________________________________________
From: Dan Tenenbaum <dtenenba at fredhutch.org>
Sent: Friday, March 4, 2016 10:46 PM
To: Marini, Federico
Cc: Martin Morgan; bioc-devel
Subject: Re: [Bioc-devel] Imports, depends and warnings
Yes, it looks like devel_sequencing has not updated for a while. I'll look into
that.
Dan
----- Original Message -----
From: "Federico Marini" <marinif at uni-mainz.de>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Cc: "Martin Morgan" <Martin.Morgan at RoswellPark.org>, "bioc-devel"
<bioc-devel at r-project.org>
Sent: Friday, March 4, 2016 1:40:54 PM
Subject: Re: [Bioc-devel] Imports, depends and warnings
Hi Dan,
I pulled the devel_sequencing image - took the most up to date a couple of days
ago.
Probably even if the rocker/rstudio-daily is indeed updated daily the bioc
container isn't?
Federico
________________________________________
From: Dan Tenenbaum <dtenenba at fredhutch.org>
Sent: Friday, March 4, 2016 10:05 PM
To: Marini, Federico
Cc: Martin Morgan; bioc-devel
Subject: Re: [Bioc-devel] Imports, depends and warnings
Can you be more specific about which docker image you pulled?
Dan
----- Original Message -----
From: "Federico Marini" <marinif at uni-mainz.de>
To: "Martin Morgan" <Martin.Morgan at roswellpark.org>, "bioc-devel"
<bioc-devel at r-project.org>
Sent: Thursday, March 3, 2016 1:20:46 AM
Subject: Re: [Bioc-devel] Imports, depends and warnings
You're right, sorry for the misunderstanding.
By updating to a more recent R devel the warning disappears. I probably
should do it more often for development sakes ...
Side question but related to this, shouldn't the R version in the
current docker container for devel_* be the R devel? On the one I pulled
recently, I recall there was the R-3.2.2 - and then I reverted back to
the "local" development environment.
Federico
On 03.03.16 10:08, Morgan, Martin wrote:
Your description is not clear enough. See the github repository branch
https://github.com/mtmorgan/PkgA/tree/import-conflict
which imports NMF and ggplot2 without any warning during
R CMD build PkgA
R CMD check PkgA_0.0.1.tar.gz
with
$ R --version|head -n3
R Under development (unstable) (2016-02-27 r70232) -- "Unsuffered Consequences"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
________________________________________
From: Federico Marini <marinif at uni-mainz.de>
Sent: Thursday, March 3, 2016 3:44 AM
To: Morgan, Martin; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Imports, depends and warnings
With the minimal working example, alone the importing of NMF raises the
warning, so I guess this is due to that particular package.
Should I contact the author of that in hope he adapts its NAMESPACE to
have some nicer behavior? (or would be *just that* warning "fine" for
the Bioc ecosystem?)
Cheers,
Federico
On 02.03.16 20:41, Morgan, Martin wrote:
I think the only unavoidable case is when the package you import 'does it
wrong'. If that's not the case, then please provide an (easy-to-reproduce --
start with a simple package.skeleton() and add a couple of Imports: and
import() statements, rather than providing your current package).
Martin
________________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Federico Marini
<marinif at uni-mainz.de>
Sent: Wednesday, March 2, 2016 10:53 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Imports, depends and warnings
Hi Bioconductors,
I'm on a good way to finalize the pcaExplorer package I presented at the
recent Bioc Developers Meeting.
Trying to keep check and BiocCheck always in the background of my head,
as well as trying to be a good 'package neighbour', I am dealing with
the issue of some "Warning: replacing previous import by..." messages,
when building/loading/checking.
From my understanding, there might be some cases where this can not be
fixed, probably because an imported package in turn imports itself
another one entirely, making my own import redundant (e.g., ggplot2 for
plotting and NMF for aheatmap give this part:
Warnung: replacing previous import by ?ggplot2::unit? when loading ?NMF?
Warnung: replacing previous import by ?ggplot2::arrow? when loading ?NMF?
This happens even if I specifically just use importFrom in the NAMESPACE.
I'm kind of puzzled on this, so I thought I'd better ask out for some
expert advice on the ML. If required, I could put the package in a
GitHub repository.
Thank you in advance for any help you can provide!
Federico
--
Federico Marini, M.Sc.
Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
Division Biostatistics and Bioinformatics
University Medical Center of the Johannes Gutenberg University Mainz
Postal address: 55101 Mainz
Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
Phone: +49 (0) 6131 17-8108
Fax: +49 (0) 6131 17-2968
Web: www.imbei.uni-mainz.de
E-Mail: marinif at uni-mainz.de
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Federico Marini, M.Sc.
Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
Division Biostatistics and Bioinformatics
University Medical Center of the Johannes Gutenberg University Mainz
Postal address: 55101 Mainz
Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
Phone: +49 (0) 6131 17-8108
Fax: +49 (0) 6131 17-2968
Web: www.imbei.uni-mainz.de
E-Mail: marinif at uni-mainz.de
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.
--
Federico Marini, M.Sc.
Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
Division Biostatistics and Bioinformatics
University Medical Center of the Johannes Gutenberg University Mainz
Postal address: 55101 Mainz
Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
Phone: +49 (0) 6131 17-8108
Fax: +49 (0) 6131 17-2968
Web: www.imbei.uni-mainz.de
E-Mail: marinif at uni-mainz.de
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