0Ok, thanks.
I have tried all suggested by you. But no package or function detected to
be dependent on BiocInstaller or Bioclite.
I have tested on both windows and linux OSs, but none shown any warning
related to these deprecated packages. Everything working fine on my PCs but
not able to pass through CRAN check at the CRAN organisation.
On Mon, 12 Nov 2018, 5:45 pm Martin Morgan <mtmorgan.b...@gmail.com wrote:
> I cannot tell whether this will be helpful or not. It looks to me like the
> warning occurs when one of your dependencies uses BiocInstaller. You could
> create a database of all available packages
>
> chooseCRANmirror()
> chooseBioCmirror()
> db = available.packages()
>
> find the installation dependencies of your package dependencies
>
> flds = c("Depends", "Imports", "LinkingTo")
> pkgs = read.dcf("DESCRIPTION", flds)[, flds]
> pkgs = trimws(unlist(strsplit(pkgs, ","), use.names = FALSE))
> pkgs = pkgs[!is.na(pkgs)]
>
> and discover which references BiocInstaller
>
> deps = tools::package_dependencies(pkgs, db, recursive = TRUE)
> unlist(deps)["BiocInstaller" %in% unlist(deps)]
>
> But actually when I run this with version 2.2 of your package I don't see
> a dependency on BiocInstaller (other than in your own package).
>
> Martin
>
> On 11/11/18, 9:55 PM, "R-package-devel on behalf of dhamma pal" <
> r-package-devel-boun...@r-project.org on behalf of dhammap...@uohyd.ac.in>
> wrote:
>
> The latest version donot use BIOCINSTALLER or bioclite, still getting a
> warning.
>
> Errors are not detected in the current version, i.e. 2.3 version of
> maGUI.
> But errors are getting reported in the earlier version i.e., 2.2 which
> is
> not the making the current version to pass through the CRAN. I have
> tried
> to submit the corrected package with version 2.2 to rectify the
> errors,
> but getting overriden error. Now how to ugrade maGUI to 2.3?
> Thanks in advance.
>
>
> ---------- Forwarded message ---------
> From: <lig...@statistik.tu-dortmund.de>
> Date: Thu, 8 Nov 2018, 1:12 pm
> Subject: [CRAN-pretest-archived] CRAN submission maGUI 2.3
> To: <dhammap...@uohyd.ac.in>
> Cc: <cran-submissi...@r-project.org>
>
>
> Dear maintainer,
>
> package maGUI_2.3.tar.gz does not pass the incoming checks
> automatically,
> please see the following pre-tests:
> Windows: <
>
> https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/Windows/00check.log
> >
> Status: 1 WARNING, 1 NOTE
> Debian: <
>
> https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/Debian/00check.log
> >
> Status: 1 NOTE
>
> Last released version's CRAN status: ERROR: 2
> See: <https://CRAN.R-project.org/web/checks/check_results_maGUI.html>
>
> CRAN Web: <https://cran.r-project.org/package=maGUI>
>
> Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help
> on
> the R-package-devel mailing list:
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> If you are fairly certain the rejection is a false positive, please
> reply-all to this message and explain.
>
> More details are given in the directory:
> <
>
> https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/
> >
> The files will be removed after roughly 7 days.
>
> No strong reverse dependencies to be checked.
>
> Best regards,
> CRAN teams' auto-check service
> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
> Check: CRAN incoming feasibility, Result: NOTE
> Maintainer: 'Dhammapal Bharne <dhammap...@uohyd.ac.in>'
>
> New submission
>
> Package was archived on CRAN
>
> CRAN repository db overrides:
> X-CRAN-Comment: Archived on 2018-11-01 as check warnings were not
> corrected despite a month's notice.
>
> Needed change for BioC 3.8
>
> Flavor: r-devel-windows-ix86+x86_64
> Check: whether package can be installed, Result: WARNING
> Found the following significant warnings:
> Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the
> 'BiocManager' CRAN
> See 'd:/RCompile/CRANincoming/R-devel/maGUI.Rcheck/00install.out' for
> details.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
On 12 Nov 2018 5:45 pm, "Martin Morgan" <mtmorgan.b...@gmail.com> wrote:
I cannot tell whether this will be helpful or not. It looks to me like the
warning occurs when one of your dependencies uses BiocInstaller. You could
create a database of all available packages
chooseCRANmirror()
chooseBioCmirror()
db = available.packages()
find the installation dependencies of your package dependencies
flds = c("Depends", "Imports", "LinkingTo")
pkgs = read.dcf("DESCRIPTION", flds)[, flds]
pkgs = trimws(unlist(strsplit(pkgs, ","), use.names = FALSE))
pkgs = pkgs[!is.na(pkgs)]
and discover which references BiocInstaller
deps = tools::package_dependencies(pkgs, db, recursive = TRUE)
unlist(deps)["BiocInstaller" %in% unlist(deps)]
But actually when I run this with version 2.2 of your package I don't see a
dependency on BiocInstaller (other than in your own package).
Martin
On 11/11/18, 9:55 PM, "R-package-devel on behalf of dhamma pal" <
r-package-devel-boun...@r-project.org on behalf of dhammap...@uohyd.ac.in>
wrote:
The latest version donot use BIOCINSTALLER or bioclite, still getting a
warning.
Errors are not detected in the current version, i.e. 2.3 version of
maGUI.
But errors are getting reported in the earlier version i.e., 2.2 which
is
not the making the current version to pass through the CRAN. I have
tried
to submit the corrected package with version 2.2 to rectify the errors,
but getting overriden error. Now how to ugrade maGUI to 2.3?
Thanks in advance.
---------- Forwarded message ---------
From: <lig...@statistik.tu-dortmund.de>
Date: Thu, 8 Nov 2018, 1:12 pm
Subject: [CRAN-pretest-archived] CRAN submission maGUI 2.3
To: <dhammap...@uohyd.ac.in>
Cc: <cran-submissi...@r-project.org>
Dear maintainer,
package maGUI_2.3.tar.gz does not pass the incoming checks
automatically,
please see the following pre-tests:
Windows: <
https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/Windows/00check.log
>
Status: 1 WARNING, 1 NOTE
Debian: <
https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/Debian/00check.log
>
Status: 1 NOTE
Last released version's CRAN status: ERROR: 2
See: <https://CRAN.R-project.org/web/checks/check_results_maGUI.html>
CRAN Web: <https://cran.r-project.org/package=maGUI>
Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help
on
the R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please
reply-all to this message and explain.
More details are given in the directory:
<
https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/
>
The files will be removed after roughly 7 days.
No strong reverse dependencies to be checked.
Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Dhammapal Bharne <dhammap...@uohyd.ac.in>'
New submission
Package was archived on CRAN
CRAN repository db overrides:
X-CRAN-Comment: Archived on 2018-11-01 as check warnings were not
corrected despite a month's notice.
Needed change for BioC 3.8
Flavor: r-devel-windows-ix86+x86_64
Check: whether package can be installed, Result: WARNING
Found the following significant warnings:
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the
'BiocManager' CRAN
See 'd:/RCompile/CRANincoming/R-devel/maGUI.Rcheck/00install.out' for
details.
[[alternative HTML version deleted]]
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R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
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