Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

Thanks for checking; minfi reads some (but not this exact one) of these IDATs as part of the build process. On Mon, Apr 11, 2016 at 8:18 PM, Henrik Bengtsson < henrik.bengts...@gmail.com> wrote: > No worries. Glad to hear it WS just a hiccup. > > Henrik > On Apr 11, 2016 4:53 PM, "Dan Tenenbaum"

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

No worries. Glad to hear it WS just a hiccup. Henrik On Apr 11, 2016 4:53 PM, "Dan Tenenbaum" wrote: > I upgraded to r70462 and I cannot reproduce it now either. I guess it was > an issue in R-alpha, since fixed. > Sorry for the trouble. > > Dan > > > - Original

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

I upgraded to r70462 and I cannot reproduce it now either. I guess it was an issue in R-alpha, since fixed. Sorry for the trouble. Dan - Original Message - > From: "Henrik Bengtsson" > To: "Dan Tenenbaum" > Cc: "Maarten van Iterson"

Re: [Bioc-devel] import except on Window Machine

On Mon, Apr 11, 2016 at 2:54 PM, Hervé Pagès wrote: > Hi Michael, > > On 04/11/2016 01:23 PM, Michael Lawrence wrote: >> >> Yes, you're right, sorry. I didn't realize that the generic is always >> exported from a package defining methods on the generic. > > > What's the

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

I'm not an OS X user, but two things you might look into/help you troubleshoot: 1. Because you said it only happens when you try to overwrite an existing PDF, could it be that there is another process holding onto (=locking) the PDF file that you're trying to write to? For instance, are you

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

I *cannot* reproduce this: % R --vanilla ## The IDAT file > pathname <- system.file(package="minfiData", "extdata", "5723646053", > "5723646053_R05C02_Grn.idat") > file.info(pathname)$size [1] 8091452 > unname(tools::md5sum(pathname)) [1] "dfc33fdaf3e91d872be896643a0c837f" >

Re: [Bioc-devel] import except on Window Machine

Hi Michael, On 04/11/2016 01:23 PM, Michael Lawrence wrote: Yes, you're right, sorry. I didn't realize that the generic is always exported from a package defining methods on the generic. What's the rationale behind this feature? It seems to be a recurrent source of surprise and confusion. In

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

Dear Wolfgang, Thanks for your response. No, I haven't tried doing the complete reinstallation as you suggest. If I recall correctly, this has happened on previous occasions but like I said in my email it's not all that disruptive to my workflow. It's more like a 'first world problem'. I was

Re: [Bioc-devel] Using Git with Bioconductor SVN repositories

>From your git log excerpt it looks like there has been some non-linear commit >history. svn does not like this. You may need to follow the instructions here: https://www.bioconductor.org/developers/how-to/git-mirrors/#dealing-with-prior-history--merge-conflicts Dan - Original Message

Re: [Bioc-devel] package submission - problem with vignette

Dear Dan, Many thanks, apparently I just had to update one of the knitr-associated components. I hope it will go through now. Many thanks again and enjoy your evening, Lara 2016-04-11 17:39 GMT+01:00 Dan Tenenbaum : > > > - Original Message - > > From: "Dan

Re: [Bioc-devel] import except on Window Machine

Michael, Thanks for confirming! Best, Julie On 4/11/16 4:23 PM, "Michael Lawrence" wrote: >Yes, you're right, sorry. I didn't realize that the generic is always >exported from a package defining methods on the generic. That can make >the exceptions more difficult

Re: [Bioc-devel] import except on Window Machine

Yes, you're right, sorry. I didn't realize that the generic is always exported from a package defining methods on the generic. That can make the exceptions more difficult to maintain. A better syntax for this case might have been: import(cranPackage, override=values) But we have to live with

Re: [Rd] Understanding POSIXct creation on different OSes.

Bumping this up to the front again ... because it exhibits a difference in behaviour of R across OSs. Such a 'feature' may not be desirable. On 4 April 2016 at 18:00, Arunkumar Srinivasan wrote: | Hello, | | Following Dirk's post here: https://github.com/Rdatatable/data.table/issues/1619 | we

Re: [Bioc-devel] import except on Window Machine

Thanks Michael! FYI, I would get a warning message if I did not use import(IRanges, except=values). Best, Julie On 4/11/16 2:40 PM, "Michael Lawrence" wrote: >On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum >wrote: >> In that output you

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

Dear Neil Have you tried with completely uninstalling your R, and reinstalling a more recent version (e.g. 3.2.4 right now). And then the same with your operating system - OS X is currently at 10.11.4. There is likely not much interest (or benefit) in chasing such things in obsolete versions.

Re: [Bioc-devel] import except on Window Machine

On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum wrote: > In that output you sent me, it's still using roxygen (via devtools) to create > the namespace. Try creating it manually and see if you still get the same > error. > > What does your NAMESPACE look like anyway? > >

Re: [Bioc-devel] import except on Window Machine

In that output you sent me, it's still using roxygen (via devtools) to create the namespace. Try creating it manually and see if you still get the same error. What does your NAMESPACE look like anyway? Looking at the NAMESPACE for CRISPRseek, the instances of the 'except' syntax look like

Re: [Bioc-devel] import except on Window Machine

# ##BUILT & RELOAD ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer * installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ ERROR: failed to lock directory ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for modifying Try

Re: [Bioc-devel] import except on Window Machine

Dear Karim, I edit NAMESPACE manually and here is my R sessionInfo. R Under development (unstable) (2016-04-03 r70416) Platform: x86_64-apple-darwin12.5.0 (64-bit) Running under: OS X 10.8.5 (Mountain Lion) Best regards, Julie From: Karim Mezhoud

Re: [Bioc-devel] import except on Window Machine

roxygen2 does not support the new syntax. Do you still get the same error if you write your NAMESPACE manually? - Original Message - > From: "Karim Mezhoud" > To: "Dan Tenenbaum" > Cc: "Lihua Zhu" , "Michael Lawrence"

Re: [Bioc-devel] import except on Window Machine

> sessionInfo() R version 3.3.0 beta (2016-04-06 r70435) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.3 (El Capitan) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum wrote:

Re: [Bioc-devel] import except on Window Machine

Karim, What is the sessionInfo() in your R-3.3? It might be too old to have the new feature. It needs to be at svn rev r70426 or newer. Dan - Original Message - > From: "Karim Mezhoud" > To: "Lihua Zhu" > Cc: "Dan Tenenbaum"

Re: [Bioc-devel] import except on Window Machine

Dear Julie, Are you using roxigen2 to edit NAMESPACE file? Are you using R 3.4? Thanks In my case, When I used R 3.3 I get this error: ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer * installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ *

[Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

Dear colleagues, I wish to report a problem I encounter when trying to save a graphic to file. When I produce a graphic and try to save it R becomes unresponsive and I must force quit, and then restart R. The problem occurs when I try to overwrite an existing graphic: for example when I made

Re: [Bioc-devel] import except on Window Machine

Thanks, Dan! Best, Julie On 4/11/16 12:22 PM, "Dan Tenenbaum" wrote: >The windows machine is still running an older version of R that does not >support this NAMESPACE syntax. I will update it this week. >Dan > > >- Original Message - >> From: "Lihua Zhu"

Re: [Bioc-devel] package submission - problem with vignette

It means that when you run R CMD build YourPackageName, the vignette is not built. It simply looks in the output of R CMD build for a line that starts: * creating vignettes ... If this line is present, it means `R` has not detected that a vignette needs to be built. It's `REQUIRED` that

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

The problem seems to have to do with illuminaio and possibly minfiData; it can be reduced to / reproduced by the following: library(illuminaio) file <- "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat" illuminaio:::readIDAT_nonenc(file) Specifically

Re: [Bioc-devel] import except on Window Machine

The windows machine is still running an older version of R that does not support this NAMESPACE syntax. I will update it this week. Dan - Original Message - > From: "Lihua Zhu" > To: "bioc-devel" > Cc: "Michael Lawrence"

[Bioc-devel] import except on Window Machine

Michael, For some reason, adding except clause in import in the NAMESPACE file gives error on window server, although it runs fine on Linux and Mac OS X. http://bioconductor.org/checkResults/devel/bioc-LATEST/CRISPRseek/moscato2-buildsrc.html Here is the line that gives error.

[Bioc-devel] package submission - problem with vignette

Dear BiocDevel, I have a question regarding the submission of my package; thank you very much in advance. I have submitted my package to Bioconductor a few days ago and it passed build, check and bioccheck. Now, that I had to change just one line in my R code and submitted it again, I get an

Re: [Bioc-devel] mascato2 check error

- Original Message - > From: "Karim Mezhoud" > To: "bioc-devel" > Sent: Monday, April 11, 2016 5:52:43 AM > Subject: [Bioc-devel] mascato2 check error > Dear BioC devel, > I did not understand the following error check message. >

Re: [R-pkg-devel] [R-SIG-Finance] [VC++ calling R] How to create a real-time interactive ticking time-series chart using dygraph via RInside?

Please choose *one* _relevant_ mailing list. Spamming 5 (!) mailing lists fragments the conversation and makes things difficult for everyone involved. On Mon, Apr 11, 2016 at 10:03 AM, Mike Deanza wrote: > Hi all, > > > I am trying to figure out how to do this in R

Re: [Rd] [R-SIG-Finance] [VC++ calling R] How to create a real-time interactive ticking time-series chart using dygraph via RInside?

Please choose *one* _relevant_ mailing list. Spamming 5 (!) mailing lists fragments the conversation and makes things difficult for everyone involved. On Mon, Apr 11, 2016 at 10:03 AM, Mike Deanza wrote: > Hi all, > > > I am trying to figure out how to do this in R

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

> Ravi Varadhan > on Mon, 11 Apr 2016 12:42:35 + writes: > all.equal.eigen() should also accommodate complex vectors, right? > Ravi Yes, definitely. The ?eigen help page does nicely mention that in the complex the eigen vectors are even less

[Bioc-devel] mascato2 check error

Dear BioC devel, I did not understand the following error check message. http://www.bioconductor.org/checkResults/3.3/bioc-LATEST/canceR/moscato2-checksrc.html Any suggestion is welcome. Thank you Karim ### Running command: ### ### rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

all.equal.eigen() should also accommodate complex vectors, right? Ravi From: R-devel on behalf of Martin Maechler Sent: Monday, April 11, 2016 3:08 AM To: William Dunlap Cc: r-devel; Jeroen Ooms

[Bioc-devel] moscato2 Windows build error reading IDAT file

Dear all, My package MethylAid does not pass check on moscato2. I got "Error in while (m%/%128 == 1) { : argument is of length zero Calls: summarize ... readIDAT_nonenc -> lapply -> FUN -> readField -> readString" the summarize function calls read.metharray.exp from minfi which calls

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

> William Dunlap via R-devel > on Mon, 4 Apr 2016 12:26:38 -0700 writes: >> If I recall correctly, some eigen vectors had their >> direction flipped (negative values became positive and >> vice versa). Did you notice anything of this kind when