Dear Bioconductor Core Team,
I am the maintainer of cliqueMS. The package was flagged to deprecation
but I have been able to fix the error that was causing the failure in
the checks. I just had to remove a dependency that is no longer on CRAN
and replace for a package available there. After
В Thu, 25 Apr 2024 11:54:49 -0700
Bryan Hanson пишет:
> So my version of gs blows things up!
The relatively good news is that GhostScript is not solely to blame. A
fresh build of "GPL Ghostscript 10.03.0 (2024-03-06)" was able to
reduce the files to 16..70% of their original size on my
Thank you so much Ivan for investigating. I didn’t even notice the *increase*!
The results of the tests you requested are very interesting:
R > tools::compactPDF("doc", gs_quality = "none", verbose = TRUE)
qs_quality="none" : use_gs=FALSE, use_qpdf=TRUE
#{pdf}s = length(paths) = 8
-
В Thu, 25 Apr 2024 08:54:41 -0700
Bryan Hanson пишет:
> 'gs+qpdf' made some significant size reductions:
> compacted 'Vig_02_Conceptual_Intro_PCA.pdf' from 432Kb to 143Kb
> compacted 'Vig_03_Step_By_Step_PCA.pdf' from 414Kb to 101Kb
> compacted 'Vig_04_Scores_Loadings.pdf' from
I forgot to mention that the BLOSUM and PAM substitution matrices have
also moved from Biostrings to the new pwalign package.
37 software packages were affected by this move (see list below). All of
them have been fixed. If you maintain one of them, please resync your
GitHub repo with the repo
On Thu, Apr 25, 2024 at 4:24 AM Ivan Krylov via R-devel
wrote:
>
> On Wed, 24 Apr 2024 15:31:39 -0500 (CDT)
> luke-tierney--- via R-devel wrote:
>
> > We would be better off (in my view, not necessarily shared by others
> > in R-core) if we could get to a point where:
> >
> > all entry
On 4/25/24 07:04, Kurt Hornik wrote:
...
> Sure, I'll look into adding something. (Too late for 4.4.0, of course.)
>
> Best
> -k
Great. Thanks!
H.
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
I have a peculiar problem regarding vignette compaction. Package LearnPCA has 8
vignettes. I am working on the devel branch with code at
https://github.com/bryanhanson/LearnPCA/tree/devel.
The problem is that at CRAN and on win-builder they detect that 5/8 vignettes
need to be compacted.
On Thu, 25 Apr 2024 14:45:04 +0200
Jeroen Ooms wrote:
> Thoughts?
How verboten would it be to create an empty external pointer object,
add it to the preserved list, and set an on-exit finalizer to clean up
the curl multi-handle? As far as I can tell, the internet module is not
supposed to be
> Hervé Pagès writes:
> On 4/24/24 23:07, Kurt Hornik wrote:
>>> Hervé Pagès writes:
>>> Hi Kurt,
>>> Is it intended that numeric_version() returns an error by default on
>>> non-character input in R 4.4.0?
>> Dear Herve, yes, that's the intention.
>>
>>> It seems that I can turn this
> Dirk Eddelbuettel writes:
> Hi Kurt,
> On 25 April 2024 at 08:07, Kurt Hornik wrote:
> | > Hervé Pagès writes:
> |
> | > Hi Kurt,
> | > Is it intended that numeric_version() returns an error by default on
> | > non-character input in R 4.4.0?
> |
> | Dear Herve, yes, that's the
A clean build solves it for me too. Thank you!
(I need to add this to my "have you tried turning it off and back on
again?" list ...)
Ben
On 2024-04-25 8:07 a.m., luke-tier...@uiowa.edu wrote:
I saw it also on some of my Ubuntu builds, but the issue went away
after a make clean/make,
I'd like to raise this again now that 4.4 is out.
Below is a more complete patch which includes a function to properly
cleanup libcurl when R quits. Implementing this is a little tricky
because libcurl is a separate "module" in R, perhaps there is a better
way, but this works:
view:
Hi Kurt,
On 25 April 2024 at 08:07, Kurt Hornik wrote:
| > Hervé Pagès writes:
|
| > Hi Kurt,
| > Is it intended that numeric_version() returns an error by default on
| > non-character input in R 4.4.0?
|
| Dear Herve, yes, that's the intention.
|
| > It seems that I can turn this into
I saw it also on some of my Ubuntu builds, but the issue went away
after a make clean/make, so maybe give that a try.
Best,
luke
On Wed, 24 Apr 2024, Ben Bolker wrote:
I'm using bleeding-edge R-devel, so maybe my build is weird. Can anyone
else reproduce this?
View() seems to crash on
On Wed, 24 Apr 2024 15:31:39 -0500 (CDT)
luke-tierney--- via R-devel wrote:
> We would be better off (in my view, not necessarily shared by others
> in R-core) if we could get to a point where:
>
> all entry points listed in installed header files can be used in
> packages, at least
No, that’s absolutely fine. I actually had forgotten that substitution matrices
were also used in the examples of msaMuscle(). Thanks for fixing!
Cheers, Ulrich
From: Hervé Pagès
Sent: Thursday, April 25, 2024 10:11 AM
To: ulr...@bodenhofer.com
Cc: bioc-devel@r-project.org; 'Martin Grigorov'
Good. I also just pushed 2 additional small tweaks (commits 0e98500 and
84c8ed5) right after you pushed yours. Hopefully I didn't step on your toes.
H.
On 4/25/24 01:04, Ulrich Bodenhofer wrote:
>
> Great, thanks, Hervé! I also made two more fixes and pushed them.
>
> Cheers, Ulrich
>
>
Great, thanks, Hervé! I also made two more fixes and pushed them.
Cheers, Ulrich
From: Hervé Pagès
Sent: Thursday, April 25, 2024 9:52 AM
To: ulr...@bodenhofer.com
Cc: bioc-devel@r-project.org; 'Martin Grigorov'
Subject: Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
I'm done. Please resync you GitHub repo.
Best,
H.
On 4/25/24 00:14, Ulrich Bodenhofer wrote:
>
> Great, thanks, Hervé, so I’ll simply wait for the update. If there is
> anything I should do, just let me know.
>
> Thanks and best regards,
>
> Ulrich
>
> *From:*Hervé Pagès
> *Sent:* Thursday,
Great, thanks, Hervé, so I’ll simply wait for the update. If there is anything
I should do, just let me know.
Thanks and best regards,
Ulrich
From: Hervé Pagès
Sent: Thursday, April 25, 2024 9:06 AM
To: ulr...@bodenhofer.com; 'Martin Grigorov'
Cc: bioc-devel@r-project.org
Subject:
Hi Ulrich,
Yes the substitution matrices are now in pwalign. I'm taking care of
msa. Sorry for that.
Best,
H.
On 4/24/24 23:25, Ulrich Bodenhofer wrote:
> Ah, thank you very much, sorry for having overlooked this! Yes, that seems
> the source of the problem. Hervé, should I wait for your
On 4/24/24 23:07, Kurt Hornik wrote:
>> Hervé Pagès writes:
>> Hi Kurt,
>> Is it intended that numeric_version() returns an error by default on
>> non-character input in R 4.4.0?
> Dear Herve, yes, that's the intention.
>
>> It seems that I can turn this into a warning by setting
>>
On Wed, 24 Apr 2024 19:35:42 -0400
Ben Bolker wrote:
> I'm using bleeding-edge R-devel, so maybe my build is weird. Can
> anyone else reproduce this?
>
>View() seems to crash on just about anything.
Not for me, sorry.
If you have a sufficiently new processor, you can use `rr` [*] to
Ah, thank you very much, sorry for having overlooked this! Yes, that seems the
source of the problem. Hervé, should I wait for your update or rather change
the package myself? The latter won’t be a problem for me. I suppose it is just
about adding ‘pwalign’ as an additional dependency, right?
> Hervé Pagès writes:
> Hi Kurt,
> Is it intended that numeric_version() returns an error by default on
> non-character input in R 4.4.0?
Dear Herve, yes, that's the intention.
> It seems that I can turn this into a warning by setting
>
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