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 <sshshoh1...@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.
>>
>>
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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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