Sorry. I am wrong. The issue is not related to as.data.frame(). It seems to be related to DataFrame naming conflict between s4vectors and SparkR. Refer to https://issues.apache.org/jira/browse/SPARK-12148
From: Sun, Rui [mailto:rui....@intel.com] Sent: Wednesday, March 16, 2016 9:33 AM To: Alex Kozlov <ale...@gmail.com>; roni <roni.epi...@gmail.com> Cc: user@spark.apache.org Subject: RE: sparkR issues ? I have submitted https://issues.apache.org/jira/browse/SPARK-13905 and a PR for it. From: Alex Kozlov [mailto:ale...@gmail.com] Sent: Wednesday, March 16, 2016 12:52 AM To: roni <roni.epi...@gmail.com<mailto:roni.epi...@gmail.com>> Cc: Sun, Rui <rui....@intel.com<mailto:rui....@intel.com>>; user@spark.apache.org<mailto:user@spark.apache.org> Subject: Re: sparkR issues ? Hi Roni, you can probably rename the as.data.frame in $SPARK_HOME/R/pkg/R/DataFrame.R and re-install SparkR by running install-dev.sh On Tue, Mar 15, 2016 at 8:46 AM, roni <roni.epi...@gmail.com<mailto:roni.epi...@gmail.com>> wrote: Hi , Is there a work around for this? Do i need to file a bug for this? Thanks -R On Tue, Mar 15, 2016 at 12:28 AM, Sun, Rui <rui....@intel.com<mailto:rui....@intel.com>> wrote: It seems as.data.frame() defined in SparkR convers the versions in R base package. We can try to see if we can change the implementation of as.data.frame() in SparkR to avoid such covering. From: Alex Kozlov [mailto:ale...@gmail.com<mailto:ale...@gmail.com>] Sent: Tuesday, March 15, 2016 2:59 PM To: roni <roni.epi...@gmail.com<mailto:roni.epi...@gmail.com>> Cc: user@spark.apache.org<mailto:user@spark.apache.org> Subject: Re: sparkR issues ? This seems to be a very unfortunate name collision. SparkR defines it's own DataFrame class which shadows what seems to be your own definition. Is DataFrame something you define? Can you rename it? On Mon, Mar 14, 2016 at 10:44 PM, roni <roni.epi...@gmail.com<mailto:roni.epi...@gmail.com>> wrote: Hi, I am working with bioinformatics and trying to convert some scripts to sparkR to fit into other spark jobs. I tries a simple example from a bioinf lib and as soon as I start sparkR environment it does not work. code as follows - countData <- matrix(1:100,ncol=4) condition <- factor(c("A","A","B","B")) dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~ condition) Works if i dont initialize the sparkR environment. if I do library(SparkR) and sqlContext <- sparkRSQL.init(sc) it gives following error > dds <- DESeqDataSetFromMatrix(countData, as.data.frame(condition), ~ > condition) Error in DataFrame(colData, row.names = rownames(colData)) : cannot coerce class "data.frame" to a DataFrame I am really stumped. I am not using any spark function , so i would expect it to work as a simple R code. why it does not work? Appreciate the help -R -- Alex Kozlov (408) 507-4987<tel:%28408%29%20507-4987> (650) 887-2135<tel:%28650%29%20887-2135> efax ale...@gmail.com<mailto:ale...@gmail.com> -- Alex Kozlov (408) 507-4987 (650) 887-2135 efax ale...@gmail.com<mailto:ale...@gmail.com>
