[Bioc-devel] RELEASE_3_15 branch frozen
Hello Maintainers, The branch RELEASE_3_15 is now frozen. You will not be able to push your commits to RELEASE_3_15 anymore. Please let us know if you have questions. See release schedule for other important up coming deadlines http://bioconductor.org/developers/release-schedule/ Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] RELEASE_3_15 branch frozen in a few hours
We are moving forward with the 3.16 release schedule. In roughly 4 hours the RELEASE_3_15 will be frozen and no longer accept commits. Any changes or bug corrections that are not pushed up by this time will not be in the Bioconductor 3.15 version of the package as we do not allow updates to past/frozen releases. http://bioconductor.org/developers/release-schedule/ You still may push to the Bioconductor master/devel branch at any time. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [R-pkg-devel] Invalid UTF-8
Thanks Ivan, I found two simple ways to convert this old file to UTF-8: (i) In emacs, C-x f (default is utf-8) (ii) In RStudio, set Tools-Global Options-Code-Saving- Default text encoding to UTF-8 No problem with new files. G;ran (US keyboard) Den 2022-10-17 kl. 11:18, skrev Ivan Krylov: В Mon, 17 Oct 2022 11:07:25 +0200 Göran Broström пишет: warning: invalid UTF-8 in comment [-Winvalid-utf8] (It's my name) So I wonder: How do I make valid UTF-8 in comment? The file GB_zeroin.c is saved in Latin-1 encoding. The warning should go away once you convert it to UTF-8. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Rd] Installation failure in non-UTF-8 MBCS locale
On 10/16/22 19:35, Gábor Csárdi wrote:
I am sorry, part of the output is garbled, as the email's encoding is
different, but the error is hopefully still clear.
This is Ubuntu 20.04, yesterday's R devel or R release, in the zh_CN locale.
The zh_CN.UTF-8 locale is fine, and it is a much better option, so I
am not sure if this is considered to be a bug.
Right, one should use UTF-8 (on all platforms) as the locale encoding.
For historical reasons, one can still parse UTF-8 when R is running e.g.
in Latin 1 locale. This is still supported as older Windows systems
don't use UTF-8 as the native encoding, yet.
When R runs in a non-UTF-8 multi-byte locale, it cannot parse UTF-8 R
input files. This is due to how the parser works and supporting that
would require a major rewrite which would not be worth the effort
(instead effort has been spent on supporting UTF-8 as the native
encoding on Windows).
Best
Tomas
install.packages("evaluate")
��װ��'/root/R/x86_64-pc-linux-gnu-library/4.3'
(��Ϊ'lib'û�б�ָ��)
�Կ�URL��https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/evaluate_0.17.tar.gz'
Content type 'binary/octet-stream' length 25984 bytes (25 KB)
==
downloaded 25 KB
* installing *source* package 'evaluate' ...
** �ɹ���'evaluate'MD5�ͼ���
** using staged installation
Warning in parse(con, encoding = "UTF-8") :
argument encoding="UTF-8" is ignored in MBCS locales
Error : invalid multibyte character in parser (:11:32)
ERROR: installing package DESCRIPTION failed for package 'evaluate'
* removing '/root/R/x86_64-pc-linux-gnu-library/4.3/evaluate'
���صij���
'/tmp/Rtmp3O0zlO/downloaded_packages'��
Warning message:
In install.packages("evaluate") : ��װ��'evaluate'ʱ�˳�??��ֵ0
R-release produces the same error.
Dockerfile to reproduce this:
FROM ubuntu:20.04
RUN apt-get -y update && apt-get -y install curl locales
RUN curl -Ls
https://github.com/r-lib/rig/releases/download/latest/rig-linux-latest.tar.gz
| tar xz -C /usr/local
RUN rig add devel
RUN rig add release
RUN locale-gen zh_CN
RUN uname -a
RUN R -q -e 'sessionInfo()'
RUN LC_ALL=zh_CN R -q -e 'install.packages("evaluate")'
G.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [R-pkg-devel] Invalid UTF-8
В Mon, 17 Oct 2022 11:07:25 +0200 Göran Broström пишет: > warning: invalid UTF-8 in comment [-Winvalid-utf8] > (It's my name) > > So I wonder: How do I make valid UTF-8 in comment? The file GB_zeroin.c is saved in Latin-1 encoding. The warning should go away once you convert it to UTF-8. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Invalid UTF-8
Hello, I suddenly get Warnings from CRAN (clang): warning: invalid UTF-8 in comment [-Winvalid-utf8] (It's my name) So I wonder: How do I make valid UTF-8 in comment? (I already have "Encoding: UTF-8" in the DESCRIPTION file) Thanks, Göran __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[Rd] Installation failure in non-UTF-8 MBCS locale
I am sorry, part of the output is garbled, as the email's encoding is
different, but the error is hopefully still clear.
This is Ubuntu 20.04, yesterday's R devel or R release, in the zh_CN locale.
The zh_CN.UTF-8 locale is fine, and it is a much better option, so I
am not sure if this is considered to be a bug.
> install.packages("evaluate")
��װ��'/root/R/x86_64-pc-linux-gnu-library/4.3'
(��Ϊ'lib'û�б�ָ��)
�Կ�URL��https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/evaluate_0.17.tar.gz'
Content type 'binary/octet-stream' length 25984 bytes (25 KB)
==
downloaded 25 KB
* installing *source* package 'evaluate' ...
** �ɹ���'evaluate'MD5�ͼ���
** using staged installation
Warning in parse(con, encoding = "UTF-8") :
argument encoding="UTF-8" is ignored in MBCS locales
Error : invalid multibyte character in parser (:11:32)
ERROR: installing package DESCRIPTION failed for package 'evaluate'
* removing '/root/R/x86_64-pc-linux-gnu-library/4.3/evaluate'
���صij���
'/tmp/Rtmp3O0zlO/downloaded_packages'��
Warning message:
In install.packages("evaluate") : ��װ��'evaluate'ʱ�˳�??��ֵ0
R-release produces the same error.
Dockerfile to reproduce this:
FROM ubuntu:20.04
RUN apt-get -y update && apt-get -y install curl locales
RUN curl -Ls
https://github.com/r-lib/rig/releases/download/latest/rig-linux-latest.tar.gz
| tar xz -C /usr/local
RUN rig add devel
RUN rig add release
RUN locale-gen zh_CN
RUN uname -a
RUN R -q -e 'sessionInfo()'
RUN LC_ALL=zh_CN R -q -e 'install.packages("evaluate")'
G.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] tools:: extracting pkg dependencies from DCF
Gabriel and Simon
I completely agree with what you are saying.
The thing is that obtaining recursive deps, all/most whatever, is already
well supported in core R. What is missing is just this single functionality
I am requesting.
If you will look into the branch you can see there is mirror.packages
function meant to mirror a slice of CRAN. It is doing exactly what you
described: package_dependencies; to obtain recursive deps, then download
all, etc.
I would love to have this function provided by core R as well, but we need
to start somewhere.
There are other use cases as well.
For example CI, where one wants to install all/most dependencies and then
run R CMD check. Then we don't worry about recursive deps are they will be
resolved automatically.
I don't think it's reasonable to force users to use 3rd party packages to
handle such a common and simple use case. Otherwise one has to hard code
deps in CI script. Not robust at all.
packages.dcf and repos.dcf makes all that way easier, and are solid base
for building customized orchestration like mirroring slice of CRAN.
Best regards
Jan
On Sun, Oct 16, 2022, 01:31 Simon Urbanek
wrote:
> Jan,
>
> I think using a single DCF as input is not very practical and would not be
> useful in the context you describe (creating self contained repos) since
> they typically concern a list of packages, but essentially splitting out
> the part of install.packages() which determines which files will be pulled
> from where would be very useful as it would be trivial to use it to create
> repository (what we always do in corporate environments) instead of
> installing the packages. I suspect that install packages is already too
> complex so instead of adding a flag to install.packages one could move that
> functionality into a separate function - we all do that constantly for the
> sites we manage, so it would be certainly something worthwhile.
>
> Cheers,
> Simon
>
>
> > On Oct 15, 2022, at 7:14 PM, Jan Gorecki wrote:
> >
> > Hi Gabriel,
> >
> > It's very nice usage you provided here. Maybe instead of adding new
> > function we could extend packages_depenedncies then? To accept file path
> to
> > dsc file.
> >
> > What about repos.dcf? Maybe additional repositories could be an attribute
> > attached to returned character vector.
> >
> > The use case is to, for a given package sources, obtain its dependencies,
> > so one can use that for installing them/mirroring CRAN subset, or
> whatever.
> > The later is especially important for a production environment where one
> > wants to have fixed version of packages, and mirroring relevant subset of
> > CRAN is the most simple, and IMO reliable, way to manage such
> environment.
> >
> > Regards
> > Jan
> >
> > On Fri, Oct 14, 2022, 23:34 Gabriel Becker
> wrote:
> >
> >> Hi Jan and Jan,
> >>
> >> Can you explain a little more what exactly you want the non-recursive,
> >> non-version aware dependencies from an individual package for?
> >>
> >> Either way package_dependencies will do this for you* with a little
> >> "aggressive convincing". It wants output from available.packages, but
> who
> >> really cares what it wants? It's a function and we are people :)
> >>
> >>> library(tools)
> >>> db <- read.dcf("~/gabe/checkedout/rtables_clean/DESCRIPTION")
> >>> package_dependencies("rtables", db, which = intersect(c("Depends",
> >> "Suggests", "Imports", "LinkingTo"), colnames(db)))
> >> $rtables
> >> [1] "methods""magrittr" "formatters" "dplyr" "tibble"
> >> [6] "tidyr" "testthat" "xml2" "knitr" "rmarkdown"
> >> [11] "flextable" "officer""stats" "htmltools" "grid"
> >>
> >>
> >> The only gotcha that I see immediately is that "LinkingTo" isn't always
> >> there (whereas it is with real output from available.packages). If you
> >> know your package doesn't have that (or that it does) at call time ,
> this
> >> becomes a one-liner:
> >>
> >> package_dependencies("rtables", db =
> >> read.dcf("~/gabe/checkedout/rtables_clean/DESCRIPTION"), which =
> >> c("Depends", "Suggests", "Imports"))
> >> $rtables
> >> [1] "methods""magrittr" "formatters" "dplyr" "tibble"
> >> [6] "tidyr" "testthat" "xml2" "knitr" "rmarkdown"
> >> [11] "flextable" "officer""stats" "htmltools" "grid"
> >>
> >> You can also trick it a slightly different way by giving it what it
> >> actually wants
> >>
> >>> tdir <- tempdir()
> >>> file.copy("~/gabe/checkedout/rtables_clean/DESCRIPTION",
> file.path(tdir,
> >> "PACKAGES"))
> >> [1] TRUE
> >>> avl <- available.packages(paste0("file://", tdir))
> >>> library(tools)
> >>> package_dependencies("rtables", avl)
> >> $rtables
> >> [1] "methods""magrittr" "formatters" "stats" "htmltools"
> >> [6] "grid"
> >>
> >>> package_dependencies("rtables", avl, which = "all")
> >> $rtables
> >> [1] "methods""magrittr" "formatters" "stats" "htmltools"
> >> [6] "grid" "dplyr" "tibble" "tidyr" "testthat"
> >> [11]
