.0 aroma.core_1.7.4
> > [7] aroma.light_1.18.2 matrixStats_0.2.2 R.rsp_0.4.0
> > [10] R.cache_0.3.0 R.filesets_0.9.0 digest_0.4.2
> > [13] R.utils_1.5.6 R.oo_1.7.4 affy_1.24.2
> > [16] R.methodsS3_1.2.1
>
> > loaded via a namespace (and not attached):
> > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.1
>
> >> traceback()
> > No traceback available
>
> > I did follow a previous forum message regarding a similar problem and
> > get the following outputs.
>
> >> library("R.utils");
> [snip]
> >> path <- "/home/elsa/probeData/tissues,coreR2,QN"
> >> print(path)
> > [1] "/home/elsa/probeData/tissues,coreR2,QN"
> >> str(file.info(path));
> > 'data.frame': 1 obs. of 10 variables:
> > $ size : num 3
> > $ isdir : logi TRUE
> > $ mode :Class 'octmode' int 1535
> > $ mtime : POSIXct, format: "2010-11-10 09:15:13"
> > $ ctime : POSIXct, format: "2010-11-10 09:16:37"
> > $ atime : POSIXct, format: "2010-11-10 09:16:37"
> > $ uid : int 341178
> > $ gid : int 341178
> > $ uname : chr "elsa"
> > $ grname: chr "elsa"
> >> print(file.access(path, mode=0));
> > /home/elsa/probeData/tissues,coreR2,QN
> > 0
> >> print(file.access(path, mode=1));
> > /home/elsa/probeData/tissues,coreR2,QN
> > 0
> >> print(file.access(path, mode=2));
> > /home/elsa/probeData/tissues,coreR2,QN
> > 0
> >> print(file.access(path, mode=4));
> > /home/elsa/probeData/tissues,coreR2,QN
> > 0
> >> print(fileAccess(path,mode=0));
> > [1] 0
> >> print(fileAccess(path,mode=1));
> > [1] 0
> >> print(fileAccess(path,mode=2));
> > [1] -1
> > Warning message:
> > In fileAccess.default(path, mode = 2) :
> > file.access(..., mode=2) and file(..., open="ab") gives different
> > results (0 != -1). Will use the file() results: /home/elsa/probeData/
> > tissues,coreR2,QN/B
> >> print(fileAccess(path,mode=4));
> > [1] 0
>
> >> print(isDirectory(path));
> > [1] TRUE
> >> print(isFile(path));
> > [1] FALSE
>
> > Looks like R.util does not have write permissions on the folder. I am
> > just not sure how i ca fix this problem.
>
> > Any help is very much appreciated.
>
> > Regards
> > Elsa Chacko
> > PhD student
> > Macquarie University
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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