t;>>>> on Wed, 5 Feb 2020 20:52:52 -0800 writes:
>
> > Yep that about sums it up.
>
> :-) ;-)
>
> Thank you, Michael !!
> I haven't laughed as much from reading e-mails in a long while !!
>
> Martin
>
>
> > On Wed, F
OK sorry for this email chain, outlook in windows 10 is definitely doing
weird stuff.
I will reopen another thread. And after understanding the joke, I thought
was a really good one XD
Best wishes.
*Stefano *
Il giorno ven 7 feb 2020 alle ore 00:24 Martin Morgan <
mtmorgan.b...@gmail.
if S4 classes are really mandatory? I need to understand
if I am forced to submit to CRAN instead (although Bioconductor would be a
good fit, sice I try to interface transcriptional analysis tools to tidy
universe)
Thanks a lot.
Stefano
[[alternative HTML version deleted]]
__
e community give me your honest opinions, I will take
them seriously and proceed.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno ven 7 feb 2020 alle ore 10:46 Martin Morgan &
ill have been resolved.
I imagine there are not many cases where a CRAN package migrated to
Bioconductor after complying with the ecosystem policies.
Thanks a lot.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical
Would this scenario satisfy " make the package _directly_ compatible with
standard Bioconductor data structures"
If an input is SummarizedExperiment return SummarizedExperiment, if the
input is a tbl_df or ttBulk, return ttBulk (?)
Best wishes.
*Stefano *
Stefano Mangiola | Po
ithub
https://github.com/stemangiola/ttBulk/issues/6
At the moment I have a custom validation function
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno sab 8
more established, upon
community feedback. The transition then will be pretty easy. When that
happens, I would be interested in having some feedback from you!
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+
(Ubuntu 18.04.3 LTS)/x86_64
OK
OK
skipped
OK
Here is the log
http://bioconductor.org/spb_reports/ttBulk_buildreport_20200212081044.html#tokay2_check_anchor
I looked online but I could not find a definitive answer. An advice will be
highly appreciated.
Thanks!
Best wishes.
*Stefano *
Thanks a lot I will try.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno ven 14 feb 2020 alle ore 02:49 Marcel Ramos <
marcel.ra...@roswellpark.org> ha scritto:
Thanks a lot to both.
I have been suggested to try
`usethis::use_pipe(export = TRUE)`
probably put in place because the task is indeed challenging.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61
;t neglect this package. It is important that it will be
included in this release of Bioconductor.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno mar 24 mar 2020 alle o
Hello,
tidybulk passed all checks now. Sorry I was waiting for a response to my
answer to a reviewer's question before sending updated versions, it was the
wrong strategy.
Please let me know if anything else is needed.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral f
denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
Thanks for the assistance.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter
OK couple of "=" were missing.
I think I completed the upload.
Thanks a lot.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno gio 26 mar 2020 alle ore 18:15 s
Hello Again,
I would be happy to submit the github master with the patch tonight if you
could please confirm the commit command. Will it be tested before
integration I assume.
Thanks a lot!
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter
eR results
#'
get_differential_transcript_abundance_bulk <- function
[...]
```
However this leads to 2 problems
1) The PDF manual includes many function that are not accessible to the
user. How can I hide documented non-exported function from the manual
2) I receive the Biocheck note. "
ter branch and I am pushing it to Bioconductor. Can I have a
RELEASE branch pushed to Bioconductor rather than my master branch?
guide: "Repeat for the release branch, replacing master with the name of
the release branch, e.g., RELEASE_3_6."
Thanks.
Best wishes.
*Stefano *
them have \Sexpr{} in the man. (only rowwise from dplyr, for which
I deleted the \Sexpr{} from the header).
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno gio 4 giu 2020
wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno gio 4 giu 2020 alle ore 23:11 Shepherd, Lori <
lori.sheph...@roswellpark.org> ha scritto:
>
> The master branch is the
unwanted
neglection (as happened to me) .
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno sab 6 giu 2020 alle ore 11:08 stefano
ha scritto:
> Thanks Lori,
>
> your emai
Hello Community,
can I link upstream/DEVELOPMENT_3_12
https://www.bioconductor.org/packages/devel/bioc/html/tidybulk.html
with a branch that is not master?
For example send a local branch called DEVELOPMENT_3_12 to be in the above
web page?
Thanks a lot.
Best wishes.
*Stefano *
Stefano
Hello,
you can use bfg-repo-cleaner ,
have a read to this document, in the section "eliminate big files from repo"
https://docs.google.com/document/d/1jxg7KCMQq3kiCcvodQk9JgtU51LqczOwLit1gHiTP4Q/edit?usp=sharing
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
nge also all assays colnames
assays(new_obj)@listData <- assays(new_obj)@listData %>% map(~ {
colnames(.x) <- unique_colnames
.x
})
new_obj
}
Is there something I am missing?
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter
Thanks Martin,
I have dropped the @ call.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
*From: *Martin Morgan
*Sent: *Wednesday, 10 March 2021 11:36 AM
*To: *stefano ; bioc
make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
[[alternative HTML version
Thanks Lori.
I rsa key had changed in my system.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno mer 10 mar 2021 alle ore 23:49 Kern, Lori <
lori.sheph...@roswellpark.
/check report for BioC 3.13 - CHECK report for
tidySummarizedExperiment on riesling1 (bioconductor.org)
<http://bioconductor.org/checkResults/devel/bioc-LATEST/tidySummarizedExperiment/riesling1-checksrc.html>Best
wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laborator
in the windows build.
Any chance this can be fixed?
Thanks a lot.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
[[alternative HTML version d
rejected] master -> master (hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:
packages/sccomp.git'
Could someone please advise? Maybe I can start the submission over?
Thanks!
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss La
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exact path to all the packages in the right order
seem crucial.
how do install.packages or biocLite know what version is required and where it
is located?
Thanks a lot
Stefano
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n the development
release.
Am I missing something or got something wrong? At what point urls are
considered stable?
Thank you very much
Best wishes
Stefano
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right that if I leave package
installation to R it won't be all that reproducible, especially when dependency
relies on CRAN packages?
cheers
Stefano
> -Original Message-
> From: Dan Tenenbaum [mailto:dtene...@fredhutch.org]
> Sent: 01 March 2016 16:01
> To: B
es or similar?
Thanks in advance for helping!
Stefano
Il giorno ven 20 mar 2020 alle ore 15:08 Mattia Furlan
ha scritto:
> Hello,
>
> I am one of the maintainers of the INSPEcT package.
>
> I noticed that the vignette building on tokay2 resulted in a timeout.
> So, I tried to
HI,
We solved a similar issue for the INSPEcT package avoiding the
parallelization in the computation of examples and vignettes. In our case
it caused the timeout in the Windows environment.
Best,
Stefano
Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. <
jianhong...@duke.edu> ha s
adding new functionalities to the package.
I tried to access, for example, the directory:
https://hedgehog.fhcrc.org/bioconductor/branches/Rpacks/
but it's forbidden to my user.
Is it possible to branch directly using the Bioc repository or do I need to
do it on my local machine?
T
r attempts to open the
website:
https://support.bioconductor.org/t/deseq2/
throwing back an error. I guess that page:
https://support.bioconductor.org/?tag=DESeq2
should be opened instead.
Best regards,
Stefano
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