Re: [Bioc-devel] Bioconductor Git: Online interface

On Tue, Feb 11, 2020 at 2:42 PM Martin Morgan wrote: > > (sending again from / to an appropriate email address, sorry for the noise) > > Henrik -- I appreciate the ease with which gitea can be deployed in this > one-off solution but cynically think that a real deployment would introduce >

Re: [Bioc-devel] Bioconductor Git: Online interface

(sending again from / to an appropriate email address, sorry for the noise) Henrik -- I appreciate the ease with which gitea can be deployed in this one-off solution but cynically think that a real deployment would introduce significant work, e.g., re-tooling our approach to new package

Re: [Bioc-devel] Bioconductor Git: Online interface

I wanna revive this old thread. I've used Gitea for internal git/issue trackers at the UCSF for quite a while now and it works really well. I've also looked into how easy it would be to use it for pure code exposure and it's pretty straightforward. Gitea even has built-in tools for

Re: [Bioc-devel] gds nodes dimensions are inconsistent

Hi Qian, I have modified the GDS file in the SeqArray package. "annotation/info/AA" should have fewer values than "annotation/info/AC", since it is a variable-length vector in the new GDS file. VCF format allows storing variable-length data, so SeqArray also allows variable-length data.

Re: [Bioc-devel] help

It's a NOTE, you can't change the affiliation of the authors, so ignore it. The purpose of the note is to improve readability by enabling display in fixed-width windows (e.g., in github!) so make changes that are consistent with improving readability without degrading information. Martin On

Re: [Bioc-devel] help

`sapply()` implies that you expect the result to be _s_implified, which implies that all your elements are the same length. Sounds like you want to use `lapply()` instead, to signal that it will *not* be simplified, even if by chance the elements are the same length. Martin On 2/11/20, 3:51

[Bioc-devel] help

" Avoid sapply(); use vapply()" Hi, This is a Note I received from BiocCheck() I tried to change my sapply functions to vapply; however, vapply requires knowing the exact length of the vector(list), however, my vector length are not static and variable. Therefore, vapply may not be of use for me

Re: [Rd] Minor typo in recent commit

> Hugh Parsonage writes: Thanks: fixed now. Best -k > I believe should be February 2020 not 2010 > --- a/doc/manual/R-exts.texi > +++ b/doc/manual/R-exts.texi > @@ -2631,9 +2631,9 @@ not necessarily installed) on all known @R{} > platforms. As from @R{} > 4.0.0 a C++ compiler will be

[Bioc-devel] help

Greetings, I am developing a Bioconductor package. After runningBiocCheck:::checkFormatting("CommunityAMARETTO", nlines=Inf) I receive * NOTE: Consider multiples of 4 spaces for line indents, 114 lines(3%) are not. The majority of the lines being shown are manual pages (pages in man

[Bioc-devel] help

Hi , I am developing a Bioconductor package. By runningBiocCheck:::checkFormatting("CommunityAMARETTO", nlines=Inf) I receive *NOTE: Consider shorter lines; 10 lines (0%) are > 80* * characters long.* However, all these 10 lines belong to Vignette and affiliation part and you can not

Re: [R-pkg-devel] Question regarding R package development, how to resolve "Warning: no source files found"

INSTALL will give that warning if you have a pkg/src directory that contains no files that look like C, C++, or Fortran files. Bill Dunlap TIBCO Software wdunlap tibco.com On Tue, Feb 11, 2020 at 11:58 AM Mohsen Nabian wrote: > Greetings! > > How to resolve the following warning for my R

[R-pkg-devel] Question regarding R package development, how to resolve "Warning: no source files found"

Greetings! How to resolve the following warning for my R package after running test :system2("R", paste0("CMD INSTALL -l ",Sys.getenv('R_HOME'),"/library ", pkg), stdout = "install1.txt", stderr = "install2.txt") Warning result : "Warning: no source files found" Thanks alot!

Re: [R-pkg-devel] Fwd: PDF generation issue from manual page

On 11/02/2020 12:33 p.m., neonira Arinoem wrote: Hi R gurus Got an issue risen by CRAN about using unknown characters from Latex. Here is the error message, in the context of PDF generated form manual pages *Check: PDF version of manual, Result: WARNING LaTeX errors when creating PDF

[Bioc-devel] gds nodes dimensions are inconsistent

Dear Dr. Zheng & SeqArray maintainer, I have a Bioconductor package called "GDSArray" that interfaces GDS file nodes as DelayedArray instances. In this new Bioc devel version of 3.11, this package failed all platforms. The debugging shows inconsistent dimensions calculated from different

Re: [Bioc-devel] Latest commit didn't update package

Thanks, yes, I checked the build report. And yes, I am afraid that you are right: it could have simply taken too much time. It is a package that tries to accomplish many things and I was warned during the review process that it was probably doing too much. But on the other hand, I know it is

Re: [Bioc-devel] Permission denied (publickey)

Hi Daniel, Could you try adding a new public key? Because everything on our end is fine. Best Nitesh > On Feb 11, 2020, at 1:09 PM, Danrley Fernandes wrote: > > Hi, > I'm the developer of the package rSWeeP, and I'm trying to clone my > package's repository on Bioconductor, so I can commit

[Bioc-devel] Permission denied (publickey)

Hi, I'm the developer of the package rSWeeP, and I'm trying to clone my package's repository on Bioconductor, so I can commit changes. I already have my ssh key register on the Bioconductor credentials for almost a week, but when I ask to git bash to " git remote add upstream

[R-pkg-devel] Fwd: PDF generation issue from manual page

Hi R gurus Got an issue risen by CRAN about using unknown characters from Latex. Here is the error message, in the context of PDF generated form manual pages *Check: PDF version of manual, Result: WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems.

Re: [Bioc-devel] Latest commit didn't update package

remember to visit the build report page http://bioconductor.org/checkResults/devel/bioc-LATEST/artMS/ ; perhaps your package failed to build, e.g., because one of the 187(!) dependent packages did not install correctly on the devel builder, or because of transient problems? Martin Morgan On

Re: [Bioc-devel] Bioc2020 Registration Open - Call for abstracts workshops/talks/posters Open

Hello Bioconductor developer community We wanted to remind you that Bioc2020 registration is open! Bioc2020 is accepting applications for workshops/talks/poster with the deadline March 3. Travel scholarships and Caregiver scholarships are also open with deadline March 3. We hope to see you

Re: [Bioc-devel] Latest commit didn't update package

That does seem odd. Please let us know when you see this again with examples and I can investigate more. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Rd] R with Squid proxy - invalid requests ??

On 11/02/2020 14:54, lejeczek via R-devel wrote: > dear devel, > > I thought you guys would know best - I have an R which fails to get > communicate outside via a proxy, and Squid's logs show: > > ... > > 1581432434.501  0 10.5.8.17 TAG_NONE/400 4064  %C5/%B6* - > HIER_NONE/- text/html >

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

I don't have direct experience or responsibility for this code, but it seems like R CMD build could instead create a 'whitelist' of files to copy to the build location, and do that rather than copying everything and removing things that are to be ignored. The basis for a patch might be

[Rd] R with Squid proxy - invalid requests ??

dear devel, I thought you guys would know best - I have an R which fails to get communicate outside via a proxy, and Squid's logs show: ... 1581432434.501  0 10.5.8.17 TAG_NONE/400 4064  %C5/%B6* - HIER_NONE/- text/html 1581432497.231  0 10.5.8.17 TAG_NONE/400 4570 NONE

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

It is actually rather complicated, because .Rbuildignore can have regular expressions, that refer to files or directories, and for the latter you need to ignore the whole directory. You can look up in the R source code how R does it, maybe you can reuse that code. Here is a quick and dirty

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

Something like file.copy( setdiff(list.files(recursive=TRUE)), scan(".Rbuildignore", what=character())), to = destdir) ? On 2020-02-11 8:50 a.m., Rainer Krug wrote: > Thinking about it - what would be the easiest way, to copy the package, > excluding files in .Rbuidignore, into the temp

[Rd] PDF generation issue from manual page

Hi R gurus Got an issue risen by CRAN about using unknown characters from Latex. Here is the error message *Check: PDF version of manual, Result: WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Undefined control sequence.

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

Thinking about it - what would be the easiest way, to copy the package, excluding files in .Rbuidignore, into the temp directory? I would like to use directly the .Rbuildignore file, to exclude the files from copying. Any suggestions? > On 11 Feb 2020, at 10:20, Rainer M Krug wrote: > > >

Re: [Bioc-devel] Latest commit didn't update package

It looks like it did get updated: http://bioconductor.org/checkResults/release/bioc-LATEST/artMS/ Is showing 1.4.3 which is the expected version correct? Remember it can take up to 24 hours for the build reports to pick up the new versions depending on when you pushed changes Cheers, Lori

Re: [R-pkg-devel] [EXTERNAL] R CMD build hanging for some but not all packages

Yes - I would suggest that this would be a useful change. As the files in .Rbuildignore are ignored anyway during build. So the ignoring could be done at the copying stage and not during the building stage? Rainer > On 11 Feb 2020, at 13:20, Hong Ooi wrote: > > They are scanned probably

Re: [R-pkg-devel] [EXTERNAL] Re: R CMD build hanging for some but not all packages

They are scanned probably because R CMD build does something like cp * to copy everything to a temp folder first up, before processing it. An argument could be made that it should manually loop through all files and dirs, checking each against .Rbuildignore before copying. From: Rainer M Krug

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

> On 11 Feb 2020, at 09:54, Gábor Csárdi wrote: > > On Tue, Feb 11, 2020 at 8:52 AM Rainer M Krug wrote: >> On 11 Feb 2020, at 09:42, Gábor Csárdi wrote: >> On Tue, Feb 11, 2020 at 8:38 AM Rainer M Krug wrote: >> On 10 Feb 2020, at 17:58, Gábor Csárdi wrote: >> >> Maybe you have large,

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

On Tue, Feb 11, 2020 at 8:52 AM Rainer M Krug wrote: > On 11 Feb 2020, at 09:42, Gábor Csárdi wrote: > On Tue, Feb 11, 2020 at 8:38 AM Rainer M Krug wrote: > On 10 Feb 2020, at 17:58, Gábor Csárdi wrote: > > Maybe you have large, ignored files in the package directory? R first > creates a copy

[Rd] Minor typo in recent commit

I believe should be February 2020 not 2010 --- a/doc/manual/R-exts.texi +++ b/doc/manual/R-exts.texi @@ -2631,9 +2631,9 @@ not necessarily installed) on all known @R{} platforms. As from @R{} 4.0.0 a C++ compiler will be selected only if it conforms to the 2011 standard (`C++11'). A minor

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

> On 11 Feb 2020, at 09:42, Gábor Csárdi wrote: > > On Tue, Feb 11, 2020 at 8:38 AM Rainer M Krug > wrote: >> >> >> >> On 10 Feb 2020, at 17:58, Gábor Csárdi wrote: >> >> Maybe you have large, ignored files in the package directory? R first >> creates a copy of

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

On Tue, Feb 11, 2020 at 8:38 AM Rainer M Krug wrote: > > > > On 10 Feb 2020, at 17:58, Gábor Csárdi wrote: > > Maybe you have large, ignored files in the package directory? R first > creates a copy of the whole directory and only applies `.Rbuildignore` > after that. > > THANKS - you solved my

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

> On 10 Feb 2020, at 17:58, Gábor Csárdi wrote: > > Maybe you have large, ignored files in the package directory? R first > creates a copy of the whole directory and only applies `.Rbuildignore` > after that. THANKS - you solved my question without me having to answer it. As I am using a