Re: [Bioc-devel] Updating author/maintainer info

Hi Kylie, It seems that we somehow forgot to grant you write access to your CardinalWorkflows package. This should work now. Please try again. Sorry for the inconvenience, H. On 09/21/2016 07:16 PM, Kyle Dwayne Bemis wrote: Hello, My personal information has changed and I need to update my

Re: [Bioc-devel] Updating author/maintainer info

Did you add --username xxx --password to the svn co command? On Thu, Sep 22, 2016 at 1:42 PM, Bemis, Kylie wrote: > Thanks, but when I follow the directions, it doesn’t work: > > svn: E175013: Commit failed (details follow): > svn: E175013: Unable to connect to a

Re: [Bioc-devel] Updating author/maintainer info

Thanks, but when I follow the directions, it doesn’t work: svn: E175013: Commit failed (details follow): svn: E175013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CardinalWorkflows' svn: E175013: Access to

[Bioc-devel] Updating author/maintainer info

Hello, My personal information has changed and I need to update my author/maintainer name and email address on my packages. For Cardinal, this is easy, but CardinalWorkflows is a data package, so I cannot update it myself. How can I update the data package info? Besides subscribing to the

Re: [Bioc-devel] New package deadline for this release: 26 September

Dear Martin and core members, We have a package named uSORT submitted to Bioconductor through GitHub half a month ago, FYI * Github Link: * Bioconductor submission track: Now the

Re: [Bioc-devel] lpsymphony - BiocParallel crash

On 09/21/2016 10:42 AM, Christian Arnold wrote: Dear Bioconductor developers, I am having a somewhat mysterious and challenging problem which we believe is a bug in either (1) BiocParallel or (2) the lpsymphony library from either Bioconductor or the SYMPHONY backend. Thank you for the clear

[Bioc-devel] Package pages: Link to NEWS gone?

I've noticed this for a while and thought it was a temporary glitch, or maybe I missed some announcement about it, but it appears that NEWS files are no longed listed on the Bioc package pages, e.g. https://bioconductor.org/packages/devel/bioc/html/Biobase.html. A mistake? /Henrik

Re: [Rd] error handling in strcapture

The new behavior is that it yields NAs when the pattern does not match (like strptime) and for empty captures in a matching pattern it yields the empty string, which is consistent with regmatches(). Michael On Wed, Sep 21, 2016 at 2:21 PM, William Dunlap wrote: > If there are

Re: [Rd] error handling in strcapture

If there are any matches then strcapture can see if the pattern has the same number of capture expressions as the prototype has columns and give an error if not. That seems appropriate. If there are no matches, then there is no easy way to see if the prototype is compatible with the pattern, so

Re: [Rd] error handling in strcapture

Hi Bill, Thanks, another good suggestion. strcapture() now returns NAs for non-matches. It's nice to have someone kicking the tires on that function. Michael On Wed, Sep 21, 2016 at 12:11 PM, William Dunlap via R-devel wrote: > Michael, thanks for looking at my first

Re: [Rd] Handlers in setGraphicsEventHandlers() can recursively call getGraphicsEvent(). Intended behavior?

Hi Thanks for the further analysis. Sounds reasonable to me. What would be good to get from you is: - a test that does recursive getGraphicsEvent() calls, that is fixed by your patch - a test that produces the newline prompt from getGraphicsEvent(), that is fixed by your other patch - a

[Rd] error handling in strcapture

Michael, thanks for looking at my first issue with utils::strcapture. Another issue is how it deals with lines that don't match the pattern. Currently it gives an error > strcapture("(.+) (.+)", c("One 1", "noSpaceInLine", "Three 3"), proto=list(Name="", Number=0)) Error in strcapture("(.+)

Re: [Rd] formal process for orphaning a package

I agree that the file shows the _reasons_ but that is not the same as a _process_. With the high volume of packages that the CRAN maintainers handle, an explicit procedure beyond "request it" is needed or should at least be spelled out. We have pushed everything CRAN-related else towards

Re: [Rd] strcapture enhancement

Thanks for the suggestion. Checked in that change. Michael On Wed, Sep 21, 2016 at 11:06 AM, William Dunlap via R-devel wrote: > The new strcapture function in R-devel is handy, capturing > the matches to the parenthesized subpatterns in a regular > expression in the

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

So this seems like a bug in mzR which is the main backend / parser for proteomics and metabolomics data. Someone should try to fix this. Unfortunately, mzR depends on several pieces of software which are written by other people, but bundled with the package. Martin's traceback suggests that

Re: [Rd] strcapture enhancement

Note that read.pattern in gsubfn does accept stringsAsFactors = FALSE, e.g. using your input lines and pattern: library(gsubfn) Lines <- c("Three 3", "Twenty 20") pat <- "([[:alpha:]]*) +([[:digit:]]*)" s2 <- read.pattern(text = Lines, pattern = pat, stringsAsFactors = FALSE, col.names =

[Rd] strcapture enhancement

The new strcapture function in R-devel is handy, capturing the matches to the parenthesized subpatterns in a regular expression in the columns of a data.frame, whose column names and classes are given by the 'proto' argument. E.g., > p1 <- data.frame(Name="", Number=0) >

Re: [Rd] formal process for orphaning a package

The README states clearly that a package is orphaned under any of three conditions: 1. The Maintainer requests is. 2. The maintainer email bounces 3. The maintainer is unresponsive to requests regarding the package from CRAN maintainers But I think that it is a good idea to include

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

One thing I notice is that the crash does not happen every time. I have successfully built the package on morelia by hand with "R CMD build". Similarly I can source the stangled vignette without a crash sometimes. But when it does crash, this is what I see: > source("msPurity-vignette.R",

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

Thanks for reply. Some of those errors are a bit cryptic for me also. I have not heard of the valgrind functionality before in R. I will test a few things out with valgrind and hopefully I can pinpoint the error a bit more. Thanks again. Tom On Wed, Sep 21, 2016 at 12:50 PM, Martin Morgan <

[Rd] formal process for orphaning a package

The CRAN policy page (https://cran.r-project.org/web/packages/policies.html) implies that there is a formal procedure for orphaning a package but none is mentioned in the Extensions manual (https://cran.r-project.org/doc/manuals/r-devel/R-exts.html). This page

[Bioc-devel] lpsymphony - BiocParallel crash

Dear Bioconductor developers, I am having a somewhat mysterious and challenging problem which we believe is a bug in either (1) BiocParallel or (2) the lpsymphony library from either Bioconductor or the SYMPHONY backend. The problem is, in a nutshell, that R silently crashes or, to be more

Re: [Bioc-devel] github mirror and svn out of sync

thanks Martin! Now everything is in sync again. You're right, the git commits were commited as separate svn commits; an alternative would be to use `git-merge --squash`, but I didn't try that one; so far I used `git cherry-pick` to merge a selected range of git commits into the devel branch

Re: [R-pkg-devel] doc url to vignette

Update: The https://cran.r-project.org/package=NAME/ syntax works now and is accepted. Best, Uwe Ligges On 21.09.2016 14:20, Duncan Murdoch wrote: On 21/09/2016 7:57 AM, S Ellison wrote: > How can I link to a certain page on CRAN without getting flagged for non- > canonical CRAN URL

Re: [R-pkg-devel] doc url to vignette

On 21/09/2016 7:57 AM, S Ellison wrote: > How can I link to a certain page on CRAN without getting flagged for non- > canonical CRAN URL forms? In the interests of avoiding something that may change in future if CRAN is restructured, would it be sufficient to include the link to the vignette

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

On 09/20/2016 05:18 AM, Thomas Lawson wrote: Hi BioConductor community, My package (msPurity) is passing the build on the Linux (*zin1*) and Windows servers (*moscato1*) but failing on the Mac OS X server (*morelia*). Also I cannot seem to replicate the failure either on a local installation of

[Bioc-devel] new biocView

A new biocView has been added to the list of terms: SingleCell Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or

Re: [Bioc-devel] github mirror and svn out of sync

On 09/21/2016 12:01 AM, Rainer Johannes wrote: Dear all, I recently observed that the svn and the github mirror of `ensembldb` is out of sync. Is this something specific to `ensembldb` or is this a general problem? Is there anything I could do to fix this? I think it is up-to-date now? I

Re: [R-pkg-devel] Mis-spelled word with winbuilder

On 21/09/2016 7:17 AM, Göran Broström wrote: I'm checking my package with winbuilder and get one NOTE: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Göran Broström ' Possibly mis-spelled words in DESCRIPTION: piecewise (9:43) How should it be spelled? I

Re: [Rd] Handlers in setGraphicsEventHandlers() can recursively call getGraphicsEvent(). Intended behavior?

doKeybd() gets called in CHelpKeyIn() and NHelpKeyIn() in library/grDevices/src/devWindows.c, where the call is encapsulated in an 'if (dd->gettingEvent)' block. So the only times this code ever calls doKeybd() is when gettingEvent is in fact set. Further, it's called in two locations in

Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

On 09/21/2016 06:06 AM, Moritz Gerstung wrote: Hi Dan Has this problem problem resurrected? I see many packages depending on zlibbioc fail, including gage, Rhtslib and deepSNV. http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/moscato1-install.html The situation has improved but

Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

Hi Dan Has this problem problem resurrected? I see many packages depending on zlibbioc fail, including gage, Rhtslib and deepSNV. http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/moscato1-install.html Cheers Moritz > On 1 Jun 2016, at 20:40, Dan Tenenbaum

Re: [Rd] Undocumented 'use.names' argument to c()

> David Winsemius > on Tue, 20 Sep 2016 23:46:48 -0700 writes: >> On Sep 20, 2016, at 7:18 PM, Karl Millar via R-devel wrote: >> >> 'c' has an undocumented 'use.names' argument. I'm not sure if this is >> a

Re: [Rd] Undocumented 'use.names' argument to c()

> On Sep 20, 2016, at 7:18 PM, Karl Millar via R-devel > wrote: > > 'c' has an undocumented 'use.names' argument. I'm not sure if this is > a documentation or implementation bug. It came up on stackoverflow a couple of years ago: