Re: [Rd] Very hard to reproduce bug (?) in R-devel

> > >> I've done some more investigation into the problem, and it is very difficult to pin down. What it looks like is happening is roughly like this: - `p` is an environment and `p$e` is also an environment. - There is a loop. In each iteration, it looks for one item in `p$e`, saves it in a

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Sorry I have been traveling. Will get to it soon. On Apr 4, 2017 12:58 PM, "Rainer Johannes" wrote: > Hi Herve, > > sorry for all the reds - actually I provided the patches to biovizBase and > ggbio, but it did not work out that smoothly that I hoped. For the other >

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Hi Herve, sorry for all the reds - actually I provided the patches to biovizBase and ggbio, but it did not work out that smoothly that I hoped. For the other packages that depend on ensembldb there's no problem or only small changes required (did contact the developers). Fingers crossed that

Re: [Bioc-devel] Check error on malbec2

Thank you, I changed to use tempdir(), and it works now. One more question is how to locate those outputs in temporary directory since I want users to use those outputs. Aimin On Tue, Apr 4, 2017 at 2:00 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Write and access your output

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Hi Johannes, This move is generating a lot of red today on the build report. Hopefully biovizBase and ggbio can be fixed quickly. Note that maybe a smoother path would have been to notify the maintainers of these packages first and wait that they make the required changes (i.e. to import the

Re: [Bioc-devel] Check error on malbec2

Write and access your output to a temporary directory instead using tempdir(). Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

[Bioc-devel] Check error on malbec2

In the package I am trying ti submit to bioconductor, I got the following error for check. Warning in dir.create(output.file.dir) : cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission denied' Warning in file(file, ifelse(append, "a", "w")) : cannot open file

[Bioc-devel] ensembl 87 and 88 added to AnnotationHub

Hello all, The ensembl 87 and 88 gtfs (converted to GRanges on the fly) have been added to AnnotationHub and are currently available: > library(AnnotationHub) > hub = AnnotationHub() updating metadata: retrieving 1 resource

Re: [Bioc-devel] Build error on tokay2

This is an ERROR on our tokay2 builder and we are in the process of resolving. You do not need to take any actions at this time and when it is resolved this should clear up automatically on the next build. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

[Bioc-devel] Build error on tokay2

Hi, My package BUMHMM fails to build on tokay2 with the following error message: " there is no package called 'Biobase' ". http://bioconductor.org/checkResults/3.5/bioc-LATEST/ BUMHMM/tokay2-buildsrc.html There are no problems with other platforms. It seems that many packages are encountering

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

On 4 Apr 2017, at 10:59, Stian Lågstad > wrote: Hi, Thanks again for notifying me about the changes needed in chimeraviz. Right now I'm having problems installing Gviz - I get these errors: """ No methods found in "GenomicAlignments" for

[Bioc-devel] Error when building on tokay2 for BioC 3.5

## I am resending this email as I it got rejected from posting due to "a message with identical text being posted to the list recently" (for reasons unknown to me). ## Hi, My package BUMHMM is giving an error when building on tokay2, with the error message: "there is no package called

[Bioc-devel] Error when building on tokay2 for BioC 3.5

Hi, My package BUMHMM is failing to build on tokay2, with the error: "there is no package called 'Biobase'". The package is built and checked with no problems on other platforms. The build report is here: http://bioconductor.org/checkResults/3.5/bioc-LATEST/BUMHMM/tokay2-buildsrc.html This

Re: [Rd] Potential bug in utils::citation()

> Martin Maechler > on Mon, 3 Apr 2017 10:22:52 +0200 writes: > Zhian Kamvar > on Sun, 2 Apr 2017 16:26:37 -0500 writes: >> Hi, I believe the function utils::citation() will fail if >> the package specified has two

[Rd] Bug report: POSIX regular expression doesn't match for somewhat higher values of upper bound

Dear Sirs, while > regexpr('(.{1,2})\\1', 'foo') [1] 2 attr(,"match.length") [1] 2 attr(,"useBytes") [1] TRUE yields the correct match, an incremented upper bound in > regexpr('(.{1,3})\\1', 'foo') [1] -1 attr(,"match.length") [1] -1 attr(,"useBytes") [1] TRUE incorrectly yields no match. R

[Rd] Some "lm" methods give wrong results when applied to "mlm" objects

I had a look at some influence measures, and it seems to me that currently several methods handle multiple lm (mlm) objects wrongly in R. In some cases there are separate "mlm" methods, but usually "mlm" objects are handled by the same methods as univariate "lm" methods, and in some cases this

Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

Thanks for looking into this! Maarten On Mon, Apr 3, 2017 at 7:00 PM, Hervé Pagès wrote: > Hi Maarten, > > identical() is not reliable on DNAStringSet objects or other objects > that contain external pointers as it can return false negatives as well > as false positives.