[Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble
Charlotte Soneson
ch@r|otte@one@on @end|ng |rom gm@||@com
Mon Apr 27 10:12:29 CEST 2020
Thanks both, this is very informative!
It seems to me (at least from my small example) that what causes the actual installation failure is not the “binary-before-source” installation (as Martin said, this would not fail since the binaries are not loaded), but that the source packages are installed in the wrong order. For example, in my test package the actual dependency (the TxDb package) is installed first (before the other source packages, which it needs):
https://github.com/csoneson/testpkg/runs/619407291?check_suite_focus=true#step:7:514 <https://github.com/csoneson/testpkg/runs/619407291?check_suite_focus=true#step:7:514>
The downloaded binary packages are in
C:\Users\runneradmin\AppData\Local\Temp\RtmpqM7M39\downloaded_packages
installing the source packages 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'GenomeInfoDbData', 'tibble'
I’m not sure that this is transient (sorry if I misunderstood you Martin) - if you depend on a source-only package that depends on another source-only package like in this case, it seems that the above will currently go wrong every time.
Leo, I find your stepwise approach interesting. I wonder if there would still be an issue if you, say, depend on a source-later-than-binary CRAN package that in turn depends on another source-later-than-binary CRAN package (that is, if the second step in your installation would get the order right or wrong in such a case). Or, say, if GenomeInfoDbData would depend on tibble, would they be installed in the right order (they are both installed in the CRAN step)?
In any case, my own conclusion is that I need to go back and understand better how all these things really are determined. For example, in Martin’s example below I would wonder what would be the order if it was “bar” that had a newer source version, or if both “baz” and “bar” had newer source versions, or if the dependency chain there was different…basically, why are the source packages above installed in that particular order.
Thanks!
Charlotte
> On 27 Apr 2020, at 08:02, Leonardo Collado Torres <lcolladotor using gmail.com> wrote:
>
> EDIT: I found a general solution! (workaround?) I had written a
> response, but I had an idea, tested it and a few hours later I'm
> finishing this email. It does work... although not exactly as I
> intended it to.
>
>
>
> ---
>
> Thanks Martin for looking into this =)
>
> I'll respond to your question about making things complicated for myself.
>
>
> ## General scenario
>
> The general scenario is, I have a package say `newpkg`. `newpkg` has
> dependencies (imports, suggests and/or depends) on Bioconductor
> packages. I want to test that `newpkg` passes R CMD build, check &
> BiocCheck. To do so, we need all the dependencies of `newpkg`
> available including the "suggests" ones.
>
> If `newpkg` was already available from Bioconductor, I could install
> it using BiocManager::install("newpkg"). But that's not necessarily
> the case.**
>
> One could install the dependencies for `newpkg` manually, using
> BiocManager::install(), remotes, and/or install.packages(). But then,
> you need to adapt the code again for `newerpkg`, `oldpkg`, etc.
>
> Currently, either through remotes::install_deps() or through
> remotes::dev_package_deps(dependencies = TRUE) directly (the first
> calls the second
> https://github.com/r-lib/remotes/blob/5b3da5f852772159cc2a580888e10536a43e9199/R/install.R#L193)
> Charlotte and I are getting the list of packages that `newpkg` depends
> on, then either installing them through remotes or BiocManager. This
> is failing for both of us, though in theory (as far as I know) either
> should work. Is this something that could be fixed? I don't know.++
>
>
> ## GitHub Actions
>
> Ultimately in my case, I'm trying to build a GitHub Actions workflow
> that will work for any package with Bioconductor dependencies. I'm
> nearly there, it's just this last issue about the source-only BioC
> packages (annotation, experiment, workflow). I've been doing this
> since last week and through this process I discovered some issues with
> my own packages that were masked in the Bioconductor build machines.
> Many other packages are already installed in the Bioconductor build
> machines and on my laptop, so I hadn't noticed some missing "suggests"
> dependencies on some of my packages. For example
> https://github.com/leekgroup/recount/commit/f3bdb77d789f1a8364f16b71bd344fd23ecbfda5.
>
>
> ## Some possibilities to explore
>
> Maybe what we need is some other code to process the DESCRIPTION file
> of `newpkg`, extract the list of packages explicitly mentioned on
> DESCRIPTION (removing those that are base packages, say it's 10
> packages), then just install those direct dependencies (the 10
> packages) instead of all the packages listed in the DESCRIPTION and
> their dependencies (what you can get from remotes::dev_package_deps(),
> say 100 packages) and pass this smaller list of direct dependencies to
> BiocManager::install(). However, I suspect that it won't work either,
> because again, I'm expecting (maybe incorrectly) that
> BiocManager::install() figures out the right order in which to install
> either the short or long list of packages and this is currently
> failing for the long list.
>
> Another option might involve figuring out from the full list of
> dependencies (remotes::dev_package_deps(dependencies = TRUE) ), which
> ones are available only through source (maybe those available only
> through repos BioCann, BioCexp, BioCworkflows from
> BiocManager::repositories() ) and install those first, then install
> the remaining packages that exist in the BioCsoft and CRAN
> repositories. Maybe something like:
>
> ## This doesn't work since BiocManager::install() doesn't allow using
> the `repos` argument
> deps <- remotes::dev_package_deps(dependencies = TRUE)
> BiocManager::install(deps$package[deps$diff != 0], repos =
> BiocManager::repositories()[c('BioCann', 'BioCexp', 'BioCworkflows')]
> )
> BiocManager::install(deps$package[deps$diff != 0])
>
> ## This also doesn't work since all CRAN deps are missing at this point
> remotes::install_deps( repos =
> BiocManager::repositories()[c('BioCann', 'BioCexp', 'BioCworkflows')]
> )
> remotes::install_deps()
>
>
> ## But the above lead me a solution at
> https://github.com/leekgroup/derfinderPlot/blob/8695cbee49a01d1d297042232a1593e6c94f1b41/.github/workflows/check-bioc.yml#L139-L165.
> That is, install packages in waves: first the CRAN ones, then the BioC
> source-only ones, then the BioC software ones. Doing the installation
> in this order worked for several of my packages (as many as I could
> test tonight).
>
>
> message(paste('****', Sys.time(), 'installing BiocManager ****'))
> remotes::install_cran("BiocManager")
>
> message(paste('****', Sys.time(), 'installing CRAN dependencies ****'))
> remotes::install_deps(repos = BiocManager::repositories()['CRAN'])
>
> message(paste('****', Sys.time(), 'installing BioC source-only
> dependencies ****'))
> remotes::install_deps(repos = BiocManager::repositories()[c('BioCann',
> 'BioCexp', 'BioCworkflows')])
>
> message(paste('****', Sys.time(), 'installing remaining BioC
> dependencies ****'))
> deps <- remotes::dev_package_deps(dependencies = TRUE, repos =
> BiocManager::repositories())
> BiocManager::install(deps$package[deps$diff != 0])
>
>
> I added those messages so I could find these steps on the logs more
> easily and it works for Bioconductor's devel docker, macOS and Windows
> using R 4.0 and BioC 3.11.
>
> Here are the links to one log file (Windows):
>
> 1. BiocManager:
> https://github.com/leekgroup/derfinderPlot/runs/621120165?check_suite_focus=true#step:12:40
> 2. CRAN deps: https://github.com/leekgroup/derfinderPlot/runs/621120165?check_suite_focus=true#step:12:43
> (though hm... it does install many BioC ones, not sure why)
> 3. The BioC source-only deps:
> https://github.com/leekgroup/derfinderPlot/runs/621120165?check_suite_focus=true#step:12:1219
> (hm... doesn't install anything)
> 4. BioC remaining deps:
> https://github.com/leekgroup/derfinderPlot/runs/621120165?check_suite_focus=true#step:12:1222
> This is where TxDb.Hsapiens.UCSC.hg19.knownGene gets installed;
> GenomeInfoDbData and tibble are available for GenomicFeatures at this
> point, so no errors pop up. This step also installs a few other CRAN
> deps which I'm not sure why they didn't install before.
>
>
> Best,
> Leo
>
> ** Even if it was, you might not want to actually install the package
> `newpkg` from Bioconductor/CRAN since you likely want to test the very
> latest version of `newpkg` and avoid any false negative errors where
> everything seems to work, but your code is really just checking the
> latest release version (bioc-release or bioc-devel for BioC packages)
> instead of your development version.
>
> ++ Maybe it could be fixed by adding a explicit dependency on
> GenomicFeatures to both GenomeInfoDbData and tibble, though I'm not
> sure. But it seems like fixing the order in which packages are
> installed is the more general problem.
>
>
>
>
>
>
>
> On Sun, Apr 26, 2020 at 5:53 PM Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
>>
>> I spent a bit of time not understanding why you were being so complicated -- BiocManager::install() finds all CRAN / Bioc dependencies, there's no need to use remotes at all and for debugging purposes it just seemed (still seems?) like you were making trouble for yourself.
>>
>> But eventually... I created a fake CRAN-style repository
>>
>> $ tree my_repo/
>> my_repo/
>> ├── bin
>> │ └── macosx
>> │ └── contrib
>> │ └── 4.0
>> │ └── PACKAGES
>> └── src
>> └── contrib
>> └── PACKAGES
>>
>> The plain-text PACKAGES file is an index of the packages that are supposed to be available. So under the 'bin' tree I have
>>
>> ---
>> Package: foo
>> Version: 1.0.0
>> NeedsCompilation: true
>>
>> Package: bar
>> Version: 1.0.0
>> Depends: foo
>>
>>
>> Package: baz
>> Version: 1.0.0
>> Depends: bar
>> ---
>>
>> baz depends on bar depends on foo, and binary versions are all at 1.0.0
>>
>> Under the src tree I have
>>
>> ---
>> Package: foo
>> Version: 1.0.1
>> NeedsCompilation: true
>>
>> Package: bar
>> Version: 1.0.0
>> Depends: foo
>>
>>
>> Package: baz
>> Version: 1.0.0
>> Depends: bar
>> ```
>> with a more recent src for foo at version 1.0.1. I guess this is (almost) the situation with GenomeInfoDbData / tibble.
>>
>> In an R session I have
>>
>>> available.packages(repos="file:///tmp/my_repo/")
>> Package Version Priority Depends Imports LinkingTo Suggests Enhances
>> foo "foo" "1.0.1" NA NA NA NA NA NA
>> bar "bar" "1.0.0" NA "foo" NA NA NA NA
>> baz "baz" "1.0.0" NA "bar" NA NA NA NA
>> License License_is_FOSS License_restricts_use OS_type Archs MD5sum
>> foo NA NA NA NA NA NA
>> bar NA NA NA NA NA NA
>> baz NA NA NA NA NA NA
>> NeedsCompilation File Repository
>> foo "true" NA "file:///tmp/my_repo/src/contrib"
>> bar NA NA "file:///tmp/my_repo/src/contrib"
>> baz NA NA "file:///tmp/my_repo/src/contrib"
>>
>> I'll try to 'install' baz; it'll fail because there are no packages to install, but it's still informative...
>>
>>> install.packages("baz", repos = "file:///tmp/my_repo")
>> Installing package into '/Users/ma38727/Library/R/4.0/Bioc/3.11/library'
>> (as 'lib' is unspecified)
>> also installing the dependencies 'foo', 'bar'
>>
>>
>> There is a binary version available but the source version is later:
>> binary source needs_compilation
>> foo 1.0.0 1.0.1 TRUE
>>
>> Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
>> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
>> package 'bar' does not exist on the local repository
>> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
>> package 'baz' does not exist on the local repository
>> installing the source package 'foo'
>>
>> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
>> package 'foo' does not exist on the local repository
>>
>> Note the order of downloads -- binaries first, then source as you found! (actually, this would 'work' because the binaries are installed without any test load, but in more complicated situations...)
>>
>> On the other hand, if I answer 'no' to install the more recent source packages I get
>>
>> There is a binary version available but the source version is later:
>> binary source needs_compilation
>> foo 1.0.0 1.0.1 TRUE
>> Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
>> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
>> package 'foo' does not exist on the local repository
>> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
>> package 'bar' does not exist on the local repository
>> Warning in download.packages(pkgs, destdir = tmpd, available = available, :
>> package 'baz' does not exist on the local repository
>>
>> installing in the order required for dependencies.
>>
>> If I remove baz from the source repository, I get a similar order of events, with an additional prompt about installing 'baz' from source.
>>
>> I don't actually see, from the 'Binary packages' section of ?install.packages, how to get R to respond 'no' to the prompt to install the more recent source package foo, but still install the source-only package 'baz'...
>>
>> Of course this is transient, when there more recent source than binaries; my own installation of TxDb on macOS found a binary tibble as current as the source, and went without problem.
>>
>> Martin
>>
>> On 4/26/20, 4:48 PM, "Leonardo Collado Torres" <lcolladotor using gmail.com> wrote:
>>
>> Hi everyone,
>>
>> Charlotte, thank you very much! I didn't know about that issue on
>> `remotes` and the fix attempts. Thank you for the info Martin!
>>
>> However, I have to report that it doesn't seem like switching from
>> remotes::install_deps() to BiocManager::install() fixes the issue. I
>> updated my GitHub Actions workflow to obtain the list of dependencies
>> using remotes, but install them with BiocManager::install() instead of
>> remotes::install_deps(). You can see this at
>> https://github.com/leekgroup/derfinderPlot/blob/ea58939ac6bf13cae7d26951732914d96b5f7d07/.github/workflows/check-bioc.yml#L139-L149
>> although I include the relevant lines of code below:
>>
>> ## Locate the package dependencies
>> deps <- remotes::dev_package_deps(dependencies = TRUE)
>>
>> ## Install any that need to be updated using BiocManager to avoid
>> ## the issues described at
>> ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
>> ## https://github.com/r-lib/remotes/issues/296
>> remotes::install_cran("BiocManager")
>> BiocManager::install(deps$package[deps$diff != 0])
>>
>>
>> This still leads to TxDb.Hsapiens.UCSC.hg19.knownGene failing to
>> install because GenomeInfoDbData is not available on both macOS and
>> Windows (again, this doesn't fail on the Bioconductor devel docker).
>> Here's for example the error on Windows
>> https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1077.
>> Immediately after, GenomeInfoDbData does get installed
>> https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1100
>> and after it, tibble
>> https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1174.
>>
>> Likely this issue only happens on Windows and macOS because of the
>> availability of some packages in source form and others in binary
>> form, unlike only using source versions in the Bioconductor docker
>> run. However, maybe I need some other code to get all the
>> dependencies of a given package in a different order, though I was
>> hoping that BiocManager::install() would find the right order for me
>> as it seems to try to do so already.
>>
>> Charlotte linked to
>> https://github.com/r-lib/remotes/commit/88f302fe53864e4f27fc7b3897718fea9a8b1fa9.
>> So maybe there's still something else to try to fix in remotes and/or
>> BiocManager instead of the DESCRIPTION files of other packages like I
>> initially thought of in this thread and in
>> https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016671.html.
>>
>> Best,
>> Leo
>>
>>
>>
>> On Sun, Apr 26, 2020 at 10:30 AM Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
>>>
>>> Thanks Charlotte for the detective work.
>>>
>>>
>>>
>>> Annotation packages (TxDb, org, BSgenome, and GenomeInfoDbData, for instance) are distributed only as source – this was a decision made quite a while (years) ago, to save disk space (some of these packages are large, and hosting macOS and Windows binaries in addition to source triple disk space requirements) and on the rationale that the packages do not have C-level source code so users do not need RTools or XCode (etc) to install from ‘source’. So in this context and in the face of a buggy remotes package, and installation of Bioconductor packages through non-standard approaches (BiocManager::install() for CRAN and Bioconductor packages and their dependencies use base R commands only) I guess the behavior you document is really an (ongoing?) bug in the remotes package?
>>>
>>>
>>>
>>> Over the years the distribution of source-only annotation packages has caused problems, in particular when (usually Windows) users have temporary or library paths with spaces or non-ASCII characters. I believe that this upstream bug (in R’s handling of Windows paths) has been fixed in the 4.0.0 release, but the details are quite complicated and I have not been able to follow the discussion fully.
>>>
>>>
>>>
>>> Martin
>>>
>>>
>>>
>>> From: Charlotte Soneson <charlottesoneson using gmail.com>
>>> Date: Sunday, April 26, 2020 at 5:32 AM
>>> To: Martin Morgan <mtmorgan.bioc using gmail.com>
>>> Cc: Leonardo Collado Torres <lcolladotor using gmail.com>, Bioc-devel <bioc-devel using r-project.org>
>>> Subject: Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble
>>>
>>>
>>>
>>> Hi Leo, Martin,
>>>
>>>
>>>
>>> it looks like this is related to an issue with the remotes package: https://github.com/r-lib/remotes/issues/296. It gets the installation order wrong, and tries to install source packages before binaries. This can be a problem with GenomeInfoDbData (which I think doesn’t have a binary, and which it looks like Leo is installing manually). The TxDb package also doesn’t seem to be available as a binary package, and currently the source package for tibble is newer than the Windows binary.
>>>
>>>
>>>
>>> According to the issue above, it should have been fixed in remotes v2.1.1 (https://github.com/r-lib/remotes/commit/88f302fe53864e4f27fc7b3897718fea9a8b1fa9). To try things out, I set up a minimal package with the only dependency being TxDb.Hsapiens.UCSC.hg19.knownGene (https://github.com/csoneson/testpkg), and checked it with GitHub Actions on macOS and Windows. It fails in both cases, since it’s trying to install TxDb.Hsapiens.UCSC.hg19.knownGene first (e.g. https://github.com/csoneson/testpkg/runs/619407291?check_suite_focus=true#step:7:533). If I depend instead on GenomicFeatures, everything builds fine (here we have a binary). It is using remotes v2.1.1 though, so perhaps this needs to be investigated further.
>>>
>>>
>>>
>>> Charlotte
>>>
>>>
>>>
>>> On 25 Apr 2020, at 22:20, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
>>>
>>>
>>>
>>> tibble is not a direct dependency of TxDb*.
>>>
>>>
>>> db = available.packages(repos = BiocManager::repositories())
>>> deps = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db)
>>> deps
>>>
>>> $TxDb.Hsapiens.UCSC.hg19.knownGene
>>> [1] "GenomicFeatures" "AnnotationDbi"
>>>
>>> but it is an indirect dependency
>>>
>>>
>>> deps = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db, recursive=TRUE)
>>> "tibble" %in% unlist(deps)
>>>
>>> [1] TRUE
>>>
>>> I did
>>>
>>> deps1 = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db, recursive=TRUE)
>>>
>>> deps2 = tools::package_dependencies("tibble", db, recursive=TRUE, reverse=TRUE)
>>>
>>> intersect(unlist(deps1), unlist(deps2))
>>> ## [1] "GenomicFeatures" "biomaRt" "BiocFileCache" "dbplyr"
>>> ## [5] "dplyr"
>>>
>>> I believe R checks for immediate dependencies, found all for TxDb* and GenomicFeatures available, and didn’t check further. I speculate that you removed tibble, or installed one of the packages in the above list, without satisfying the dependencies for that package. Or perhaps what the message is really trying to say is that it failed to load tibble (because it was installed in a previous version of the R toolchain?)
>>>
>>> It would be interesting to debug this further on your system, to understand the problem for other users.
>>>
>>> Martin
>>>
>>> On 4/25/20, 2:48 PM, "Bioc-devel on behalf of Leonardo Collado Torres" <bioc-devel-bounces using r-project.org on behalf of lcolladotor using gmail.com> wrote:
>>>
>>> Hi Bioc-devel,
>>>
>>> I think that there's a potential issue with either GenomicFeatures,
>>> TxDb.Hsapiens.UCSC.hg19.knownGene or an upstream package.
>>>
>>>
>>> On a fresh R 4.0 Windows installation with BioC 3.11, I get the
>>> following error message when installing
>>> TxDb.Hsapiens.UCSC.hg19.knownGene as shown at
>>> https://github.com/leekgroup/derfinderPlot/runs/618370463?check_suite_focus=true#step:13:1225.
>>>
>>>
>>> 2020-04-25T18:32:26.0765748Z * installing *source* package
>>> 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
>>> 2020-04-25T18:32:26.0769789Z ** using staged installation
>>> 2020-04-25T18:32:26.1001400Z ** R
>>> 2020-04-25T18:32:26.1044734Z ** inst
>>> 2020-04-25T18:32:26.2061605Z ** byte-compile and prepare package for
>>> lazy loading
>>> 2020-04-25T18:32:30.7296724Z ##[error]Error: package or namespace load
>>> failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc,
>>> .libPaths()), versionCheck = vI[[i]]):
>>> 2020-04-25T18:32:30.7305615Z ERROR: lazy loading failed for package
>>> 'TxDb.Hsapiens.UCSC.hg19.knownGene'
>>> 2020-04-25T18:32:30.7306686Z * removing
>>> 'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene'
>>> 2020-04-25T18:32:30.7307196Z there is no package called 'tibble'
>>> 2020-04-25T18:32:30.7310561Z ##[error]Error: package 'GenomicFeatures'
>>> could not be loaded
>>> 2020-04-25T18:32:30.7311805Z Execution halted
>>>
>>> From looking at the bioc-devel landing pages for both GenomicFeatures
>>> and TxDb.Hsapiens.UCSC.hg19.knownGene, I see that tibble is not listed
>>> as a dependency for either package.
>>>
>>> Best,
>>> Leo
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
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