[Bioc-devel] merge the release and the dev version to eliminate errors
Hi, I am trying to fix the package on new dev 3.9. The errors appears to be different from what it is in the release version 3.8. The errors in 3.9 is in window system, while the errors in 3.8 are in the other two systems. Is there a way I can merge these two? https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/mlm4omics/malbec1-install.html http://bioconductor.org/checkResults/devel/bioc-LATEST/mlm4omics/ I saw the report in 3.9 were all okay once, after I pushed the changes. Now , the vignette seems to have errors. Please advise, Irene SL Zeng From: Bioc-devel on behalf of bioc-devel-requ...@r-project.org Sent: Friday, 23 November 2018 12:05 a.m. To: bioc-devel@r-project.org Subject: Bioc-devel Digest, Vol 176, Issue 22 Send Bioc-devel mailing list submissions to bioc-devel@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioc-devel or, via email, send a message with subject or body 'help' to bioc-devel-requ...@r-project.org You can reach the person managing the list at bioc-devel-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioc-devel digest..." Today's Topics: 1. Cannot access remote upstream after changing the laptop (Tang, Wenhao) 2. Re: Cannot access remote upstream after changing the laptop (Shepherd, Lori) 3. Re: Cannot access remote upstream after changing the laptop (Turaga, Nitesh) 4. =?gb2312?b?tPC4tDogIENhbm5vdCBhY2Nlc3MgcmVtb3RlIHVw?= =?gb2312?b?c3RyZWFtIGFmdGVyIGNoYW5naW5nIHRoZSBsYXB0b3A=?= (Tang, Wenhao) 5. R 3.6 Compiling issues, are there any binaries available? (Casper Peters) 6. Re: 80% of man pages must have runnable examples (package with numerous Shiny apps) (L Rutter) 7. Re: 80% of man pages must have runnable examples (package with numerous Shiny apps) (Kevin RUE) 8. Re: Cannot access remote upstream after changing the laptop (Dario Strbenac) -- Message: 1 Date: Wed, 21 Nov 2018 13:27:47 + From: "Tang, Wenhao" To: "bioc-devel@r-project.org" Subject: [Bioc-devel] Cannot access remote upstream after changing the laptop Message-ID: Content-Type: text/plain; charset="utf-8" Hi, I am using a new laptop right now, and would like to update package using it. However I can no longer access the upstream when I "git fetch --all": wt215@DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master) $ git remote -v origin https://github.com/WT215/bayNorm.git (fetch) origin https://github.com/WT215/bayNorm.git (push) upstreamg...@git.bioconductor.org:packages/bayNorm.git (fetch) upstreamg...@git.bioconductor.org:packages/bayNorm.git (push) wt215@DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master) $ git fetch --all Fetching origin Fetching upstream g...@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. error: Could not fetch upstream Because I am using a new machine, the local SSH information may lost, which is highly likely the cause. May I ask what should I do? Thanks a lot! Best wishes, Wenhao [[alternative HTML version deleted]] -- Message: 2 Date: Wed, 21 Nov 2018 13:31:32 + From: "Shepherd, Lori" To: "Tang, Wenhao" , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] Cannot access remote upstream after changing the laptop Message-ID: Content-Type: text/plain; charset="utf-8" You can log onto the Git Credentials App at any time and add new/additional ssh-keys https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Tang, Wenhao Sent: Wednesday, November 21, 2018 8:27:47 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Cannot access remote upstream after changing the laptop Hi, I am using a new laptop right now, and would like to update package using it. However I can no longer access the upstream when I "git fetch --all": wt215@DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master) $ git remote -v origin https://github.com/WT215/bayNorm.git (fetch) origin https://github.com/WT215/bayNorm.git (push) upstreamg...@git.bioconductor.org:packages/bayNorm.git (fetch) upstreamg...@git.bioconductor.org:packages/bayNorm.git (push) wt215@DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master) $ git fetch --all Fetching origin Fetching
[Bioc-devel] Bioc 3.9 software builds Nov 23
The Linux builder for Bioc 3.9 was taking an unusually long time to complete the software builds today. Because of this, today's report will only include Windows and Mac results. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] build/check report for experimental data not updating
Hi all, I noticed that the check report for experimental data (Bioc3.9) is not updating. The snapshot date is still "Sun, 18 Nov 2018". Thanks, Carmen -- Carmen Maria Livi Post Doctoral Researcher Ferrari Lab IFOM - Fondazione Istituto firc Oncologia Molecolare Via Adamello 16 20139 Milano, Italy ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] [tryExcept] New try Function
Hi Emil,
First, thanks for the response. As you mentioned, a lot of times tryCatch
does the work, as you can return a value. However, sometimes it is useful
to assign several variables when an error occurs. You could do it with <<-,
but I prefer to reduce it's usage unless completely necessary.
I guess that the attachment was missed in the moderation. Here it is the
function:
tryExcept <- function (expr,
except = {})
{
doTryExcept <- function(expr, parentenv) {
.Internal(.addCondHands("error", list(NULL), parentenv,
environment(), FALSE))
expr
}
parentenv <- parent.frame()
doTryExcept(return(expr), parentenv)
invisible(except)
}
As you can see, the tryExcept function uses a simplified version of the
tryCatch architecture, but it allows you to pass by a second expression
that is evaluated in case an error occurs during the evaluation of the
first expression. It could even work as an infix operator:
`%except%` <- tryExcept
# dummy example
{foo <- "foo"} %except% {foo <- "foo bar"}
print(foo) # "foo"
{ foo <- "foo"
stop()
} %except% {
foo <- "foo bar"
}
print(foo) # "foo bar"
It's main downside is that you are not able to handle the error occured,
although there is the possibility to add a 'silent' parameter such as in
'try' in order to print the error if desired. All in all, this would be a
function for simple error handling, but I think it would be practical, and
you can always move to tryCatch if you need a more complex error handling.
I will be looking forward to hearing your insights.
Best,
Ernest Benedito
Missatge de Emil Bode del dia dv., 23 de nov. 2018
a les 13:17:
> Hi Ernest,
>
> To start: I don't see an attachment, I think they're not (always) allowed
> on this mailing-list. If you want to send something, text is your safest
> bet.
> But regarding the issue of tryCatch: I think you're not fully using what
> it already can do. In almost all circumstances I've encountered the
> following works fine:
> res <- tryCatch(expr, error = function(cond) {
> # a bunch of code
> # Some value to be stored in res
> })
> The only difference is that now "#abunchofcode" is run from inside a
> function, which means you're working in a different environment, and if you
> want to assign values to other variables you need to use <<- or assign.
> For a modified function, I think it would be nice if there's a way to
> supply an expression instead of a function, so that evaluation (and
> assignment!) takes place in the same environment as the main code in the
> tryCatch (in expr). Is that what you made?
> And with the current tryCatch, you could use something like this:
> res <- tryCatch(expr, error=function(e) evalq({
> # a bunch of code
> # Some value for res
> }, envir=parent.frame(4))) # The 4 is because some internal functions are
> involved, parent.frame(4) is the same environment as used by expr
>
> Although this is cumbersome, and it gets even more cumbersome if you want
> to access the error-object in #abunchofcode, or use #abunchofcode to return
> to a higher level, so I get it you're looking for a more elegant solution.
>
> Best regards,
> Emil Bode
>
> On 23/11/2018, 08:49, "R-devel on behalf of Ernest Benedito" <
> r-devel-boun...@r-project.org on behalf of ebenedi...@gmail.com> wrote:
>
> Hi everyone,
>
> When dealing with errors, sometimes I want to run a bunch of code when
> an error occurs.
> For now I usually use a structure such as:
>
> res <- tryCatch(expr, error = function(cond) cond) # or try(expr)
>
> if (inherits(res, “error”)) # or inherits(res, “try-error”)
> # a bunch of code
>
> I though it would be useful to have a function that does this
> naturally, so I came up with the attached function.
>
> I would be glad to hear your insights and if you think it would make
> sense to add this function to R.
>
> Best regards,
> Ernest
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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[Rd] R 3.5.2 scheduled for December 20
Full schedule available on developer.r-project.org -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [tryExcept] New try Function
Hi Ernest,
To start: I don't see an attachment, I think they're not (always) allowed on
this mailing-list. If you want to send something, text is your safest bet.
But regarding the issue of tryCatch: I think you're not fully using what it
already can do. In almost all circumstances I've encountered the following
works fine:
res <- tryCatch(expr, error = function(cond) {
# a bunch of code
# Some value to be stored in res
})
The only difference is that now "#abunchofcode" is run from inside a function,
which means you're working in a different environment, and if you want to
assign values to other variables you need to use <<- or assign.
For a modified function, I think it would be nice if there's a way to supply an
expression instead of a function, so that evaluation (and assignment!) takes
place in the same environment as the main code in the tryCatch (in expr). Is
that what you made?
And with the current tryCatch, you could use something like this:
res <- tryCatch(expr, error=function(e) evalq({
# a bunch of code
# Some value for res
}, envir=parent.frame(4))) # The 4 is because some internal functions are
involved, parent.frame(4) is the same environment as used by expr
Although this is cumbersome, and it gets even more cumbersome if you want to
access the error-object in #abunchofcode, or use #abunchofcode to return to a
higher level, so I get it you're looking for a more elegant solution.
Best regards,
Emil Bode
On 23/11/2018, 08:49, "R-devel on behalf of Ernest Benedito"
wrote:
Hi everyone,
When dealing with errors, sometimes I want to run a bunch of code when an
error occurs.
For now I usually use a structure such as:
res <- tryCatch(expr, error = function(cond) cond) # or try(expr)
if (inherits(res, “error”)) # or inherits(res, “try-error”)
# a bunch of code
I though it would be useful to have a function that does this naturally, so
I came up with the attached function.
I would be glad to hear your insights and if you think it would make sense
to add this function to R.
Best regards,
Ernest
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