And also,
For process(ae) getting warning messages(pls see below) it seems to be related with next command lines it does not matter? could you please take a closer look at these as well? curent sessionInfo is R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.rsp_0.19.3 aroma.light_2.0.0 matrixStats_0.10.0 [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 [7] R.filesets_2.6.0 R.utils_1.33.7 R.oo_1.18.2 [10] affxparser_1.36.0 R.methodsS3_1.6.1 loaded via a namespace (and not attached): [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4 DNAcopy_1.38.1 [5] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 tools_3.1.1 > > process(ae) Loading required package: R.rsp R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. Attaching package: ‘R.rsp’ The following object is masked from ‘package:aroma.affymetrix’: getParameter The following objects are masked from ‘package:aroma.core’: getParameters, process, write The following objects are masked from ‘package:R.filesets’: getAttribute, getAttributes, getFile, getFileSize, getHeader, nbrOfLines, setAttribute, setAttributes The following objects are masked from ‘package:R.utils’: parse, parse.default The following objects are masked from ‘package:base’: flush, parse, stop, write The following object is masked _by_ package:aroma.affymetrix: writeCdf The following object is masked _by_ package:R.utils: findFiles 20140920 19:48:32|Color maps: 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ 5_(RaGene-1_0-st-v1),residuals 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) 20140920 19:48:47|Color maps: 20140920 19:48:47|Chip type: RaGene-1_0-st-v1,r3 20140920 19:48:54|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ 5_(RaGene-1_0-st-v1),residuals 20140920 19:48:54|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) [1] FALSE Warning messages: 1: In fcn(...) : Packages reordered in search path: package:affxparser 2: In parseRepos(sets = repos, where = where, fallback = fallback, : Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’ 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = aliases, : No color maps specified. Nothing to do. 5: In parseRepos(sets = repos, where = where, fallback = fallback, : Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’ 6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' Many Thanks! Sunghee 2014년 9월 20일 토요일 오후 7시 58분 39초 UTC+9, jjspring OH 님의 말: > > > > > Thanks Henrik, > > Yes, There is no error message on the command line display(ae) but when i > open up the file under the directory (/results ... .html) with safari > Its not working and the result is not shown, > I have attached screen image file to show up, Could you please take a look > at and doublecheck? > > > Thanks a lot > > Sunghee > > > > > > > > 2014년 9월 20일 토요일 오전 8시 3분 52초 UTC+9, Henrik Bengtsson 님의 말: >> >> On Fri, Sep 19, 2014 at 8:24 AM, Henrik Bengtsson <h...@biostat.ucsf.edu> >> wrote: >> > Sorry, it took me a while to spot the actual problem; >> > >> >> display(ae) >> >> The file >> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html >> does not exist. >> > >> > (I'm surprised there is no "error" or similar generated, but it could >> > be because that message is from an external software). >> > >> > You can always open the HTML report manually just like any other HTML >> > file. You'll find it at reports\tissues/RBC,QN,RMA/ArrayExplorer.html >> > under your working directory. >> > >> > I'll investigate and fix this. >> >> It was a bug in aroma.core making display() only opening Explorer HTML >> pages on Windows. I've fixed this in aroma.core 2.12.8 and verified >> that it works on OSX. Update to via: >> >> source("http://callr.org/install#aroma.affymetrix") >> >> Thanks for reporting >> >> Henrik >> >> > >> > /Henrik >> > >> > >> > >> > On Wed, Sep 17, 2014 at 5:50 PM, jjspring OH <sshsh...@gmail.com> >> wrote: >> >> >> >> Hi, >> >> >> >> >> >> I am getting errors when i run aroma.affymetrix package for dynamic >> reports, >> >> it looks like for low level analysis, everything works well for now, >> >> Could you please take a closer look at and let me know what the >> problem is? >> >> I am running under the current directory(/foo/arom-anal/) >> >> >> >> >> >>> process(ae) >> >> Loading required package: R.rsp >> >> R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. >> >> >> >> Attaching package: ‘R.rsp’ >> >> >> >> The following object is masked from ‘package:aroma.affymetrix’: >> >> >> >> getParameter >> >> >> >> The following objects are masked from ‘package:aroma.core’: >> >> >> >> getParameters, process, write >> >> >> >> The following objects are masked from ‘package:R.filesets’: >> >> >> >> getAttribute, getAttributes, getFile, getFileSize, getHeader, >> >> nbrOfLines, setAttribute, setAttributes >> >> >> >> The following objects are masked from ‘package:R.utils’: >> >> >> >> parse, parse.default >> >> >> >> The following objects are masked from ‘package:base’: >> >> >> >> flush, parse, stop, write >> >> >> >> The following object is masked _by_ package:aroma.affymetrix: >> >> >> >> writeCdf >> >> >> >> The following object is masked _by_ package:R.utils: >> >> >> >> findFiles >> >> >> >> 20140918 09:43:05|Color maps: >> >> 20140918 09:43:05|Chip type: RaGene-1_0-st-v1,r3 >> >> 20140918 09:43:12|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ >> >> 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, >> CS _ >> >> 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, >> NS _ >> >> 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, >> NS _ >> >> 5_(RaGene-1_0-st-v1),residuals >> >> 20140918 09:43:12|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ >> >> 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ >> 8_(RaGene-1_0-st-v1), >> >> NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ >> >> 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) >> >> 20140918 09:43:20|Color maps: >> >> 20140918 09:43:20|Chip type: RaGene-1_0-st-v1,r3 >> >> 20140918 09:43:27|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ >> >> 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, >> CS _ >> >> 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, >> NS _ >> >> 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, >> NS _ >> >> 5_(RaGene-1_0-st-v1),residuals >> >> 20140918 09:43:27|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ >> >> 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ >> 8_(RaGene-1_0-st-v1), >> >> NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ >> >> 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) >> >> [1] FALSE >> >> Warning messages: >> >> 1: In fcn(...) : Packages reordered in search path: package:affxparser >> >> 2: In parseRepos(sets = repos, where = where, fallback = fallback, : >> >> Had to fall back to a set of predefined repositories (please make >> sure to >> >> set your package repositories properly, cf. ?setRepositories): CRAN: >> >> ‘@CRAN@’ -> ‘http://cran.r-project.org’ >> >> 3: In is.na(x) : is.na() applied to non-(list or vector) of type >> 'NULL' >> >> 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = >> >> aliases, : >> >> No color maps specified. Nothing to do. >> >> 5: In parseRepos(sets = repos, where = where, fallback = fallback, : >> >> Had to fall back to a set of predefined repositories (please make >> sure to >> >> set your package repositories properly, cf. ?setRepositories): CRAN: >> >> ‘@CRAN@’ -> ‘http://cran.r-project.org’ >> >> 6: In is.na(x) : is.na() applied to non-(list or vector) of type >> 'NULL' >> >>> display(ae) >> >>> The file >> >>> >> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html >> >>> does not exist. >> >> >> >> >> >> Thanks a lot in advance, >> >> >> >> Sunghee >> >> >> >> -- >> >> -- >> >> 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-af...@googlegroups.com >> >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ >> >> >> >> --- >> >> You received this message because you are subscribed to the Google >> Groups >> >> "aroma.affymetrix" group. >> >> To unsubscribe from this group and stop receiving emails from it, send >> an >> >> email to aroma-affymetr...@googlegroups.com. >> >> For more options, visit https://groups.google.com/d/optout. >> > -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.