On Sat, Mar 23, 2013 at 2:29 PM, Uma Shankavaram <uma.shankava...@gmail.com> wrote: > Dear Henrik, > > Thanks for the prompt fix. I have re-installed the library from the > source("http://aroma-project.org/hbLite.R") > hbInstall("aroma.core") > > Yes, it is working now, but there is still a small glitch. > It is failing if I pass the verbose argument. > > e.g. > process(ae, verbose = log) > > gives an error: > at #01. process(ae, verbose = log) > - process() is in environment 'aroma.core' > > Error: Argument 'verbose' is not a vector: function
So, here 'log' probably equals base::log. Use verbose=TRUE (default) or a (negative) value, e.g. verbose=-10 (verbose=-20 shows more). Is there an (online?) example showing "process(ae, verbose = log)" that needs to be corrected? /Henrik >>>>>>>>>>>>>>>>>>>>>> > However, without verbose argument, gets the result. > process(ae) > Color maps: sqrt,yellow > Chip type: GenomeWideSNP_6.Full > Samples: GSM557940, GSM557941, GSM557942 > Aliases: GSM557940, GSM557941, GSM557942 > Color maps: sqrt,yellow > Chip type: GenomeWideSNP_6.Full > Samples: GSM557940, GSM557941, GSM557942 > Aliases: GSM557940, GSM557941, GSM557942 > [1] FALSE > > > Uma > > On Sat, Mar 23, 2013 at 5:05 PM, Henrik Bengtsson > <henrik.bengts...@aroma-project.org> wrote: >> >> I've fixed this. Running. >> >> source("http://aroma-project.org/hbLite.R") >> hbInstall("aroma.core") >> >> should fix this (you'll get aroma.core v2.8.3). Please let me know if >> this solved your problem. >> >> /Henrik >> >> PS. The problem appears when installing the R-forge binary of >> aroma.core (which in turn is due to temporary updates in R.rsp, which >> [is too much to explain]). I *think* this would only hit people who >> have R-forge setup in their getOption("repos") or install directly >> from R-forge, so most people would not be affected by this. I've >> updated hbInstall() to never install from R-forge. FYI, don't install >> from R-forge, because that contains my non-official under-construction >> and non-tested updates. >> >> >> On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson >> <henrik.bengts...@gmail.com> wrote: >> > I can reproduce this - very odd. I'll investigate a fix it. In the >> > meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g. >> > >> > install.packages("aroma.core", repos="@CRAN@") >> > install.packages("aroma.affymetrix", repos="@CRAN@") >> > >> > (Add repos="@CRAN@" to make sure not to install from other >> > repositories.) >> > >> > Thanks for the report, >> > >> > Henrik >> > >> > On Sat, Mar 23, 2013 at 10:16 AM, Uma Shankavaram >> > <uma.shankava...@gmail.com> wrote: >> >> Hello, >> >> >> >> I am using aroma.affymetrix_2.8.2 package using Windows version of R to >> >> process 4 SNP6.0 cel files. >> >> I am getting an error when trying to use this function. >> >> >> >> e.g. >> >> ae <- ArrayExplorer(csR) >> >> setColorMaps(ae, "sqrt,yellow") >> >> process(ae, verbose = log) >> >> ... >> >> Error: could not find function "process" >> >> >> >> Can anyone know why there is a problem? >> >> >> >> My R session info is: >> >>> sessionInfo() >> >> R version 2.15.1 (2012-06-22) >> >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> >> >> locale: >> >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> >> States.1252 LC_MONETARY=English_United States.1252 >> >> [4] LC_NUMERIC=C LC_TIME=English_United >> >> States.1252 >> >> >> >> attached base packages: >> >> [1] stats graphics grDevices utils datasets methods base >> >> >> >> other attached packages: >> >> [1] aroma.affymetrix_2.8.2 affxparser_1.30.2 aroma.apd_0.2.3 >> >> R.huge_0.4.2 aroma.light_1.24.0 >> >> [6] aroma.core_2.8.2 matrixStats_0.6.2 R.rsp_0.8.2 >> >> R.devices_2.1.3 R.cache_0.6.8 >> >> [11] R.filesets_2.0.1 R.utils_1.19.5 R.oo_1.13.0 >> >> R.methodsS3_1.4.2 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] digest_0.6.3 PSCBS_0.30.0 tools_2.15.1 >> >> >> >> >> >> Thanks >> >> >> >> Uma >> >> >> >> -- >> >> -- >> >> 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/groups/opt_out. >> >> >> >> >> >> -- >> -- >> 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/groups/opt_out. >> >> > > > > -- > Uma > > -- > -- > 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/groups/opt_out. > > -- -- 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/groups/opt_out.