Dear Nitesh,
Could you please add a new developer to my BioC packages systemPipeR and
systemPipeRdata to provide commit/push access for the corresponding git
repositories on git.bioconductor.org. The person's name is Daniela Cassol
(new postdoc in my group) and her email is danicas...@gmail.com.
Hi all,
If you put
foo <- `[`
Somewhere in a package, it will trigger
Error in makeUsageCollector(fun, ...) : only works for closures
In BiocCheck::BiocCheck() (version 1.18.0). This comes from
if (typeof(fun) != "closure")
stop("only works for closures")
In codetools::makeUsageColle
From what I can see in scPipe, it looks to me like there’s difference in flags
for tokay1 and tokay2 (release and development).
http://bioconductor.org/checkResults/release/bioc-LATEST/scPipe/tokay1-buildbin.html
-O2 -Wall -mtune=generic
http://bioconductor.org/checkResults/devel/bioc-LATEST/scP
Thanks Val. I don�t think it�s a BiocNeighbors thing, as it doesn�t try to
customize the compilation flags or have its own Makevars. Moreover, the �-O3
-mtune=native -mtune=generic� flags seem to show up on all of my packages
containing C++11 code. Some cursory checks of other packages suggest t
Thanks! I am working to fix that!
Tiphaine
Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and M
Maybe others will have better suggestions for how to debug exactly...
I am able to reproduce the error and just with a trial and error of deleting
and adding chunks of the vignette ... it first seems to appear with the attempt
to add the figure
\begin{figure}
<>=
extdata <- system.file("extdat
Hi Michael,
I don't think we have any package that require C++14 at the moment.
I see 36 software packages that have SystemRequirements: C++11 in devel. I
agree that package authors should probably stick to that and avoid C++14 for
now.
The change I made to the build system is just a minor imp
Dear Val/Herve:
Does this mean that Bioconductor depends on C++14? Keeping up with the C++
standards is a struggle, at least for those maintaining deployments on
clusters with slow-moving enterprise linux distributions.
It would be helpful if someone could document the minimum C++ standard,
along
Hi,
Just a heads up that we won't have a build report for 3.9 today. Herve
made some changes to the build report to display the C++14 compilation
flags and I messed up the deployment. Tomorrow we should be back on
track with the report and the new C++14 flags.
Sorry for the inconvenience.
Val
Hi Christian,
This is a known - there are no Mac binaries for El Capitan for R 3.6 at
this point. We don't build Cairo from source on the Mac builder, we use
the binary from CRAN. Once CRAN makes the binary available your package
will build.
Valerie
On 12/14/18 4:37 AM, Christian Mertes w
I need more information to help you.
Please check http://bioconductor.org/developers/how-to/git/faq/, #14
especially. And any others you may need.
> On Dec 17, 2018, at 12:46 PM, Anand MT wrote:
>
> Hi Nitesh,
>
> Yes, I have pulled from upstream but still the same issue.
>
> $ git pull up
Hi Aaron,
The only compilation flags that are different for tokay1 (release) and
tokay2 (devel) are C++14 flags. BiocNeighbors is not using C++14 but
C++11 so I think the changes we discussed previously actually don't
apply to your case.
All compilation flags we use are listed at the top of th
Hi Nitesh,
Yes, I have pulled from upstream but still the same issue.
$ git pull upstream master
From git.bioconductor.org:packages/maftools
* branchmaster -> FETCH_HEAD
Already up to date.
$ git status
On branch devel
nothing to commit, working tree clean
$ git push upstream ma
Hi Micheal,
Please be informed that there can be only one “maintainer”. You may consider
having more than one collaborator on the package, which is Benjamin Haibe
Kains.
Also, the email on file for Benjamin is "bhklab.resea...@gmail.com” with the
username you have provided.
I will add the
Hi,
Have your tried the command mentioned in the error message
git pull
This is important.
Once that is done, “IF” you have merge conflicts, please do
http://bioconductor.org/developers/how-to/git/resolve-conflicts/
Best,
Nitesh
> On Dec 17, 2018, at 10:22 AM, Anand MT
Hi,
I would like to add my labs software developer to my current Bioc packages,
but he says that according to "ssh -T g...@git.bioconductor.org | grep
Meta" he does not have write access. Is there a way I can give him write
access? They want to add the email benjamin.haibe.ka...@utoronto.ca and g
Hi,
I need to advise to build my vignette. It seems that my vignette could not
build under Bioconductor 3.9. I try to find where it fails, but I don't find
the bug.
I updated my vignette last February to work with new version of BiocStyle and
it did well for Bioconductor 3.8, but it seems that
It seems like you've posted this in several locations -- stackoverflow, slack,
here. Choose one forum and stick with it, so that people do not waste their
time duplicating effort. Regardless of forum, provide a minimal reproducible
example (e.g., a stripped-down github repository) to illustrate
Hello,
We have a warning related to defining an S4 object:
Warning: undefined slot classes in definition of "MyObject": index(class
"Rcpp_ModuleClass")
More details are here:
https://stackoverflow.com/questions/53814548/rcpp-class-wrapped-in-s4-object-warning
Could anyone please help?
Many than
Thank you. I thought we had a BiocCheck for browser that would print a clearer
message. I will look into this but thank you for correcting your package.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton S
Good day,
Thanks for running it. I found the error you had happens because of an example
which used random sampling and rarely returned a zero-length result. I have
made the example deterministic so that it always succeeds.
The error you saw is not related to the problem seen on the build serve
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