[Bioc-devel] biocLite should warn when called from a non-current R version

Diego Diez diego10ruiz at gmail.com
Fri Jun 21 04:35:47 CEST 2013


however unlike an iphone Bioconductor is only (as far as I know)
supported for the current release. We all do our best to help users
when they find problems and in most cases when I have suggested they
upgrade they have done so- solving their problems. If they were more
aware of being using an unsupported outdated version of Bioconductor
then they will- at least- have the opportunity of making a reasoned
decision- maybe even upgrade before asking. Indeed people having
legitimate reasons to run an outdated version do understand they are
running an outdated version and so will ignore those messages. As for
getting a message/warning when updating packages, now it is not a
clean, message-free process already. Adding useful information will
not make it significantly cluttered in my opinion. I agree with those
that think the shortest and the most explicit the best. My suggestion:

"NOTE: You are running an outdated (unsupported) version of
Bioconductor {show versions}. Consider upgrading your system to get
all the new features and bug fixes. Please take a look at {URL} for

or similar. And include details about the implications (methods,
possible incompatibilities, etc) of doing so in the URL.

All the best,

On Fri, Jun 21, 2013 at 12:21 AM, Wolfgang Huber <whuber at embl.de> wrote:
> Hi,
> there is benefit in having newest versions, but I think we shouldn't get carried away, and find Martin's suggestion reasonable. I don't want to be told to go get an iPhone 5 every time I update an app on my iPhone 4 - even if that same app would work much better there. People may have legitimate reasons to run an 'old' R, and we are not the version police.
> Simon, I very much sympathise with your frustration about thoughtless or ignorant user questions, and I suppose you hope that this proposed change will provide a quick fix. I would have said something different above if I shared that hope, but I am not sure it would make much difference to them in practice: many would not follow that message even it were in ALL CAPS ALL ACROSS THEIR SCREEN. And at the same time shouting at people who know what they're doing is not a desirable approach.
>         Best wishes
>         Wolfgang
> On Jun 20, 2013, at 9:03 am, Simon Anders <anders at embl.de> wrote:
>> Hi Martin
>> good to see that Herve agrees with me, and I reiterate my point, because I consider this issue very important.
>> The average user does _not_ expect that a function like 'biocLite', which has the express purpose of downloading and installing packages, does not pull the newest package. I know that to you, as an an experienced Bioc person, this has become second nature, but believe me: It is unusual and very surprising for anybody used to other systems.
>> The message hence has to very clearly and unambiguously state the following fact: "The biocLite function will NOT install the most recent released versions of Bioconductor packages."
>> I insist that this should be mentioned in this direct manner. Your formulation may imply it to the careful reader but not to a user in a hurry. Merely mentioning that there are newer versions will _not_ bring across the point that calling the biocLite installation script will not install these!
>> I really do not see the problem with saying clearly that biocLite will not pull the newest version. Is this something we are ashamed of and don't want to admit straight out?
>> And I frankly see no need to warn users already in this message that updates can break existing workflows. Everybody who has ever used any software knows this.
>>  Simon
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