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[Bioc-devel] BiocManager::install

13 messages · Vincent Carey, Wolfgang Huber, Martin Morgan +3 more

Original
Wolfgang Huber
# 
Hi,

I am wondering whether:
1. it could be easier to install Bioconductor packages (devel or release) on R-devel (or other non-standard R versions) using BiocManager::install (I may be stirring a hornet?s nest with that:)
2. whether its documentation needs to be updated and/or its implementation could be deconvoluted (hopefully that?s uncontroversial). 

Re the first point, I appreciate that we?re trying to help non-expert users with simple use cases, and that we had/have a lot of trouble with users working with out-of-sync versions. OTOH, the current solution (rigid, confusing documentation, seemingly buggy implementation) seems to be standing in the way for developers, a dichotomy that we do not really want.

Of course, a workaround is
```{r}
```	
and maybe this is just the answer. So far, my workflows have been based on BiocManager::install, but I get (and cannot seem to get rid of):

```{r}
Error: Bioconductor does not yet build and check packages for R version 4.4; see
  https://bioconductor.org/install
R Under development (unstable) (2023-05-05 r84398)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Users/whuber/R.framework/Versions/4.4/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.20 fortunes_1.5-4     

loaded via a namespace (and not attached):
[1] compiler_4.4.0  tools_4.4.0     rstudioapi_0.14
``` 

I noted some discussion on this here: https://github.com/Bioconductor/BiocManager/issues/13 but this was 5 years ago.
It appears that the documentation of BiocManager::install mismatches its implementation, and overall the process for something that's conceptually quite simple seems to have become convoluted. 

One of the most helpful documentation resources on this topic btw is https://solutions.posit.co/envs-pkgs/bioconductor/ which cheerfully concludes "Working with BioConductor packages for code development is possible."

Thanks and best wishes
Wolfgang

--
Wolfgang Huber
EMBL
https://www.embl.org/groups/huber
Martin Morgan
# 
For off-piste use I would have consulted `setRepositories(graphics = FALSE)` and then

```
## use Sys.setenv() before setRepositories
Sys.setenv(R_BIOC_VERSION="3.18")
setRepositories(ind = 1:4) # CRAN plus Bioc soft, anno, and expt repos
getOption("repos")    # check
install.packages("BiocGenerics")
```

The help page ?BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS says

     ?BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS? is an environment variable
     or global ?options()? which, when set to ?FALSE?, avoids the R and
     _Bioconductor_ version checks that are done by querying an online
     configuration file. Setting
     ?BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS? to ?FALSE? can speed
     package loading when internet access is slow or non-existent, but
     may result in out-of-date information about the current release
     and development versions of _Bioconductor_. Offline users should
     set the ?BIOCONDUCTOR_CONFIG_FILE? environment variable or option
     to a ?.yaml? file similar to
     https://bioconductor.org/config.yaml for full offline use and
     version validation.

This could be clarified to more clearly indicate that BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS replaces the online version check with a local check against BIOCONDUCTOR_CONFIG_FILE; it does not disable the check. If you've copied the online file to a local file verbatim, then the same constraints are validated but without going online.

The use case that this is meant to support is when the Bioconductor repository (options(BioC_mirror = ?)) is itself off-line or not internet accessible, as might be the case in a corporate or HPC environment where a local mirror is maintained on the file system or inside a firewall.

One could hack the local config file in a more or less obvious way (replace "3.18" : "4.3" in the r_ver_for_bioc_ver section) but I would do something less easily forgotten.

FWIW I don't think BiocManager should support non-standard installations, keeping most users on track but letting the experts fend for themselves.

Martin


From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Wolfgang Huber <wolfgang.huber at embl.org>
Date: Saturday, May 6, 2023 at 4:40 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] BiocManager::install
Hi,

I am wondering whether:
1. it could be easier to install Bioconductor packages (devel or release) on R-devel (or other non-standard R versions) using BiocManager::install (I may be stirring a hornet?s nest with that:)
2. whether its documentation needs to be updated and/or its implementation could be deconvoluted (hopefully that?s uncontroversial).

Re the first point, I appreciate that we?re trying to help non-expert users with simple use cases, and that we had/have a lot of trouble with users working with out-of-sync versions. OTOH, the current solution (rigid, confusing documentation, seemingly buggy implementation) seems to be standing in the way for developers, a dichotomy that we do not really want.

Of course, a workaround is
```{r}
```
and maybe this is just the answer. So far, my workflows have been based on BiocManager::install, but I get (and cannot seem to get rid of):

```{r}
Error: Bioconductor does not yet build and check packages for R version 4.4; see
  https://bioconductor.org/install
R Under development (unstable) (2023-05-05 r84398)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Users/whuber/R.framework/Versions/4.4/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocManager_1.30.20 fortunes_1.5-4

loaded via a namespace (and not attached):
[1] compiler_4.4.0  tools_4.4.0     rstudioapi_0.14
```

I noted some discussion on this here: https://github.com/Bioconductor/BiocManager/issues/13 but this was 5 years ago.
It appears that the documentation of BiocManager::install mismatches its implementation, and overall the process for something that's conceptually quite simple seems to have become convoluted.

One of the most helpful documentation resources on this topic btw is https://solutions.posit.co/envs-pkgs/bioconductor/ which cheerfully concludes "Working with BioConductor packages for code development is possible."

Thanks and best wishes
Wolfgang

--
Wolfgang Huber
EMBL
https://www.embl.org/groups/huber

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Vincent Carey
# 
Thanks for these observations Wolfgang, I am glad I read to the end,
because as you say,

https://solutions.posit.co/envs-pkgs/bioconductor/

has lots of interesting information.  As I personally have no
experience with renv or Connect
much of the motivating detail is opaque to me.

I would question the proposition

"Given the structural differences between BioConductor and CRAN
repositories, it is not straightforward to work with both types. "

with at least 10 years of history of effective usage of both together
by many hundreds of users.  "Straightforward" is
subjective.  The existence of some shortcomings, like the specific
ones you mention, is acknowledged, and setting
up priorities to ameliorate them would be worthwhile.  Part of the
prioritization would need to be based on user
data and user experiences.  In the case of this posit.co article, what
is known about the significance of Connect
for genomic data science?  I have not had great difficulty publishing
apps to shinyapps.io that use Bioconductor
and CRAN, but perhaps it can be made easier if that is a key concern.

The problem of smoothly supporting multiple versions of R/Bioc
simultaneously is also acknowledged.  At this
time we do not have sufficient resources to make a big charge in the
direction of increasing support for this
"use case".  Users and sysadmins with sufficient expertise can
definitely accomplish much in this area, see
https://bioconductor.org/about/release-announcements/ for the map of
resources supporting this going back to
2005.  If there is a way to simplify this by using recently developed
package management strategies is would
be good to know and document.

This is a good place to continue the discussion from a developer's
perspective, but how can we get more
input from non-developer users?  And from posit.co?

"Publishing Shiny Apps that make use of BioConductor packages to
Connect is not possible for this setup.
BiocManager::install() temporarily adds the BioConductor repository
for the duration of the install process.
During the publishing process rsconnect no longer has any knowledge
about BioConductor." -- is this something
that can be remedied in BiocManager?  Are we able to test Connect for
this use case?
On Sat, May 6, 2023 at 4:40?AM Wolfgang Huber <wolfgang.huber at embl.org> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Wolfgang Huber
    

    

      
      #
    

  


  

      
Dear Martin and Vince

thank you, very insightful points. Indeed I think it?s primarily a matter of documentation and priming, and, e.g., adding Martin's lines prominently enough e.g. to https://contributions.bioconductor.org/use-devel.html and a reference to it into the manpage of BiocMananger::install.  

I acknowledge that installation and dealing with dependencies is *hard*. The relatively smooth user experience of Bioconductor, compared to other projects, is one of our greatest assets. I guess it needs constant attention on our side. One of the slogans of R/Bioconductor is ?turning users into developers? and therefore something that has useful defaults but is easy enough to customize seems desirable. In that sense, it?d be great to be able to stay with BiocManager::install and not having to abandon it in favour of base::install.packages.

The codebase behind BiocManager::install seems to have become a little?. complicated.

The documentation clarification re BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS that Martin suggests would be welcome.

Kind regards
Wolfgang

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
      #
    

  


  

      
I opened two issues for further discussion of the technical aspects.

https://github.com/Bioconductor/BiocManager/issues/165
https://github.com/Bioconductor/pkgrevdocs/issues/108

Just to be clear, as noted at the end of the second issue and on the web page you mention, a Bioconductor package developer wishing to use 'Bioc-devel' should, during the mid-April to mid-October release cycle, be using the **release** version of R. This combination of R and Bioconductor is supported by BiocManager. Similarly, in the mid-October to mid-April release cycle, the Bioconductor developer should be R-devel, and BoicManager supports this, too.

There are scenarios where a developer might wish to combine R-devel and Bioc-devel in the mid-May, to mid-October time frame, e.g., when developing a CRAN package with Bioconductor dependencies, or when conscientiously testing CRAN packages that depend on Bioconductor packages. One may also just want to be on the bleeding edge, so using R-devel and living with any consequence that arise from R / Bioconductor version mismatches. Are these less-common scenarios the one that you are engaged in?

Martin

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Wolfgang Huber <wolfgang.huber at embl.org>
Date: Saturday, May 6, 2023 at 9:43 AM
To: Vincent Carey <stvjc at channing.harvard.edu>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] BiocManager::install
Dear Martin and Vince

thank you, very insightful points. Indeed I think it?s primarily a matter of documentation and priming, and, e.g., adding Martin's lines prominently enough e.g. to https://contributions.bioconductor.org/use-devel.html and a reference to it into the manpage of BiocMananger::install.

I acknowledge that installation and dealing with dependencies is *hard*. The relatively smooth user experience of Bioconductor, compared to other projects, is one of our greatest assets. I guess it needs constant attention on our side. One of the slogans of R/Bioconductor is ?turning users into developers? and therefore something that has useful defaults but is easy enough to customize seems desirable. In that sense, it?d be great to be able to stay with BiocManager::install and not having to abandon it in favour of base::install.packages.

The codebase behind BiocManager::install seems to have become a little?. complicated.

The documentation clarification re BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS that Martin suggests would be welcome.

Kind regards
Wolfgang

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

  
  


  


      

    

    

      
      

        


  

        

      Wolfgang Huber
    

    

      
      #
    

  


  

      
Hi Martin

As you correctly point out, Bioconductor package developers are probably not those with the most relevant use cases. I think there are use cases for everyone else?anyone who decides to write code on R-devel, for whatever reason, and just wants to use a Bioconductor package between mid-April to mid-October (they could develop for CRAN, or just be a user and write scripts and packages for a private project). There are many useful packages on Bioconductor that are of general interest, even for people whose work does not center around Bioconductor or biology (say, ggtree, rhdf5, sparseMatrixStats, EBImage, ?)

I added these ponderings also to https://github.com/Bioconductor/pkgrevdocs/issues/108 

Thanks and best wishes
Wolfgang


(PS in my particular case yesterday, it was just that my R-devel is better maintained (built from source etc) and has in its library some (non-BioC) packages with complex systems dependencies that I need for a workflow I am working on, packages that currently elude me on my binary installation of R4.3. And then in addition I just wanted to *use* a package from Bioconductor and didn?t like how clumsy that experience was.)

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Martin Maechler
    

    

      
      #
    

  


  

          

      
      
      
    

        
> Hi Martin As you correctly point out, Bioconductor package
    > developers are probably not those with the most relevant
    > use cases. I think there are use cases for everyone
    > else?anyone who decides to write code on R-devel, for
    > whatever reason, and just wants to use a Bioconductor
    > package between mid-April to mid-October (they could
    > develop for CRAN, or just be a user and write scripts and
    > packages for a private project). There are many useful
    > packages on Bioconductor that are of general interest,
    > even for people whose work does not center around
    > Bioconductor or biology (say, ggtree, rhdf5,
    > sparseMatrixStats, EBImage, ?)

    > I added these ponderings also to
    > https://github.com/Bioconductor/pkgrevdocs/issues/108

    > Thanks and best wishes Wolfgang

As the older ones among you know, I've been a BioC developer
only many years ago ('hexbin' e.g.), but as an R package
maintainer and co-maintainer and R Core team member,
I really like to chime in here, declaring that it *has* been
quite painful for me over the years to test CRAN packages which
depend on BioC packages - with R-devel -- which is my primary R
version for testing, notably also for testing potential changes in R
across many packages, etc.
Notably during this half of the year where there is no
"official" way how to correctly install current Bioconductor packages 
(in their own package library, as I always do) under R-devel.

If I'd be able to sum up the time lost over this issue for the last say 10
years, it would add to a full working day at least. ...

(and I have added a comment also in the above issue #108)


    > (PS in my particular case yesterday, it was just that my
    > R-devel is better maintained (built from source etc) and
    > has in its library some (non-BioC) packages with complex
    > systems dependencies that I need for a workflow I am
    > working on, packages that currently elude me on my binary
    > installation of R4.3. And then in addition I just wanted
    > to *use* a package from Bioconductor and didn?t like how
    > clumsy that experience was.)

My other experience is that I always have to help people in my
group to install our pcalg CRAN package because it depends
e.g. on Bioc packages 'graph' and 'Rgraphviz' .. and on their
laptops they somehow don't have the correct  getOption("repos")
or there are other reasons why install.packages('pcalg')
does not find its Bioc dependencies.
On our Linux desktop+server environment, I do setup
    options(repos = ....)
such that everything works .. but alas, also *not* when in
R-devel but when you develop a package for CRAN / or only just
follow the more wide recommendation to also check your package
with current R-devel, then non-expert package developers need a
lot of stamina if their package depends (directly or
recursively) on a Bioc package....
which is really unfortunate and tends to put the Bioconductor
project in a shady light it really has not deserved at all!

Martin

--
Martin Maechler
ETH Zurich  and  R Core team
  


    >> Il giorno 06.05.2023, alle ore 16:45, Martin Morgan
    >> <mtmorgan.bioc at gmail.com> ha scritto:
    >> 
    >> I opened two issues for further discussion of the
    >> technical aspects.
    >> https://github.com/Bioconductor/BiocManager/issues/165
    >> https://github.com/Bioconductor/pkgrevdocs/issues/108
    >> Just to be clear, as noted at the end of the second issue
    >> and on the web page you mention, a Bioconductor package
    >> developer wishing to use 'Bioc-devel' should, during the
    >> mid-April to mid-October release cycle, be using the
    >> **release** version of R. This combination of R and
    >> Bioconductor is supported by BiocManager. Similarly, in
    >> the mid-October to mid-April release cycle, the
    >> Bioconductor developer should be R-devel, and BoicManager
    >> supports this, too.  There are scenarios where a
    >> developer might wish to combine R-devel and Bioc-devel in
    >> the mid-May, to mid-October time frame, e.g., when
    >> developing a CRAN package with Bioconductor dependencies,
    >> or when conscientiously testing CRAN packages that depend
    >> on Bioconductor packages. One may also just want to be on
    >> the bleeding edge, so using R-devel and living with any
    >> consequence that arise from R / Bioconductor version
    >> mismatches. Are these less-common scenarios the one that
    >> you are engaged in?  Martin From: Bioc-devel
    >> <bioc-devel-bounces at r-project.org> on behalf of Wolfgang
    >> Huber <wolfgang.huber at embl.org> Date: Saturday, May 6,
    >> 2023 at 9:43 AM To: Vincent Carey
    >> <stvjc at channing.harvard.edu> Cc: bioc-devel at r-project.org
    >> <bioc-devel at r-project.org> Subject: Re: [Bioc-devel]
    >> BiocManager::install Dear Martin and Vince
    >> 
    >> thank you, very insightful points. Indeed I think it?s
    >> primarily a matter of documentation and priming, and,
    >> e.g., adding Martin's lines prominently enough e.g. to
    >> https://contributions.bioconductor.org/use-devel.htmland
    >> a reference to it into the manpage of
    >> BiocMananger::install.
    >> 
    >> I acknowledge that installation and dealing with
    >> dependencies is *hard*. The relatively smooth user
    >> experience of Bioconductor, compared to other projects,
    >> is one of our greatest assets. I guess it needs constant
    >> attention on our side. One of the slogans of
    >> R/Bioconductor is ?turning users into developers? and
    >> therefore something that has useful defaults but is easy
    >> enough to customize seems desirable. In that sense, it?d
    >> be great to be able to stay with BiocManager::install and
    >> not having to abandon it in favour of
    >> base::install.packages.
    >> 
    >> The codebase behind BiocManager::install seems to have
    >> become a little?. complicated.
    >> 
    >> The documentation clarification re
    >> BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS that Martin
    >> suggests would be welcome.
    >> 
    >> Kind regards Wolfgang
    >> 
    >> 
    >> 
    >> 
    >> 
    >> 
    >> > Il giorno 06.05.2023, alle ore 13:05, Vincent Carey
    >> <stvjc at channing.harvard.edu> ha scritto:
    >> > 
    >> > Thanks for these observations Wolfgang, I am glad I
    >> read to the end, > because as you say,
    >> > 
    >> > https://solutions.posit.co/envs-pkgs/bioconductor/
    >> > 
    >> > has lots of interesting information.  As I personally
    >> have no > experience with renv or Connect > much of the
    >> motivating detail is opaque to me.
    >> > 
    >> > I would question the proposition
    >> > 
    >> > "Given the structural differences between BioConductor
    >> and CRAN > repositories, it is not straightforward to
    >> work with both types. "
    >> > 
    >> > with at least 10 years of history of effective usage of
    >> both together > by many hundreds of users.
    >> "Straightforward" is > subjective.  The existence of some
    >> shortcomings, like the specific > ones you mention, is
    >> acknowledged, and setting > up priorities to ameliorate
    >> them would be worthwhile.  Part of the > prioritization
    >> would need to be based on user > data and user
    >> experiences.  In the case of this posit.co article, what
    >> > is known about the significance of Connect > for
    >> genomic data science?  I have not had great difficulty
    >> publishing > apps to shinyapps.io that use Bioconductor >
    >> and CRAN, but perhaps it can be made easier if that is a
    >> key concern.
    >> > 
    >> > The problem of smoothly supporting multiple versions of
    >> R/Bioc > simultaneously is also acknowledged.  At this >
    >> time we do not have sufficient resources to make a big
    >> charge in the > direction of increasing support for this
    >> > "use case".  Users and sysadmins with sufficient
    >> expertise can > definitely accomplish much in this area,
    >> see >
    >> https://bioconductor.org/about/release-announcements/ for
    >> the map of > resources supporting this going back to >
    >> 2005.  If there is a way to simplify this by using
    >> recently developed > package management strategies is
    >> would > be good to know and document.
    >> > 
    >> > This is a good place to continue the discussion from a
    >> developer's > perspective, but how can we get more >
    >> input from non-developer users?  And from posit.co?
    >> > 
    >> > "Publishing Shiny Apps that make use of BioConductor
    >> packages to > Connect is not possible for this setup.  >
    >> BiocManager::install() temporarily adds the BioConductor
    >> repository > for the duration of the install process.  >
    >> During the publishing process rsconnect no longer has any
    >> knowledge > about BioConductor." -- is this something >
    >> that can be remedied in BiocManager?  Are we able to test
    >> Connect for > this use case?
    >> > 
    >> > 
    >> > On Sat, May 6, 2023 at 4:40?AM Wolfgang Huber

        
>> <wolfgang.huber at embl.org> wrote:

        
>> >> 
    >> >> Hi,
    >> >> 
    >> >> I am wondering whether: >> 1. it could be easier to
    >> install Bioconductor packages (devel or release) on
    >> R-devel (or other non-standard R versions) using
    >> BiocManager::install (I may be stirring a hornet?s nest
    >> with that:) >> 2. whether its documentation needs to be
    >> updated and/or its implementation could be deconvoluted
    >> (hopefully that?s uncontroversial).
    >> >> 
    >> >> Re the first point, I appreciate that we?re trying to
    >> help non-expert users with simple use cases, and that we
    >> had/have a lot of trouble with users working with
    >> out-of-sync versions. OTOH, the current solution (rigid,
    >> confusing documentation, seemingly buggy implementation)
    >> seems to be standing in the way for developers, a
    >> dichotomy that we do not really want.
    >> >> 
    >> >> Of course, a workaround is >> ```{r} >>>
    >> install.packages("ggtree", repos = c(?@CRAN@",
    >> "https://bioconductor.org/packages/3.18/bioc") >> ``` >>
    >> and maybe this is just the answer. So far, my workflows
    >> have been based on BiocManager::install, but I get (and
    >> cannot seem to get rid of):
    >> >> 
    >> >> ```{r} >>>
    >> options(BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE)
    >> >>> BiocManager::install("ggtree", version = "devel") >>
    >> Error: Bioconductor does not yet build and check packages
    >> for R version 4.4; see >>
    >> https://bioconductor.org/install
    >> >> 
    >> >>> sessionInfo() >> R Under development (unstable)
    >> (2023-05-05 r84398) >> Platform: aarch64-apple-darwin20
    >> (64-bit) >> Running under: macOS Ventura 13.3.1
    >> >> 
    >> >> Matrix products: default >> BLAS:
    >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    >> >> LAPACK:
    >> /Users/whuber/R.framework/Versions/4.4/Resources/lib/libRlapack.dylib;
    >> LAPACK version 3.11.0
    >> >> 
    >> >> locale: >> [1]
    >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    >> >> 
    >> >> time zone: Europe/Berlin >> tzcode source: internal
    >> >> 
    >> >> attached base packages: >> [1] stats graphics
    >> grDevices utils datasets methods base
    >> >> 
    >> >> other attached packages: >> [1] BiocManager_1.30.20
    >> fortunes_1.5-4
    >> >> 
    >> >> loaded via a namespace (and not attached): >> [1]
    >> compiler_4.4.0 tools_4.4.0 rstudioapi_0.14 >> ```
    >> >> 
    >> >> I noted some discussion on this here:
    >> https://github.com/Bioconductor/BiocManager/issues/13 but
    >> this was 5 years ago.  >> It appears that the
    >> documentation of BiocManager::install mismatches its
    >> implementation, and overall the process for something
    >> that's conceptually quite simple seems to have become
    >> convoluted.
    >> >> 
    >> >> One of the most helpful documentation resources on
    >> this topic btw is
    >> https://solutions.posit.co/envs-pkgs/bioconductor/ which
    >> cheerfully concludes "Working with BioConductor packages
    >> for code development is possible."
    >> >> 
    >> >> Thanks and best wishes >> Wolfgang
    >> >> 
    >> >> --
    >> >> Wolfgang Huber >> EMBL >>
    >> https://www.embl.org/groups/huber
    >> >> 
    >> >> _______________________________________________ >>
    >> Bioc-devel at r-project.org mailing list >>
    >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
    >> > 
    >> > -- 
    >> > The information in this e-mail is intended only for
    >> th...{{dropped:17}}
    >> 
    >> _______________________________________________
    >> Bioc-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel

  
  


  


      

    

    
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      Kasper Daniel Hansen
    

    

      
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Could we get a list of use cases from Wolfgang? I am confused about what
the issue is. Is the issue that it is painful to work with R-devel in the
"off" 6-months? If so, I agree that it should be easier (even if we don't
recommend it). But I am having a hard time parsing the email.

I can recognize Martin M's wish: a way to run Bioc-release on R-devel; that
seems sensible to me.

Best,
Kasper

On Tue, May 9, 2023 at 3:46?AM Martin Maechler <maechler at stat.math.ethz.ch>
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      Wolfgang Huber
    

    

      
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Hi Kasper

My use case is simple: anyone who works with R-devel and wants to use a package on Bioconductor from April to October.
Many of the 2230 packages in our repository are useful outside of the BiocGenerics, IRanges, SummarizedExperiment core world. 
E.g., to name a few, BiocParallel, illuminaio, rhdf5, EBImage, ggtree, edgeR, limma, qvalue, sparseMatrixStats, ? and I do not think ?we? should recommend people who want to use these which version of R they must use. Btw these examples are all ?highly downloaded?.

I fully understand the wish to make people use coherent versions of packages and R for situations where lots of interdependent packages, classes, methods etc. are imported. 
But sometimes, people just need one or two packages, and then R?s built-in dependency management works just fine and the current BiocManager approach is needlessly intrusive.

It?s as bad as having made me wonder whether to recommend authors of packages that do not directly build upon BiocGenerics, IRanges etc. to submit them to CRAN, to increase potential user base (b/c installation from Bioconductor can be such a pain). And that?s really not the place I want to be.

Thanks and best wishes
Wolfgang

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Kasper Daniel Hansen
    

    

      
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It seems totally sensible to be able to use BiocManager to install either
bioc-release or bioc-devel at any time, provided you're running R-devel.
First, by definition, R-devel is always >= the R used for release / devel
and Second, it is reasonable to assume users of R-devel to know what they
are doing.

I am unsure if you're arguing for anything else.

Best,
Kasper

On Thu, May 11, 2023 at 10:25?AM Wolfgang Huber <wolfgang.huber at embl.org>
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      Wolfgang Huber
    

    

      
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Hi Kasper,

Nope, that?s it. Was I so unclear?

	Wolfgang.

  
  


  


      

    

    

      
      

        


  

        

      Klaus Schliep
    

    

      
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Hi all,
no real contribution to this discussion, just some appreciation to all your
hard work.
I just wish CRAN had something like a proper release cycle for packages. I
contribute to two packages phangorn and ape, which have a decent number of
reverse dependencies. So you can't introduce any breaking changes (as there
is no devel branch) without contacting all maintainers and fixing some/most
reverse dependencies yourself. Also whenever CRAN introduces a change to
R-devel which causes an error of your package, one and sometime all
maintainers of dependent packages might get an email stating to fix this
within 2 weeks. This however has nothing to do with their release cycle of
the new R version itself. I wonder how many packages have been taken from
CRAN and how much total unnecessary frustration this causes?
Have a nice weekend.
Kind regards,
Klaus Schliep

On Sat, May 6, 2023 at 10:40?AM Wolfgang Huber <wolfgang.huber at embl.org>
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      Wolfgang Huber
    

    

      
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Dear Klaus

Good points. I am not trying to ?poach? anything here, and guess you have discussed this, but with this number of reverse dependencies, it sounds like the maintainers, contributors and users of ape and phangorn could benefit from putting the packages on Bioconductor?