Hi.
On Wed, Nov 10, 2010 at 12:58 AM, Elsa Chacko <elsa.cha...@gmail.com> wrote:
> 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.
That was a patch for R.utils 1.5.1 and you've already got R.utils
1.5.6. Using that code had no affect on your issue.
> But then i came across a Disk quota exceeded, which i guess is upto
> the sys admin to fix...
So that was the real cause.
Thanks for reporting back.
/Henrik
>
> 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.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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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