Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
On 10.08.2023 at 17:56 Neal Fultz wrote: In the past, I've extracted the pre-built debian packages into the user's personal folder, instead of installing them via apt. It worked (but it was not fun), and was pretty manual. That might interact a bit better with some of the third party tools for dealing with dependencies in shiny apps, compared to system-wide installs; ymmv. Thank you for the suggestion. My implemented approach works indeed similar to this. After moving this discussion to R-SIG-Debian (https://stat.ethz.ch/pipermail/r-sig-debian/2023-August/thread.html), Dirk Eddelbuettel suggested five different approaches. I made indeed a snapshot (a local copy) of the complete "site-library" folder to another place of the file system (e.g. "site-library-snapshot"). In the .Renviron file of the shiny user, the environment variable R_LIBS_USER then points to this location. The base packages from "library" are conservative, so I decided to use them from the original position. Finally, an rmarkdown script provided by the shiny-server can report the value of .libPaths() and versions and locations of installed packages: installed.packages()[,2:3] This works well, except for a package that contained relative symbolic links to the file system. Thomas __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN
Dirk, thanks - one of those annoying cases where a script works in the login shell, but not in the cron job -- hopefully fixed. Cheers, Simon > On 9/08/2023, at 12:45 AM, Dirk Eddelbuettel wrote: > > > Simon, > > This is still an issue for arm64. Uploaded tiledb and RQuantLib yesterday, > both already built binaries for macOS (thank you!) but on the x86_64 ones are > on the results page. Can you take another peek at this? > > Thanks so much, Dirk > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Rd] feature request: optim() iteration of functions that return multiple values
Another option that is similar to Enrico's is to use object oriented
programming with R6 or reference objects. I prefer the R6 package
(which will still use an environment like Enrico, but with some
different syntax and a little easier if you want to do this multiple
times.
Here is some example code (this grows the vectors inefficiently, which
could be improved, but it is fast as is):
library(R6)
RB <- R6Class("RB",
public=list(
x = numeric(0),
y = numeric(0),
val=numeric(0),
fun = function(x) {
x1 <- x[1]
x2 <- x[2]
self$x <- c(self$x, x1)
self$y <- c(self$y, x2)
ans <- 100*(x2-x1*x1)^2 + (1-x1)^2
self$val <- c(self$val, ans)
ans
}
)
)
rb1 <- RB$new()
optim(c(-1.2, 1), rb1$fun)
plot(rb1$x, rb1$y, type='l')
rb2 <- RB$new()
optim(c(0,1), rb2$fun)
lines(rb2$x, rb2$y, col='blue')
library(optimx)
rb3 <- RB$new()
optimr(c(-1.2,1), rb3$fun)
lines(rb3$x, rb3$y, col='red')
rb4 <- RB$new()
optimr(c(-1.2,1), rb4$fun, method='hjn')
lines(rb4$x, rb4$y, col='forestgreen')
On Fri, Aug 4, 2023 at 2:22 AM Enrico Schumann wrote:
>
> On Thu, 03 Aug 2023, Sami Tuomivaara writes:
>
> > Dear all,
> >
> > I have used optim a lot in contexts where it would
> > useful to be able to iterate function myfun that, in
> > addition to the primary objective to be minimized
> > ('minimize.me'), could return other values such as
> > alternative metrics of the minimization, informative
> > intermediate values from the calculations, etc.
> >
> > myfun <- function()
> > {
> > ...
> > return(list(minimize.me = minimize.me, R2 = R2, pval = pval, etc.))
> > }
> >
> > During the iteration, optim could utilize just the first value from the
> > myfun return list; all the other values calculated and returned by myfun
> > could be ignored by optim.
> > After convergence, the other return values of myfun
> > could be finally extracted and appended into the optim
> > return value (which is a list) as additional entry
> > e.g.: $aux <- list(R2, pval, etc.), (without
> > 'minimize.me' as it is already returned as $value).
> >
> > The usual ways for accessing optim return values, e.g.,
> > $par, $value, etc. are not affected. Computational
> > cost may not be prohibitive either. Is this feasible
> > to consider?
> >
>
> If you only wish to store additional information, you could do
> so with an environment, without changing optim. For instance,
> like so (using the first example from ?optim):
>
> data <- new.env()
> data$i <- 0
> data$fun.value <- numeric(1000)
>
> fr <- function(x, data) { ## Rosenbrock Banana function
> x1 <- x[1]
> x2 <- x[2]
> ans <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
> data$i <- data$i + 1
> data$fun.value[data$i] <- ans
> ans
> }
> optim(c(-1.2,1), fr, data = data)
> ## $par
> ## [1] 1.000260 1.000506
> ##
> ## $value
> ## [1] 8.825241e-08
> ##
> ## $counts
> ## function gradient
> ## 195 NA
> ##
> ##
>
> data$i
> ## 195
>
> plot(data$fun.value[1:data$i])
>
>
>
>
> --
> Enrico Schumann
> Lucerne, Switzerland
> http://enricoschumann.net
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com
__
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[Rd] as.matrix.dist patch (performance)
Please find attached a small patch to improve the performance of
as.matrix.dist(). It's a tiny bit more involved than the current code
but does bring a reasonable speed improvement for larger objects
(remaining comparable for smaller ones).
Example:
set.seed(1)
dat <- matrix(rnorm(2), ncol = 2);
system.time(as.matrix(dist(dat)))
As of r84931:
user system elapsed
3.370 1.154 4.535
With this patch:
user system elapsed
1.925 0.754 2.685
Submitting here in the first instance but happy to move to Bugzilla if
more appropriate.
Cheers
Tim
Index: src/library/stats/R/dist.R
===
--- src/library/stats/R/dist.R (revision 84931)
+++ src/library/stats/R/dist.R (working copy)
@@ -49,10 +49,13 @@
{
size <- attr(x, "Size")
df <- matrix(0, size, size)
-lower <- row(df) > col(df)
+idx <- seq_len(size)
+d1 <- unlist(lapply(idx[-1L], seq.int, to = size, by = 1L))
+d2 <- rep.int(idx[-size], times = rev(idx[-size]))
+lower <- cbind(d1,d2)
+upper <- cbind(d2,d1)
df[lower] <- x ## preserving NAs in x
-df <- t(df)
-df[lower] <- x
+df[upper] <- x
labels <- attr(x, "Labels")
dimnames(df) <-
if(is.null(labels)) list(seq_len(size), seq_len(size)) else list(labels,labels)
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Re: [Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?
I just want to add my 2 cents that I think it would be very useful and
beneficial to improve S4 to surface that information as well.
More information about the way that the dispatch failed would be of great
help in situations like the one Michael pointed out.
~G
On Thu, Aug 10, 2023 at 9:59 AM Michael Chirico via R-devel <
r-devel@r-project.org> wrote:
> I forwarded that along to the original reporter with positive feedback
> -- including the argument names is definitely a big help for cuing
> what exactly is missing.
>
> Would a patch to do something similar for S4 be useful?
>
> On Thu, Aug 10, 2023 at 6:46 AM Hadley Wickham
> wrote:
> >
> > Hi Michael,
> >
> > I can't help with S4, but I can help to make sure this isn't a problem
> > with S7. What do you think of the current error message? Do you see
> > anything obvious we could do to improve?
> >
> > library(S7)
> >
> > dbGetQuery <- new_generic("dbGetQuery", c("conn", "statement"))
> > dbGetQuery(connection = NULL, query = NULL)
> > #> Error: Can't find method for generic `dbGetQuery(conn, statement)`:
> > #> - conn : MISSING
> > #> - statement: MISSING
> >
> > Hadley
> >
> > On Wed, Aug 9, 2023 at 10:02 PM Michael Chirico via R-devel
> > wrote:
> > >
> > > I fielded a debugging request from a non-expert user today. At root
> > > was running the following:
> > >
> > > dbGetQuery(connection = conn, query = query)
> > >
> > > The problem is that they've named the arguments incorrectly -- it
> > > should have been [1]:
> > >
> > > dbGetQuery(conn = conn, statement = query)
> > >
> > > The problem is that the error message "looks" highly confusing to the
> > > untrained eye:
> > >
> > > Error in (function (classes, fdef, mtable) : unable to find an
> > > inherited method for function ‘dbGetQuery’ for signature ‘"missing",
> > > "missing"’
> > >
> > > In retrospect, of course, this makes sense -- the mis-named arguments
> > > are getting picked up by '...', leaving the required arguments
> > > missing.
> > >
> > > But I was left wondering how we could help users right their own ship
> here.
> > >
> > > Would it help to mention the argument names? To include some code
> > > checking for weird combinations of missing arguments? Any other
> > > suggestions?
> > >
> > > Mike C
> > >
> > > [1]
> https://github.com/r-dbi/DBI/blob/97934c885749dd87a6beb10e8ccb6a5ebea3675e/R/dbGetQuery.R#L62-L64
> > >
> > > __
> > > R-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
> >
> > --
> > http://hadley.nz
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?
I forwarded that along to the original reporter with positive feedback
-- including the argument names is definitely a big help for cuing
what exactly is missing.
Would a patch to do something similar for S4 be useful?
On Thu, Aug 10, 2023 at 6:46 AM Hadley Wickham wrote:
>
> Hi Michael,
>
> I can't help with S4, but I can help to make sure this isn't a problem
> with S7. What do you think of the current error message? Do you see
> anything obvious we could do to improve?
>
> library(S7)
>
> dbGetQuery <- new_generic("dbGetQuery", c("conn", "statement"))
> dbGetQuery(connection = NULL, query = NULL)
> #> Error: Can't find method for generic `dbGetQuery(conn, statement)`:
> #> - conn : MISSING
> #> - statement: MISSING
>
> Hadley
>
> On Wed, Aug 9, 2023 at 10:02 PM Michael Chirico via R-devel
> wrote:
> >
> > I fielded a debugging request from a non-expert user today. At root
> > was running the following:
> >
> > dbGetQuery(connection = conn, query = query)
> >
> > The problem is that they've named the arguments incorrectly -- it
> > should have been [1]:
> >
> > dbGetQuery(conn = conn, statement = query)
> >
> > The problem is that the error message "looks" highly confusing to the
> > untrained eye:
> >
> > Error in (function (classes, fdef, mtable) : unable to find an
> > inherited method for function ‘dbGetQuery’ for signature ‘"missing",
> > "missing"’
> >
> > In retrospect, of course, this makes sense -- the mis-named arguments
> > are getting picked up by '...', leaving the required arguments
> > missing.
> >
> > But I was left wondering how we could help users right their own ship here.
> >
> > Would it help to mention the argument names? To include some code
> > checking for weird combinations of missing arguments? Any other
> > suggestions?
> >
> > Mike C
> >
> > [1]
> > https://github.com/r-dbi/DBI/blob/97934c885749dd87a6beb10e8ccb6a5ebea3675e/R/dbGetQuery.R#L62-L64
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> http://hadley.nz
__
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Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
In the past, I've extracted the pre-built debian packages into the user's personal folder, instead of installing them via apt. It worked (but it was not fun), and was pretty manual. That might interact a bit better with some of the third party tools for dealing with dependencies in shiny apps, compared to system-wide installs; ymmv. On Wed, Aug 9, 2023 at 8:00 AM Thomas Petzoldt < thomas.petzo...@tu-dresden.de> wrote: > Hi Dirk, > > thank you very much dirk for the quick response. I was aware that > r-package-devel may not be the optimal place ;-) but hoped to address > the right audience between r-devel and r-help. > > Many thanks also for the suggestions, especially r2u and sorry for > confusing the name of Michael. > > Thomas > > Am 09.08.2023 um 16:41 schrieb Dirk Eddelbuettel: > > On 9 August 2023 at 16:26, Thomas Petzoldt wrote: > > | I am running a couple of shiny servers with several apps that are > based > > | around own CRAN packages. It worked stable for years, but due to the > > | growing number of packages, the compile time for regular manual package > > | installation and updates became inconvenient. > > | > > | Therefore, I have been very happy to use pre-compiled packages from the > > | c2d4u repository: deb > > | https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu/ jammy > main > > > > These days you also have r2u which has all of CRAN ie 20k binaries > (each, for > > two Ubuntu flavors). See https://eddelbuettel.github.io/r2u > > > > | This is indeed a great service, thanks to Dirk Edelbuettel, mark Rutter > > > > That would be Michael Rutter. > > > > | and the complete team! The downside is, that now the r-cran-* binaries > > | are installed automatically, together with the system update. I > > | experienced now repeated cases that crashed some of the shiny apps, > > | mainly due to conflicts between the binary packages and other packages > > | installed from sources. > > > > If you use r2u (as I do on a laptop, an ec2 server, all my CI testing for > > work and testing for months now) you get all packages and do not need to > > mix. Try r2u, it's good. > > > > | My question: what is best practise, to disallow automatic updates for > > | all r-cran-* packages? Uncommenting the complete package source in the > > | apt/sources.list.d/cd4u...list file? Fiddling around with > > | /etc/apt/preferences ? > > | > > | The ideal approach would be to put a plain textfile of all installed > > | r-cran packages somewhere to the system, where packages that are to be > > | upgraded (or oppositely: pinned) are just commented or outcommented. > > > > That is very Debian / Ubuntu specific question. Can I ask you to bring > it to > > the dedicated list r-sig-debian ? > > > > From the top of my head I can think of setting package status 'hold' (a > > simpler per-package approach) or setting specific apt pinning values to > not > > alter packages from specific repos, see the manual pages. > > > > But please ask on r-sig-debian. This list is for generic R packaging > questions. > > > > Thanks, Dirk > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Rd] Improving user-friendliness of S4 dispatch failure when mis-naming arguments?
Hi Michael,
I can't help with S4, but I can help to make sure this isn't a problem
with S7. What do you think of the current error message? Do you see
anything obvious we could do to improve?
library(S7)
dbGetQuery <- new_generic("dbGetQuery", c("conn", "statement"))
dbGetQuery(connection = NULL, query = NULL)
#> Error: Can't find method for generic `dbGetQuery(conn, statement)`:
#> - conn : MISSING
#> - statement: MISSING
Hadley
On Wed, Aug 9, 2023 at 10:02 PM Michael Chirico via R-devel
wrote:
>
> I fielded a debugging request from a non-expert user today. At root
> was running the following:
>
> dbGetQuery(connection = conn, query = query)
>
> The problem is that they've named the arguments incorrectly -- it
> should have been [1]:
>
> dbGetQuery(conn = conn, statement = query)
>
> The problem is that the error message "looks" highly confusing to the
> untrained eye:
>
> Error in (function (classes, fdef, mtable) : unable to find an
> inherited method for function ‘dbGetQuery’ for signature ‘"missing",
> "missing"’
>
> In retrospect, of course, this makes sense -- the mis-named arguments
> are getting picked up by '...', leaving the required arguments
> missing.
>
> But I was left wondering how we could help users right their own ship here.
>
> Would it help to mention the argument names? To include some code
> checking for weird combinations of missing arguments? Any other
> suggestions?
>
> Mike C
>
> [1]
> https://github.com/r-dbi/DBI/blob/97934c885749dd87a6beb10e8ccb6a5ebea3675e/R/dbGetQuery.R#L62-L64
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Bioc-devel] [+externe Mail+] Re: pwOmics package get error message for Linux check
Dear Maren,
Do you need more help with this ?
Both https://code.bioconductor.org/browse/pwOmics/commits/devel and
https://github.com/MarenS2/pwOmics don't have the change yet.
Regards,
Martin
On Tue, Aug 8, 2023 at 3:39 PM Sitte, Maren <
maren.si...@med.uni-goettingen.de> wrote:
> Dear Martin,
>
>
> thank you very much for the quick response.
>
> I will apply your advice and add the package to "Suggests".
>
>
> Kind regards
>
> Maren
>
>
> --
>
> NGS Integrative Genomics (NIG), Core Unit
> Department of Human Genetics
> University Medical Center Göttingen (UMG)
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
> Contact : 0551 39-60778
> --
> *Von:* Martin Grigorov
> *Gesendet:* Dienstag, 8. August 2023 14:36:27
> *An:* Sitte, Maren
> *Cc:* Schoeps, Torsten; bioc-devel@r-project.org
> *Betreff:* [+externe Mail+] Re: [Bioc-devel] pwOmics package get error
> message for Linux check
>
> Hi,
>
> On Tue, 8 Aug 2023 at 12:32, Sitte, Maren <
> maren.si...@med.uni-goettingen.de> wrote:
>
>> Dear Bioconductor Developers,
>>
>>
>> I received an email that my package "pwOmics" gets an error in the check
>> under Linux.
>> Install and build gets an OK, but check shows an error.
>>
>> I had a look and the problem seems to be:
>>
>> > BiocGenerics:::testPackage("pwOmics")
>> Error in library("RUnit", quietly = TRUE) :
>> there is no package called 'RUnit'
>> Calls: -> library
>> Execution halted
>>
>> I checked and the RUnit package is still available on Bioconductor and
>> can still be installed. So I can't fully understand the error message.
>> Could you help me resolve this error message?
>
>
> You need to add RUnit in the list of “Suggests” in the DESCRIPTION file.
>
> Regards,
> Martin
>
>
>>
>> Thank you for the support!
>> Kind regards
>> Maren
>>
>>
>> --
>>
>> NGS Integrative Genomics (NIG), Core Unit
>> Department of Human Genetics
>> University Medical Center Göttingen (UMG)
>> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
>> Contact : 0551 39-60778
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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Re: [Bioc-devel] Omada package failing due to removed dependency
Hi, All is green at https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/ Regards, Martin On Thu, Aug 10, 2023 at 9:44 AM Sokratis Kariotis < sokratiskario...@gmail.com> wrote: > Hey all, > > Is this fixed now? I think I can see all pass, but on the actual website > its still on error. Thanks! > > Cheers, > Sokratis > > On Tue, Aug 1, 2023 at 4:25 PM Sokratis Kariotis < > sokratiskario...@gmail.com> wrote: > >> Hey, >> >> I believe I have resolved the conflicts and now can run: *git push >> upstream main:devel* >> with Everything up-to-date as a result. However, *git push origin main* >> does not yield >> anything and it keeps hanging without a message. I checked >> https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/ >> and the last commit is April. >> >> >> On Mon, Jul 31, 2023 at 10:01 PM Kern, Lori < >> lori.sheph...@roswellpark.org> wrote: >> >>> You'll need to find the merge conflicts and resolve them. Recommit those >>> files and then it should go. >>> >>> Lori Shepherd - Kern >>> >>> Bioconductor Core Team >>> >>> Roswell Park Comprehensive Cancer Center >>> >>> Department of Biostatistics & Bioinformatics >>> >>> Elm & Carlton Streets >>> >>> Buffalo, New York 14263 >>> -- >>> *From:* Bioc-devel on behalf of >>> Sokratis Kariotis >>> *Sent:* Monday, July 31, 2023 7:27 AM >>> *To:* Martin Grigorov >>> *Cc:* bioc-devel@r-project.org >>> *Subject:* Re: [Bioc-devel] Omada package failing due to removed >>> dependency >>> >>> Tried but its Already up to date. >>> >>> On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, >> > >>> wrote: >>> >>> > Hi Sokratis, >>> > >>> > You need to do "git pull --rebase" before trying to push. >>> > Most probably the version has been bumped upstream. >>> > >>> > Regards, >>> > Martin >>> > >>> > On Mon, Jul 31, 2023 at 2:16 PM Sokratis Kariotis < >>> > sokratiskario...@gmail.com> wrote: >>> > >>> >> Hey all, >>> >> >>> >> I created a new key and now I can commit etc but there is a conflict >>> that >>> >> is not allowing me to go ahead. >>> >> >>> >> My commands: >>> >> git add . >>> >> git commit -m "Update metrics" >>> >> git push upstream main:devel >>> >> >>> >> *The above results in the following error:* >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> *Enumerating objects: 19, done.Counting objects: 100% (17/17), >>> done.Delta >>> >> compression using up to 16 threadsCompressing objects: 100% (11/11), >>> >> done.Writing objects: 100% (11/11), 4.78 KiB | 4.78 MiB/s, done.Total >>> 11 >>> >> (delta 7), reused 0 (delta 0), pack-reused 0remote: Error: You cannot >>> push >>> >> without resolving merge conflicts.remote:remote: Please check the >>> files in >>> >> the commit pushed to the git-serverremote: for merge conflict markers >>> like >>> >> '<<<', '', '>>>'.remote:To >>> >> git.bioconductor.org:packages/omada ! [remote rejected] main -> devel >>> >> (pre-receive hook declined)error: failed to push some refs to >>> >> 'git.bioconductor.org:packages/omada'* >>> >> >>> >> >>> >> >>> >> On Mon, Jul 31, 2023 at 3:36 PM Mike Smith >>> wrote: >>> >> >>> >> > Hi Sokratis, >>> >> > >>> >> > Everything in Bioconductor is built around the central Bioconductor >>> git >>> >> > repositories. The only way to get changes out to users is to commit >>> >> them >>> >> > to git.bioconductor.org and then the build system will pick those >>> up, >>> >> run >>> >> > the tests and checks, create new versions of packages, and make them >>> >> > available for distribution. >>> >> > >>> >> > Perhaps you can include the git command you're running to submit the >>> >> > changes and a copy of the exact error you're receiving. That might >>> help >>> >> > the team suggest a solution. >>> >> > >>> >> > Best regards, >>> >> > Mike >>> >> > >>> >> > On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis < >>> >> > sokratiskario...@gmail.com> wrote: >>> >> > >>> >> >> Hey both, >>> >> >> >>> >> >> I have edited the package code but I'm having some difficulties >>> >> pushing it >>> >> >> to trigger another build (github passphrase). Is there another way >>> to >>> >> >> trigger the build? Thanks! >>> >> >> >>> >> >> Cheers, >>> >> >> Sokratis >>> >> >> >>> >> >> On Wed, Jul 12, 2023 at 1:43 AM Kern, Lori < >>> >> lori.sheph...@roswellpark.org >>> >> >> > >>> >> >> wrote: >>> >> >> >>> >> >> > We can give you a little more time (a few weeks) to fix the >>> package >>> >> but >>> >> >> > please fix as soon as possible to avoid deprecation. >>> >> >> > >>> >> >> > Cheers, >>> >> >> > >>> >> >> > Lori Shepherd - Kern >>> >> >> > >>> >> >> > Bioconductor Core Team >>> >> >> > >>> >> >> > Roswell Park Comprehensive Cancer Center >>> >> >> > >>> >> >> > Department of Biostatistics & Bioinformatics >>> >> >> > >>> >> >> > Elm & Carlton Streets >>> >> >> > >>> >> >> > Buffalo, New York 14263 >>> >> >> > -- >>> >> >> > *From:* Sokratis Kariotis >>> >> >> > *Sent:*
Re: [Bioc-devel] Omada package failing due to removed dependency
Hey all, Is this fixed now? I think I can see all pass, but on the actual website its still on error. Thanks! Cheers, Sokratis On Tue, Aug 1, 2023 at 4:25 PM Sokratis Kariotis wrote: > Hey, > > I believe I have resolved the conflicts and now can run: *git push > upstream main:devel* > with Everything up-to-date as a result. However, *git push origin main* > does not yield > anything and it keeps hanging without a message. I checked > https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/ > and the last commit is April. > > > On Mon, Jul 31, 2023 at 10:01 PM Kern, Lori > wrote: > >> You'll need to find the merge conflicts and resolve them. Recommit those >> files and then it should go. >> >> Lori Shepherd - Kern >> >> Bioconductor Core Team >> >> Roswell Park Comprehensive Cancer Center >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> -- >> *From:* Bioc-devel on behalf of >> Sokratis Kariotis >> *Sent:* Monday, July 31, 2023 7:27 AM >> *To:* Martin Grigorov >> *Cc:* bioc-devel@r-project.org >> *Subject:* Re: [Bioc-devel] Omada package failing due to removed >> dependency >> >> Tried but its Already up to date. >> >> On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, >> wrote: >> >> > Hi Sokratis, >> > >> > You need to do "git pull --rebase" before trying to push. >> > Most probably the version has been bumped upstream. >> > >> > Regards, >> > Martin >> > >> > On Mon, Jul 31, 2023 at 2:16 PM Sokratis Kariotis < >> > sokratiskario...@gmail.com> wrote: >> > >> >> Hey all, >> >> >> >> I created a new key and now I can commit etc but there is a conflict >> that >> >> is not allowing me to go ahead. >> >> >> >> My commands: >> >> git add . >> >> git commit -m "Update metrics" >> >> git push upstream main:devel >> >> >> >> *The above results in the following error:* >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *Enumerating objects: 19, done.Counting objects: 100% (17/17), >> done.Delta >> >> compression using up to 16 threadsCompressing objects: 100% (11/11), >> >> done.Writing objects: 100% (11/11), 4.78 KiB | 4.78 MiB/s, done.Total >> 11 >> >> (delta 7), reused 0 (delta 0), pack-reused 0remote: Error: You cannot >> push >> >> without resolving merge conflicts.remote:remote: Please check the >> files in >> >> the commit pushed to the git-serverremote: for merge conflict markers >> like >> >> '<<<', '', '>>>'.remote:To >> >> git.bioconductor.org:packages/omada ! [remote rejected] main -> devel >> >> (pre-receive hook declined)error: failed to push some refs to >> >> 'git.bioconductor.org:packages/omada'* >> >> >> >> >> >> >> >> On Mon, Jul 31, 2023 at 3:36 PM Mike Smith >> wrote: >> >> >> >> > Hi Sokratis, >> >> > >> >> > Everything in Bioconductor is built around the central Bioconductor >> git >> >> > repositories. The only way to get changes out to users is to commit >> >> them >> >> > to git.bioconductor.org and then the build system will pick those >> up, >> >> run >> >> > the tests and checks, create new versions of packages, and make them >> >> > available for distribution. >> >> > >> >> > Perhaps you can include the git command you're running to submit the >> >> > changes and a copy of the exact error you're receiving. That might >> help >> >> > the team suggest a solution. >> >> > >> >> > Best regards, >> >> > Mike >> >> > >> >> > On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis < >> >> > sokratiskario...@gmail.com> wrote: >> >> > >> >> >> Hey both, >> >> >> >> >> >> I have edited the package code but I'm having some difficulties >> >> pushing it >> >> >> to trigger another build (github passphrase). Is there another way >> to >> >> >> trigger the build? Thanks! >> >> >> >> >> >> Cheers, >> >> >> Sokratis >> >> >> >> >> >> On Wed, Jul 12, 2023 at 1:43 AM Kern, Lori < >> >> lori.sheph...@roswellpark.org >> >> >> > >> >> >> wrote: >> >> >> >> >> >> > We can give you a little more time (a few weeks) to fix the >> package >> >> but >> >> >> > please fix as soon as possible to avoid deprecation. >> >> >> > >> >> >> > Cheers, >> >> >> > >> >> >> > Lori Shepherd - Kern >> >> >> > >> >> >> > Bioconductor Core Team >> >> >> > >> >> >> > Roswell Park Comprehensive Cancer Center >> >> >> > >> >> >> > Department of Biostatistics & Bioinformatics >> >> >> > >> >> >> > Elm & Carlton Streets >> >> >> > >> >> >> > Buffalo, New York 14263 >> >> >> > -- >> >> >> > *From:* Sokratis Kariotis >> >> >> > *Sent:* Monday, July 10, 2023 10:27 AM >> >> >> > *To:* Kern, Lori >> >> >> > *Cc:* Oleksii Nikolaienko ; >> >> >> > bioc-devel@r-project.org >> >> >> > *Subject:* Re: [Bioc-devel] Omada package failing due to removed >> >> >> > dependency >> >> >> > >> >> >> > Hey both, >> >> >> > >> >> >> > I have checked the package license (GPL) and it should be fine to >> use >> >> >> the >> >> >> > code. However, I am having difficulty finding the
