Re: [Bioc-devel] Something about time out errors

2017-03-27 Thread Dan Tenenbaum
- Original Message - > From: "Martin Morgan" > To: "Rainer Johannes" > Cc: "Aimin Yan" , "bioc-devel" > > Sent: Monday, March 27, 2017 12:29:49 PM > Subject: Re: [Bioc-devel] Something about time out errors > On 03/27/2017 12:57 PM, Rainer Johannes wrote: >> Do you have code fetching

Re: [Bioc-devel] Something about time out errors

2017-03-27 Thread Martin Morgan
On 03/27/2017 12:57 PM, Rainer Johannes wrote: Do you have code fetching data from web resources? I also sometimes get timeout errors on ensembldb and I guess it's because in some unit tests I'm fetching data from the ensembl ftp server. Testing web resources is a pretty interesting topic. I

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-27 Thread Michael Lawrence
Actually, I don't see where the package itself is loaded in the vignette. If it were, this error would not occur. Unsurprisingly, I get this when trying to run the vignette code: Warning message: In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found I noticed that pathprintGEOData

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-27 Thread Marcel Ramos
Hi Sokratis, You can resolve this issue by moving `SummarizedExperiment` to the Suggests field and including a `library(SummarizedExperiment)` call in your vignette. Best regards, Marcel On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis mailto:s.kario...@sheffield.ac.uk>> wrote: Hey,

Re: [Bioc-devel] Something about time out errors

2017-03-27 Thread Rainer Johannes
Do you have code fetching data from web resources? I also sometimes get timeout errors on ensembldb and I guess it's because in some unit tests I'm fetching data from the ensembl ftp server. jo > On 27 Mar 2017, at 18:37, Martin Morgan wrote: > > On 03/27/2017 12:22 PM, Aimin Yan wrote: >> I

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-27 Thread Michael Lawrence
I committed a fix into R trunk with a regression test. On Mon, Mar 27, 2017 at 8:41 AM, Michael Lawrence wrote: > My bad guys, I'll fix when I get to work. > > On Mon, Mar 27, 2017 at 3:59 AM, Martin Morgan > wrote: >> On 03/22/2017 01:12 PM, Hervé Pagès wrote: >>> >>> Hi Martin, >>> >>> On 03/2

Re: [Bioc-devel] Something about time out errors

2017-03-27 Thread Martin Morgan
On 03/27/2017 12:22 PM, Aimin Yan wrote: I am submitting a R package to bioconductor. but I got time out errors when I performed R CMD check. Is there a possible way that I can set up time to allow more time for R CMD check? Or I have to use examples that they do not cost large time. Submitte

[Bioc-devel] Something about time out errors

2017-03-27 Thread Aimin Yan
I am submitting a R package to bioconductor. but I got time out errors when I performed R CMD check. Is there a possible way that I can set up time to allow more time for R CMD check? Or I have to use examples that they do not cost large time. Thank you for your help Aimin [[alternati

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-27 Thread Michael Lawrence
My bad guys, I'll fix when I get to work. On Mon, Mar 27, 2017 at 3:59 AM, Martin Morgan wrote: > On 03/22/2017 01:12 PM, Hervé Pagès wrote: >> >> Hi Martin, >> >> On 03/22/2017 03:17 AM, Martin Maechler wrote: Andrzej Oleś on Wed, 22 Mar 2017 10:29:57 +0100 writes

[Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-27 Thread Sokratis Kariotis
Hey, I have submitted the package pathprintGEOData, which got accepted, but the build/check report is now producing the following error: *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics: chunk 1 Error in assays(result) : could not find function "assays"* *assays

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-27 Thread Martin Morgan
On 03/22/2017 01:12 PM, Hervé Pagès wrote: Hi Martin, On 03/22/2017 03:17 AM, Martin Maechler wrote: Andrzej Oleś on Wed, 22 Mar 2017 10:29:57 +0100 writes: > Just for the record, on R-3.3.2 Herve's code fails with the following error: > Error in x[TRUE] <- new("A") : > incom