Hey, Henrik
Thanks so much for your suggestion! Actually it is a disk problem, I use the
network hard driver to read and write then I have this error, although I
have the authority to read, write and create files in that driver. After I
set the directory to a local driver and move files to the new driver, there
isn't error at all.
I followed your suggestion to run the R codes. Here it is.
It looks like the test code works well, am I right?
> library("R.utils");
>
> path <- "Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1";
> print(path);
[1] "Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1"
>
> # Get file-system information about the directory
> str(file.info(path));
'data.frame': 1 obs. of 7 variables:
$ size : num 0
$ isdir: logi TRUE
$ mode :Class 'octmode' int 511
$ mtime: POSIXct, format: "2007-04-30 17:48:15"
$ ctime: POSIXct, format: "2007-04-27 23:00:44"
$ atime: POSIXct, format: "2007-04-27 23:00:44"
$ exe : chr "no"
>
> # Check access rights using plain R
> print(file.access(path, mode=0));
Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1
0
> print(file.access(path, mode=1));
Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1
0
> print(file.access(path, mode=2));
Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1
-1
> print(file.access(path, mode=4));
Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1
0
>
> # Check access rights using R.utils
> print(fileAccess(path, mode=0));
[1] 0
> print(fileAccess(path, mode=1));
[1] -1
Warning message:
In fileAccess.default(path, mode = 1) :
file.access() and file.info() gives different results for mode=1 (0 !=
-1). Will use the file.info() results.
> print(fileAccess(path, mode=2));
Y:/cchen/AS&Methy/probeData/tissues,RBC/HuGene-1_0-st-v1
-1
> print(fileAccess(path, mode=4));
[1] 0
>
> # More troubleshooting
> print(isDirectory(path));
[1] TRUE
> print(isFile(path));
[1] FALSE
>
> # Trying to create a file
> pathname <- file.path(path, "dummy.txt");
> cat(file=pathname, "Hello world!\n");
> str(file.info(pathname));
'data.frame': 1 obs. of 7 variables:
$ size : num 14
$ isdir: logi FALSE
$ mode :Class 'octmode' int 438
$ mtime: POSIXct, format: "2007-04-30 17:55:18"
$ ctime: POSIXct, format: "2007-04-30 17:48:15"
$ atime: POSIXct, format: "2007-04-30 17:48:15"
$ exe : chr "no"
> print(readLines(pathname));
[1] "Hello world!"
On Sat, Sep 4, 2010 at 6:25 PM, Henrik Bengtsson <henrik.bengts...@gmail.com
> wrote:
> 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/
>
--
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/
