Re: [Bioc-devel] Distinction between release and devel package websites
to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave
Re: [Bioc-devel] Distinction between release and devel package websites
systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing
Re: [Bioc-devel] Distinction between release and devel package websites
- Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: bioc-devel@r-project.org Sent: Wednesday, July 23, 2014 6:41:06 PM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Date: Wed, 23 Jul 2014 11:33:44 -0700 From: Martin Morgan mtmor...@fhcrc.org To: Matthew McCall mcca...@gmail.com, Michael Lawrence lawrence.mich...@gene.com Cc: bioc-devel@r-project.org bioc-devel@r-project.org Subject: Re: [Bioc-devel] Distinction between release and devel package websites Message-ID: 53d8.1090...@fhcrc.org Content-Type: text/plain; charset=windows-1252; format=flowed Dan has implemented these changes. Go to the Bioconductor home page and in the search box at the top right enter supraHex (winner of the ISMB 2014 Best Artwork Award! Check out the URL on the package landing page). You'll see that the first link is to supraHex, and the second to supraHex (development version). On the supraHex (development version) page you'll see text indicating that you're looking at the development version, and for the release you should go somewhere else. Further down the installation instructions are now in their own section, adding a little more emphasis. The Documentation section includes instructions -- browseVignettes(supraHex) -- for getting your version of the vignettes. The 'download' section is now called 'Package Archives'. The Package Archives section starts with a sentence pointing to Installation instructions. Mousing over one of the links pops up a tool tip encouraging you once again to use biocLite. Relevant changes also apply to release landing pages. As Vince mentioned, it is REALLY IMPORTANT that users do not mix release and devel versions of packages in a single library. Even if it 'works for package X', this invariably leads to incompatibilities and confusion. For those users wanting new features, tell them to switch to using the development version, e.g., as outlined at http://bioconductor.org/packages/release/bioc/html/supraHex.html Thanks for your input, Martin Hi, I just caught up to date with this conversation and I like the implemented changes. Great job! I hope that they will be effective. Just some minor details: * Maybe the tooltip over the zip and tarball links when on a devel page can show a link to http://bioconductor.org/developers/how-to/useDevel/ Alternatively, the link could be under the Package Archives section by modifying Follow Installation instructions to use this package in your R session. to something like Follow Installation instructions to use this package in your R session. Verify that you are using the devel version. * I was looking forward to the svn links (for devel pages), are you still going to add them? If not, I understand that they are not necessary. I just added this, a Browse/checkout source link in the package archives section. This is for release packages as well as devel. There's no such link for annotation packages because those don't live in svn.. Dan Also, about svn, well I guess that I'm from the more recent group that knows git/Mercurial but never learned svn (hence why I haven't followed up on Hervé's suggestion in an earlier thread). I thought I wasn't going to need to (thanks to the Git-SVN bridge!), but well, seems like I'll at least need to learn some basic svn. Finally, regarding the issue of pushing new features to devel versions (and not release), I understand the reasons for doing so. In my case, what I have been trying to do to minimize major differences between the versions is to keep working on the package outside of BioC until we are more confident on its stability. Kind of pre-devel. Pre-devel users (just a handful) can then install it via devtools::install_github(). I understand that not every package workflow is like this, but well, it could be a suggestion worth mentioning at http://www.bioconductor.org/developers/package-guidelines/ Though of course, maybe it's better to have pre-devel packages be submitted to BioC-devel and drive all the traffic through BioC. Just some thoughts. Cheers, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r
Re: [Bioc-devel] Distinction between release and devel package websites
- Original Message - From: James W. MacDonald jmac...@uw.edu To: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de Cc: Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 9:26:13 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? I tend to agree with this... Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). There is such a note, but it's often ignored, as you point out. Dan Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel packagewebsites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page
Re: [Bioc-devel] Distinction between release and devel package websites
Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Cheers, Andrzej On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we
Re: [Bioc-devel] Distinction between release and devel package websites
Agreed. Disabling the links is a good idea. There's really no good reason for someone to install packages manually. If a user really wants to mix release/devel, it is still technically possible but this change would strongly discourage it. For ensuring the user notices that a page is for the devel version , I'm still in favor of the simple notification box. Probably without the option to hide forever. On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release
Re: [Bioc-devel] Distinction between release and devel package websites
- Original Message - From: Andrzej Oleś andrzej.o...@gmail.com To: James W. MacDonald jmac...@uw.edu Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:14:05 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. Why would you want to do that? That's the kind of thing that gets people into trouble. Anyway, the packages would still be downloadable, and the link location could be figured out, but I don't think we need to make it easier for people to do the wrong thing by providing links. Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. There are also design considerations; I'm not sure a different background color would look good. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2 Home These are all great ideas for making the release and devel pages look different from each other, and maybe we'll consider some of them, but the real problem is people downloading packages from these pages--and they could run into the same problems by downloading packages from the release landing page (if, for example, they are running BioC devel, or some version that's earlier than the current release). I don't think any of the measures will be as effective as simply removing the links and replacing them with instructions on installing the package via biocLite(). Dan Cheers, Andrzej On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional
Re: [Bioc-devel] Distinction between release and devel package websites
- Original Message - From: Matthew McCall mcca...@gmail.com To: Michael Lawrence lawrence.mich...@gene.com Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:49:39 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites I hope the package source link is not on the proposed list of links to remove. I often use these links to browse through the source code of packages to learn from others' work. Also, it seems that making the source code (even slightly) less accessible would go against the principle of open source software. There is no package source link (unless you mean the source tarball) but I think it would be good to add a link directly to the package source in svn. That would make the source even easier to browse than it is now (you would now have to download and untar a tarball first). Dan Best, Matt On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Agreed. Disabling the links is a good idea. There's really no good reason for someone to install packages manually. If a user really wants to mix release/devel, it is still technically possible but this change would strongly discourage it. For ensuring the user notices that a page is for the devel version , I'm still in favor of the simple notification box. Probably without the option to hide forever. On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want
Re: [Bioc-devel] Distinction between release and devel package websites
Just check out from svn to get the source... way easier to keep up to date, and if you notice an issue, easier to make a patch. On Tue, Jul 22, 2014 at 10:49 AM, Matthew McCall mcca...@gmail.com wrote: I hope the package source link is not on the proposed list of links to remove. I often use these links to browse through the source code of packages to learn from others' work. Also, it seems that making the source code (even slightly) less accessible would go against the principle of open source software. Best, Matt On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Agreed. Disabling the links is a good idea. There's really no good reason for someone to install packages manually. If a user really wants to mix release/devel, it is still technically possible but this change would strongly discourage it. For ensuring the user notices that a page is for the devel version , I'm still in favor of the simple notification box. Probably without the option to hide forever. On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages
Re: [Bioc-devel] Distinction between release and devel package websites
The current link to the source tarball is called Package Source hence the quotes. Yes, I could check out the package using svn, but when browsing through a Bioconductor workflow, there are these handy links to the package pages that let me download and browse the source tarball without having to type anything. I like the idea of replacing the source tarball link with a link to the package source in svn. Best, Matt On Tue, Jul 22, 2014 at 1:58 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Just check out from svn to get the source... way easier to keep up to date, and if you notice an issue, easier to make a patch. On Tue, Jul 22, 2014 at 10:49 AM, Matthew McCall mcca...@gmail.com wrote: I hope the package source link is not on the proposed list of links to remove. I often use these links to browse through the source code of packages to learn from others' work. Also, it seems that making the source code (even slightly) less accessible would go against the principle of open source software. Best, Matt On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Agreed. Disabling the links is a good idea. There's really no good reason for someone to install packages manually. If a user really wants to mix release/devel, it is still technically possible but this change would strongly discourage it. For ensuring the user notices that a page is for the devel version , I'm still in favor of the simple notification box. Probably without the option to hide forever. On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21
Re: [Bioc-devel] Distinction between release and devel package websites
I just want to add the perspective that I often browse package documentation vignettes from the website rather than accessing it from the R command line. Sometimes it's just easier or more convenient to view it in a browser. So, when doing this, I sometimes accidentally get the wrong documentation (devel instead of release or vice versa) and end up wondering why the vignette isn't working on my system. So it's just just a problem of downloading the source code. - Original Message - From: Andrzej Oleś andrzej.o...@gmail.com To: James W. MacDonald jmac...@uw.edu Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:14:05 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. Why would you want to do that? That's the kind of thing that gets people into trouble. Anyway, the packages would still be downloadable, and the link location could be figured out, but I don't think we need to make it easier for people to do the wrong thing by providing links. Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. There are also design considerations; I'm not sure a different background color would look good. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2 Home These are all great ideas for making the release and devel pages look different from each other, and maybe we'll consider some of them, but the real problem is people downloading packages from these pages--and they could run into the same problems by downloading packages from the release landing page (if, for example, they are running BioC devel, or some version that's earlier than the current release). I don't think any of the measures will be as effective as simply removing the links and replacing them with instructions on installing the package via biocLite(). Dan Cheers, Andrzej On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links
Re: [Bioc-devel] Distinction between release and devel package websites
Thanks everyone for the input. We'll make some changes (over the next day or so), and then iterate on those as needed. Specifically 1. text after the package title indicating when the user is on the 'developer' page, with link to a 'stable release version'. 2. more prominent Installation header 3. Rename 'Package Downloads' to something less appealing, add text to indicate that the correct way to install a package is to follow Installation instructions, add pop-up interstitial to each of the gz/zip/tgz links to try to further clarify installation. We might tell google not to index devel packages (but then packages added during a particular release cycle aren't indexed until the next release). We will not change the color of the devel landing page (because color would not have meaning to the uninitiated). Interesting also that one source of problem is the _vignettes_, not the landing page. Maybe we could add a browseVignettes() code chunk. Martin On 07/22/2014 11:10 AM, Matthew McCall wrote: The current link to the source tarball is called Package Source hence the quotes. Yes, I could check out the package using svn, but when browsing through a Bioconductor workflow, there are these handy links to the package pages that let me download and browse the source tarball without having to type anything. I like the idea of replacing the source tarball link with a link to the package source in svn. Best, Matt On Tue, Jul 22, 2014 at 1:58 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Just check out from svn to get the source... way easier to keep up to date, and if you notice an issue, easier to make a patch. On Tue, Jul 22, 2014 at 10:49 AM, Matthew McCall mcca...@gmail.com wrote: I hope the package source link is not on the proposed list of links to remove. I often use these links to browse through the source code of packages to learn from others' work. Also, it seems that making the source code (even slightly) less accessible would go against the principle of open source software. Best, Matt On Tue, Jul 22, 2014 at 1:22 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Agreed. Disabling the links is a good idea. There's really no good reason for someone to install packages manually. If a user really wants to mix release/devel, it is still technically possible but this change would strongly discourage it. For ensuring the user notices that a page is for the devel version , I'm still in favor of the simple notification box. Probably without the option to hide forever. On Tue, Jul 22, 2014 at 9:26 AM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops
Re: [Bioc-devel] Distinction between release and devel package websites
Hi Andrzej, On 07/22/2014 10:14 AM, Andrzej Oleś wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I was thinking of something like this: http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/ Just a demo. This will be reset to the usual background tomorrow. Cheers, H. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Cheers, Andrzej On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip
Re: [Bioc-devel] Distinction between release and devel package websites
Dear Dan, James, Michael, Matt, thank you, I see your point but I'm afraid I must disagree with you. I've had this situation numerous times that I have added/fixed something in the devel branch of a package and had to advice the users to use this latest version. Needless to say, they were typically using the release branch, and it was a relatively painless procedure for them to pick the tarball from the devel landing page and proceed with manual installation. Of course, this could be also achieved by installing from the svn, however, this is not very welcome from the user's perspective. Please correct me if I'm wrong, but to my knowledge there is no build-in mechanism in 'biocLite' facilitating the above described scenario. Therefore, I think that it could be useful to have an 'useDevel' argument to biocLite() allowing for the installation of a specific package(s) from the devel rather than from the release branch without having to switch to devel completely. As this would be an optional argument defaulting to FALSE I wouldn't be worried by potential abuse, at least not more than by having the devel packages exposed on the website. As an additional precaution measure we could issue a warning and ask the user to confirm that (s)he is aware of the risks and wants to proceed. As Matt pointed out, direct links to package source tarballs are very useful for quick and lightweight inspection of package code. This approach combined with opening the files directly with an archive browser is particularly appealing, as it saves one from dealing with manual svn checkout and the cleanup afterwards. Please note that replacing the prebuild tarball with a link to the SVN has the caveat of getting potantially broken code. Tarballs which make it through to the website guarantee that the package at least builds. Best, Andrzej On Tue, Jul 22, 2014 at 7:57 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: James W. MacDonald jmac...@uw.edu To: Andrzej Oleś andrzej.o...@gmail.com Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:51:35 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi Andrzej, On 7/22/2014 1:14 PM, Andrzej Oleś wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. I'm not sure I think this is a compelling reason for keeping the links. If someone is sophisticated enough to install a devel version of a package into their release install, then surely they are sophisticated enough to get it from svn? Or to know how to find the link to the tarball. Dan It has always struck me as odd that we try time and again to get people to use biocLite() to install packages, yet make it so easy for people to ignore this advice. Best, Jim Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Cheers, Andrzej On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also
Re: [Bioc-devel] Distinction between release and devel package websites
Hi Andrzej, - Original Message - From: Andrzej Oleś andrzej.o...@gmail.com To: Dan Tenenbaum dtene...@fhcrc.org Cc: James W. MacDonald jmac...@uw.edu, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 2:06:25 PM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Dear Dan, James, Michael, Matt, thank you, I see your point but I'm afraid I must disagree with you. I've had this situation numerous times that I have added/fixed something in the devel branch of a package and had to advice the users to use this latest version. Needless to say, they were typically using the release branch, and it was a relatively painless procedure for them to pick the tarball from the devel landing page and proceed with manual installation. Of course, this could be also achieved by installing from the svn, however, this is not very welcome from the user's perspective. Please correct me if I'm wrong, but to my knowledge there is no build-in mechanism in 'biocLite' facilitating the above described scenario. Therefore, I think that it could be useful to have an 'useDevel' argument to biocLite() allowing for the installation of a specific package(s) from the devel rather than from the release branch without having to switch to devel completely. As this would be an optional argument defaulting to FALSE I wouldn't be worried by potential abuse, at least not more than by having the devel packages exposed on the website. As an additional precaution measure we could issue a warning and ask the user to confirm that (s)he is aware of the risks and wants to proceed. If a user wants to use a devel package they should be using BioC-devel. We explain on the web site how to run both BioC-devel and BioC-release on the same machine. Installing a devel package into an otherwise release installation is going to cause problems and defeats the entire purpose of having a devel branch. As Matt pointed out, direct links to package source tarballs are very useful for quick and lightweight inspection of package code. This approach combined with opening the files directly with an archive browser is particularly appealing, as it saves one from dealing with manual svn checkout and the cleanup afterwards. Please note that replacing the prebuild tarball with a link to the SVN has the caveat of getting potantially broken code. Tarballs which make it through to the website guarantee that the package at least builds. I think we're going to leave the links there but put in some sort of popup explaining that you should really use biocLite() unless you have some special reason for downloading the tarball. Dan Best, Andrzej On Tue, Jul 22, 2014 at 7:57 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: James W. MacDonald jmac...@uw.edu To: Andrzej Oleś andrzej.o...@gmail.com Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:51:35 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi Andrzej, On 7/22/2014 1:14 PM, Andrzej Oleś wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. I'm not sure I think this is a compelling reason for keeping the links. If someone is sophisticated enough to install a devel version of a package into their release install, then surely they are sophisticated enough to get it from svn? Or to know how to find the link to the tarball. Dan It has always struck me as odd that we try time and again to get people to use biocLite() to install packages, yet make it so easy for people to ignore this advice. Best, Jim Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being
Re: [Bioc-devel] Distinction between release and devel package websites
Andrzej, If you have the an important enough bugfix the correct procedure is to commit it to the release branch. Then users would simply update the package via biocLite. Note that this should be fixes ONLY. No new features. Regardless of how much the users want them, those belong in dev. ~G On Tue, Jul 22, 2014 at 2:06 PM, Andrzej OleÅ andrzej.o...@gmail.com wrote: Dear Dan, James, Michael, Matt, thank you, I see your point but I'm afraid I must disagree with you. I've had this situation numerous times that I have added/fixed something in the devel branch of a package and had to advice the users to use this latest version. Needless to say, they were typically using the release branch, and it was a relatively painless procedure for them to pick the tarball from the devel landing page and proceed with manual installation. Of course, this could be also achieved by installing from the svn, however, this is not very welcome from the user's perspective. Please correct me if I'm wrong, but to my knowledge there is no build-in mechanism in 'biocLite' facilitating the above described scenario. Therefore, I think that it could be useful to have an 'useDevel' argument to biocLite() allowing for the installation of a specific package(s) from the devel rather than from the release branch without having to switch to devel completely. As this would be an optional argument defaulting to FALSE I wouldn't be worried by potential abuse, at least not more than by having the devel packages exposed on the website. As an additional precaution measure we could issue a warning and ask the user to confirm that (s)he is aware of the risks and wants to proceed. As Matt pointed out, direct links to package source tarballs are very useful for quick and lightweight inspection of package code. This approach combined with opening the files directly with an archive browser is particularly appealing, as it saves one from dealing with manual svn checkout and the cleanup afterwards. Please note that replacing the prebuild tarball with a link to the SVN has the caveat of getting potantially broken code. Tarballs which make it through to the website guarantee that the package at least builds. Best, Andrzej On Tue, Jul 22, 2014 at 7:57 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: James W. MacDonald jmac...@uw.edu To: Andrzej OleÅ andrzej.o...@gmail.com Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:51:35 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi Andrzej, On 7/22/2014 1:14 PM, Andrzej OleÅ wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. I'm not sure I think this is a compelling reason for keeping the links. If someone is sophisticated enough to install a devel version of a package into their release install, then surely they are sophisticated enough to get it from svn? Or to know how to find the link to the tarball. Dan It has always struck me as odd that we try time and again to get people to use biocLite() to install packages, yet make it so easy for people to ignore this advice. Best, Jim Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html
Re: [Bioc-devel] Distinction between release and devel package websites
While mixing release and devel may work in specific cases, enabling it in the specific case means also enabling it in general. And in general, it will break and cause frustration and hardship for both users and developers. The other way to access source code is through R itself. On Tue, Jul 22, 2014 at 2:06 PM, Andrzej OleÅ andrzej.o...@gmail.com wrote: Dear Dan, James, Michael, Matt, thank you, I see your point but I'm afraid I must disagree with you. I've had this situation numerous times that I have added/fixed something in the devel branch of a package and had to advice the users to use this latest version. Needless to say, they were typically using the release branch, and it was a relatively painless procedure for them to pick the tarball from the devel landing page and proceed with manual installation. Of course, this could be also achieved by installing from the svn, however, this is not very welcome from the user's perspective. Please correct me if I'm wrong, but to my knowledge there is no build-in mechanism in 'biocLite' facilitating the above described scenario. Therefore, I think that it could be useful to have an 'useDevel' argument to biocLite() allowing for the installation of a specific package(s) from the devel rather than from the release branch without having to switch to devel completely. As this would be an optional argument defaulting to FALSE I wouldn't be worried by potential abuse, at least not more than by having the devel packages exposed on the website. As an additional precaution measure we could issue a warning and ask the user to confirm that (s)he is aware of the risks and wants to proceed. As Matt pointed out, direct links to package source tarballs are very useful for quick and lightweight inspection of package code. This approach combined with opening the files directly with an archive browser is particularly appealing, as it saves one from dealing with manual svn checkout and the cleanup afterwards. Please note that replacing the prebuild tarball with a link to the SVN has the caveat of getting potantially broken code. Tarballs which make it through to the website guarantee that the package at least builds. Best, Andrzej On Tue, Jul 22, 2014 at 7:57 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: James W. MacDonald jmac...@uw.edu To: Andrzej OleÅ andrzej.o...@gmail.com Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr...@embl.de, Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 10:51:35 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi Andrzej, On 7/22/2014 1:14 PM, Andrzej OleÅ wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. I'm not sure I think this is a compelling reason for keeping the links. If someone is sophisticated enough to install a devel version of a package into their release install, then surely they are sophisticated enough to get it from svn? Or to know how to find the link to the tarball. Dan It has always struck me as odd that we try time and again to get people to use biocLite() to install packages, yet make it so easy for people to ignore this advice. Best, Jim Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2
Re: [Bioc-devel] Distinction between release and devel package websites
Hi Hervé, thank you for the demo! Yes, this is definitely much more clear than just a different color. Maybe we could first implement this idea on the build/check report websites and see how the uptake will be? I always keep getting confused by the colors which keep changing with every release cycle anyway... Cheers, Andrzej On Tue, Jul 22, 2014 at 10:04 PM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Andrzej, On 07/22/2014 10:14 AM, Andrzej Oleś wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful. I was thinking of something like this: http://www.bioconductor.org/checkResults/3.0/data-experiment-LATEST/ Just a demo. This will be reset to the usual background tomorrow. Cheers, H. I would rather recommend emphasizing the distinction between release and devel in clear text across the package landing page, possibly in multiple places, e.g. somewhere close to the actual package version number; for instance, add the word devel after the version number with a tooltip which will give some explanation/warning that this is not the stable release version. The concept of a notification box is far from ideal because it tends to be annoing to the user and once dismissed 'forever' the user won't be warned in the future. I think that the actual problem arises from the fact that the release landing pages are not clearly prioritized over the devel ones. Maybe this could be addressed by preventing the devel pages from being harvested by google? It could make also sense to emphasize (bold face, color, ...) the package release landing page on the result list returned by the search engine on the BioC website. Currently, the results for release and devel differ only in their relative path, which can be easily overlooked, and both say Package Home, see example below: Bioconductor - DESeq2 - /packages/release/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Bioconductor - DESeq2 - /packages/devel/bioc/html/DESeq2.html Bioconductor - DESeq2 Home Cheers, Andrzej On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald jmac...@uw.edu wrote: Given that we have an ongoing problem with people inadvisedly clicking and installing things, is there a good rationale for allowing them to do so? Perhaps the landing page for each package should be stripped of links and replaced with some indication of the availability for each package on the various operating systems. There could also be a note indicating that people can install using biocLite(). Best, Jim On 7/22/2014 11:48 AM, Dan Tenenbaum wrote: Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more different from each other, but I think something needs to be done about the second problem as well. Perhaps a popup that comes up when you click on a package tarball saying The best way to install this is with biocLite(); are you sure you want to download it? Whatever we do probably won't happen until after BioC2014. Dan - Original Message - From: Julian Gehring julian.gehr...@embl.de To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence lawrence.mich...@gene.com, Vincent Carey st...@channing.harvard.edu Cc: bioc-devel@r-project.org Sent: Tuesday, July 22, 2014 8:07:29 AM Subject: Re: [Bioc-devel] Distinction between release and devel package websites Hi, Tooltips that appear while hovering over selected links are easy to miss. This alone will likely not be clear enough. We should convey the information that the entire website presents a different version of the package. The idea of a notification box that can be made visible by the individual user seems tempting. One can combine this with an optional cookie, to remember the state between browser sessions. Changing the layout of the devel page itself will also be helpful to make the distinction more pronounced. Hopefully we could approach this in a way that maintains the nice design of the bioc website. Best Julian On 21.07.2014 21:50, Hervé Pagès wrote: Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21
Re: [Bioc-devel] Distinction between release and devel package websites
Hi Martin, thank you! On Tue, Jul 22, 2014 at 9:01 PM, Martin Morgan mtmor...@fhcrc.org wrote: We might tell google not to index devel packages (but then packages added during a particular release cycle aren't indexed until the next release). This adds to the complexity and I'm not sure how hard this would be to implement, but maybe for the packages which didn't make it to the release yet we could allow to index the devel landing pages? Any plans on addressing the distinction between release/devel in the output from the search engine on the BioC website? Best, Andrzej ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
Hi Dan, Michael, Julian, Thank's for keeping the links to the tarballs! I don't argue that mixing release and devel is a good idea in general. Rather, that for some users this might be the best compromise between the following two objectives: 1. a stable working environment 2. the possibility to use or just quickly check a specific new feature available in the devel version of package X Switching entirely to devel is quite often a no-no for them because of the unstable nature of the devel branch. And maintaining both release and devel only adds to their frustration. As a developer I would like to have the freedom to advise people on using the latest devel version of my package regardless of whether they are running release or devel if I think that this is safe for them, which is typically the case for many upstream packages without (many) reverse dependencies. I don't see the point of unnecessary obstructing this approach and I'm not sure I understand why there is such an outrage about mixing release and devel. In contrary, quite often this can be much safer than switching between BioC branches. I personally do not want to find myself in a position when I advice a user to switch to BioC devel because of some new function from my package he/she would like to give a try only to learn that this broke his/hers scripts (due to the changes in some other packages). To sum up, I believe that mixing release and devel might be beneficial in some specific cases similar to the above described one and it's important that the infrastructure allows leveraging this approach, e.g. by providing direct access to devel tarballs. Cheers, Andrzej On Tue, Jul 22, 2014 at 11:12 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi Andzrej, thank you, I see your point but I'm afraid I must disagree with you. I've had this situation numerous times that I have added/fixed something in the devel branch of a package and had to advice the users to use this latest version. Needless to say, they were typically using the release branch, and it was a relatively painless procedure for them to pick the tarball from the devel landing page and proceed with manual installation. Of course, this could be also achieved by installing from the svn, however, this is not very welcome from the user's perspective. I'm not sure I understand to need to mix devel and release. If there is a bug in the release branch, it should be also patched there. And if users need the features of the devel branch, they would have to switch to devel anyway. Best Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
On Tue, Jul 22, 2014 at 7:10 PM, Andrzej OleÅ andrzej.o...@gmail.com wrote: Hi Dan, Michael, Julian, Thank's for keeping the links to the tarballs! I don't argue that mixing release and devel is a good idea in general. Rather, that for some users this might be the best compromise between the following two objectives: 1. a stable working environment 2. the possibility to use or just quickly check a specific new feature available in the devel version of package X IMHO this is the road to ruin. Switching entirely to devel is quite often a no-no for them because of the unstable nature of the devel branch. And maintaining both release I personally have never done the homework required to have both branches on hand with convenient updating. It is surely feasible and I would imagine a number of folks reading this have done it for themselves. It is probably not trivial to do it portably but a doc with suggestions for key platforms would be a nice contribution. I used to have Rrel and Rdev scripts that made it work and that is easily worked out but it is not very elegant and transitioning to new releases of R is laborious. and devel only adds to their frustration. As a developer I would like to have the freedom to advise people on using the latest devel version of my package regardless of whether they are running release or devel if I think that this is safe for them, which is typically the case for many upstream packages without (many) reverse dependencies. I don't see the point of unnecessary obstructing this approach and I'm not sure I understand why there is such an outrage about mixing release and devel. In contrary, quite often this can be much safer than Depends on your definition of safety. I think that we have gained much from the clean separation, in terms of user support effort and freedom to experiment in devel. Experts can do what they like and deal with the consequences themselves, but the general approach to the user community should be principled and it should be: 1) in general, use release branch and report bugs and see that they are fixed in a timely way; if they are not, let the core know -- 2) if you expect help, do all package installations via biocLite() -- 3) we like seeing mileage on the devel branch and encourage its use for novel features, but it needs to be used with the appropriate version of R and the devel package set. switching between BioC branches. I personally do not want to find myself in a position when I advice a user to switch to BioC devel because of some new function from my package he/she would like to give This is an engineering commitment to a stable release branch. No new features, only bug fixes. We have benefited from this immensely. a try only to learn that this broke his/hers scripts (due to the changes in some other packages). To sum up, I believe that mixing release and devel might be beneficial in some specific cases similar to the above described one and it's important that the infrastructure allows leveraging this approach, e.g. by providing direct access to devel tarballs. Cheers, Andrzej On Tue, Jul 22, 2014 at 11:12 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi Andzrej, thank you, I see your point but I'm afraid I must disagree with you. I've had this situation numerous times that I have added/fixed something in the devel branch of a package and had to advice the users to use this latest version. Needless to say, they were typically using the release branch, and it was a relatively painless procedure for them to pick the tarball from the devel landing page and proceed with manual installation. Of course, this could be also achieved by installing from the svn, however, this is not very welcome from the user's perspective. I'm not sure I understand to need to mix devel and release. If there is a bug in the release branch, it should be also patched there. And if users need the features of the devel branch, they would have to switch to devel anyway. Best Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Distinction between release and devel package websites
Hi, In addition to these suggestions, how about using a special background color for package landing pages in devel? Cheers, H. On 07/21/2014 07:32 PM, Michael Lawrence wrote: Or an unobtrusive notification box that drops down from the top of the page, saying something like this is devel; there would be a dismiss button and a checkbox for whether to show again. The user is free to simply ignore it and proceed as normal. On Mon, Jul 21, 2014 at 7:10 PM, Vincent Carey st...@channing.harvard.edu wrote: how about a tooltip that reads installation via biocLite() is the recommended approach to Bioconductor software acquisition, other approaches may lead to inconsistent package-sets that appears when a reader hovers over a tarball. i would imagine that this is how the wrong package gets installed, by manually using an inappropriate tarball. wrong documentation is not so easy but the doc on the devel branch might have a different tooltip cautioning the readers to be sure they want to read the doc on the devel version. On Mon, Jul 21, 2014 at 9:39 PM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Can we make the package websites for the devel and release version of a package more distinguishable? To elaborate on this: In the past, I have seen several users having problems with using bioconductor because they ended up on the wrong page (mostly the devel page when they would have needed the release). This resulted in getting the wrong documentation or installing the wrong package. The pages are well designed, and there is no reason to change this. However, the websites for the devel and release version of a package look almost identical, and that these two get confused seems to happen to many users (me included). If you search for a package within the bioc website, the release version always comes first in the search results. If you are coming from the outside (e.g. google), this may not be the case. In fact, googling a few packages names often returned only the devel page in the top 10 search results. What are the feelings regarding this? We could add a header section on the devel page that states that this is an unstable version not meant to be used in production settings, and provide a link to the respective release version? Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
