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.
You received this message because you are subscribed to the Google Groups
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