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. >> >> > You received this message because you are subscribed to the Google Groups >> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go tohttp://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/ > -- 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/