Hi,
let's troubleshoot this one. It may have to do with R having problems
retrieving the correct file access information from drives mounted on
(Samba?) network drives. We basically assert that there is write
access to directories before starting; this is done in order not to
create broken results but also in order to give more informative error
messages. In your case it seems that this test fails. The actual
tests are done by R and the R.utils package and has nothing to do with
the aroma framework. So, let try the below first and let me know what
the output is:
library("R.utils");
path <- "Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1";
print(path);
# Get file-system information about the directory
str(file.info(path));
# Check access rights using plain R
print(file.access(path, mode=0));
print(file.access(path, mode=1));
print(file.access(path, mode=2));
print(file.access(path, mode=4));
# Check access rights using R.utils
print(fileAccess(path, mode=0));
print(fileAccess(path, mode=1));
print(fileAccess(path, mode=2));
print(fileAccess(path, mode=4));
# More troubleshooting
print(isDirectory(path));
print(isFile(path));
# Trying to create a file
pathname <- file.path(path, "dummy.txt");
cat(file=pathname, "Hello world!\n");
str(file.info(pathname));
print(readLines(pathname));
Let me know what you get on all these. That should narrow down the issue.
/Henrik
On Fri, Sep 3, 2010 at 10:36 AM, chen chao <chench...@gmail.com> wrote:
> Hi, Henrik
> My working directory is "Y:/cchen/AS&Methy", so CDF file is in
> "Y:/cchen/AS&Methy/annotationData/chipTypes/HuGene-1_0-st-v1"
> and CEL files are at "Y:/cchen/AS&Methy/rawData/tissues/HuGene-1_0-st-v1/"
> The unwritable folder is
> "Y:\cchen\AS&Methy\probeData\tissues,RBC\HuGene-1_0-st-v1", I think it is
> going to save the background correction data. Although it exists, no files
> are created in that file.
>> getwd()
> [1] "Y:/cchen/AS&Methy"
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
> attached base packages:
> [1] stats graphics grDevices datasets grid utils methods
> base
> other attached packages:
> [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1
> matrixStats_0.2.1
> [8] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
> digest_0.4.2 GenomeGraphs_1.8.0 biomaRt_2.4.0
> FIRMAGene_0.9.5
> [15] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-3 tools_2.11.1 XML_3.1-1
>
> On Fri, Sep 3, 2010 at 11:02 AM, Henrik Bengtsson <h...@stat.berkeley.edu>
> wrote:
>>
>> Hi,
>>
>> Q1. What is your sessionInfo() when the error occurs.
>>
>> Q2. What is your working directories, i.e. what does print(getwd()) give?
>>
>> /Henrik
>>
>> On Fri, Sep 3, 2010 at 8:23 AM, AlexChen <chench...@gmail.com> wrote:
>> > Hi,
>> >
>> > I want to use FIRMAGene package (http://bioinf.wehi.edu.au/folders/
>> > firmagene/sup3_04feb2010.R) to analysis alternative splice in my data,
>> > but got a problem.
>> >
>> > here is my code:
>> >
>> > library(FIRMAGene)
>> > library(GenomeGraphs)
>> > library(aroma.affymetrix)
>> > verbose <- Arguments$getVerbose(-30); timestampOn(verbose)
>> > affxparser::convertCdf("./annotationData/chipTypes/HuGene-1_0-st-v1/
>> > HuGene-1_0-st-v1.cdf","./annotationData/chipTypes/HuGene-1_0-st-v1/
>> > HuGene-1_0-st-v1.cdf")
>> > cdf<-AffymetrixCdfFile$byChipType("HuGene-1_0-st-v1",verbose=verbose)
>> > cs<-AffymetrixCelSet$byName("tissues",cdf=cdf,verbose=verbose)
>> > bc <- RmaBackgroundCorrection(cs)
>> >
>> > #works well but...
>> > csBC <- process(bc,verbose=verbose)
>> > 20100903 09:54:16|Background correcting data set...
>> > Error in list(`process(bc, verbose = verbose)` = <environment>,
>> > `process.RmaBackgroundCorrection(bc, verbose = verbose)` =
>> > <environment>, :
>> >
>> > [2010-09-03 09:54:17] Exception: No write permission for directory:
>> > probeData/tissues,RBC/HuGene-1_0-st-v1
>> > at throw(Exception(...))
>> > at throw.default("No write permission for directory: ", path)
>> > at throw("No write permission for directory: ", path)
>> > at getWritablePathname.Arguments(static, file = "dummy-not-created",
>> > path = path, ...)
>> > at getWritablePathname(static, file = "dummy-not-created", path =
>> > path, ...)
>> > at method(static, ...)
>> > at Arguments$getWritablePath(path)
>> > at bgAdjustRma.AffymetrixCelSet(NA, path = "probeData/tissues,RBC/
>> > HuGene-1_0-st-v1", verbose = TRUE, overwrite = FALSE, subsetToUpdate =
>> > NULL, typesToUpdate = "pm", addJitter
>> > at bgAdjustRma(NA, path = "probeData/tissues,RBC/HuGene-1_0-st-v1",
>> > verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
>> > typesToUpdate = "pm", addJitter = FALSE, jitterSd
>> > at do.call("bgAdjustRma", args = args)
>> > at process.RmaBackgroundCorrection(bc, verbose = verbose)
>> > at process(bc, verbose = verbose)
>> > 20100903 09:54:17|Background correcting data set...done
>> >
>> > The folder "probeData/tissues,RBC/HuGene-1_0-st-v1" has been created,
>> > and indeed writable when I created one new txt file as a test. But the
>> > no written permission problem is still there. Any suggestions? Thanks
>> > so much.
>> >
>> > --
>> > 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
>> "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/
>
>
>
> --
> Chen, Chao
> Psychiatry
> University of Chicago
> 924 E 57th St, Chicago, IL 60637
> U. S. A.
> MOE Key Laboratory of Contemporary Anthropology and Center for
> Evolutionary Biology,
> School of Life Sciences and Institutes of Biomedical Sciences,
> Fudan University
> 220# Handan Road, Shanghai (200433)
> P.R.China
>
> --
> 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
"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/
