Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'
i think this is an interesting analysisi have not viewed talk but it
seems to me this could be a nice r journal paperquerying jim h on fate
of itdepends seems in orderthe topic is central to robustness of
ecosystem so i hope some tools can come out of this
On Wed, Feb 12, 2020 at 12:13 PM Robert Castelo
wrote:
> Martin, Vince, Sean,
>
> thank you very much for your comments and suggestions, i've looked at
> the package 'itdepends' from Jim Hester, this was a great suggestion. i
> actually found a talk he gave about it on rstudioconf2019, here:
>
>
> https://resources.rstudio.com/rstudio-conf-2019/it-depends-a-dialog-about-dependencies
>
> i recommend watching it to anyone interested in this thread, i think
> pretty much tackles the most important issues we're concerned as
> developers, regarding dependencies.
>
> ironically, the package 'itdepends' doesn't seem to be actively
> developed: it's not part of CRAN, the GitHub repo hasn't been updated in
> the last 5 months, it has 10 open issues for 5 closed ones and i've
> experienced that some functions break in the current R-devel.
>
> i also didn't know about 'BiocPkgTools' and this seems to be the right
> home for adding the kind of functionality we're talking about, although
> i would think the same for 'itdepends' if it would be pushed to CRAN at
> some point.
>
> i've invested some time to develop what it constitutes at the moment my
> own needs on this subject. in case this is useful to anyone i've made a
> GitHub gist available here:
>
> https://gist.github.com/rcastelo/7429d05178ddb57a38bd42093c2ddfe2
>
> i haven't attempted to integrate this into 'BiocPkgTools' and do a pull
> request because of two reasons:
>
> 1. if i try to fetch the dependencies from CRAN, as well as from BioC
> (which is the only default), i get an error:
>
> library(BiocPkgTools)
>
> df <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"))
> Error in url(viewsFileUrl) : invalid 'description' argument
>
> 2. because some of the calls break 'itdepends' in R-devel, this would
> also break 'BiocPkgTools' in R-devel. i'm also not sure how feasible it
> is for a BioC package to have a package dependency outside CRAN and BioC.
>
> my initial motivation for all this was that the installation of
> 'GenomicScores' was breaking in one of our servers because of
> compilation problems with the package 'Matrix'. this was surprising to
> me because i wasn't expecting to have that dependency. after the first
> exchange of messages in this thread, using the code we wrote, i
> identified that only a few lines in the source of 'GenomicScores' were
> leading to that dependency upstream. i could replace them and get rid of
> that dependency and actually other ones.
>
> i've tried to provide a first attempt for a general approach to this
> situation. first we should source the gist:
>
> devtools::source_gist("rcastelo/depburden.R")
>
> then build a database of dependencies information:
>
> repos <- BiocManager::repositories()[c("BioCsoft", "CRAN")]
> db <- utils::available.packages(repos=repos)
>
> and now the important part consists of the following three steps:
>
> 1. identify the burden of dependencies of a package, e.g., "GenomicScores"
>
> pkgDepMetrics("GenomicScores", db)
>ImportedBy Exported Usage DepOverlap
> Biobase1 128 0.781250 0.0250
> BSgenome 1 93 1.075269 0.3625
> XML2 175 1.142857 0.0125
> IRanges4 254 1.574803 0.0375
> BiocGenerics 5 139 3.597122 0.0125
> GenomicRanges 4 104 3.846154 0.1125
> S4Vectors 11 262 4.198473 0.0250
> GenomeInfoDb 5 53 9.433962 0.0750
> AnnotationHub 4 33 12.121212 0.6875
> BiostringsNA 240NA 0.0750
>
> following Jim's recommendations on his talk, concretely those in minute
> 16, this function reports the number of function calls to a dependency
> and the number of exported functions by that dependency. the column
> 'Usage' is the percentage of those imported calls to the exposed
> functionality by the dependency. for instance, if i want to get rid of
> 'AnnotationHub' i'd have to implement in my package about the 12% of the
> functionality exported by 'AnnotationHub'.
>
> the column 'DepOverlap' shows the overlap between the dependency graph
> of the analyzed package and the dependency graph of the dependency in
> that row. this is calculated as a Jaccard index (intersection of
> vertices divided by the union) where 0 would correspond to disjoint
> graphs and 1 to identical ones.
>
> from these numbers i can see that, for instance, i'm importing just one
> function call from 'BSgenome' (about 1% of its functionality), while the
> dependency burden of 'BSGenome' overlaps more than 1/3 of the total
> burden of the package. this is to me a good candidate to explore in the
> following
Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Thanks a lot to both.
I have been suggested to try
`usethis::use_pipe(export = TRUE)`
probably put in place because the task is indeed challenging.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno gio 13 feb 2020 alle ore 18:29 Felix Ernst <
felix.gm.er...@outlook.com> ha scritto:
> Hi,
>
> I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to
> implicit for anyone's taste, \code{\link[magrittr:pipe]{\%>\%}} should also
> work in this case.
>
> The case above is used for a package external link. For an internal
> explicit link use \code{\link[=something]{or other}}.
>
> Felix
>
> -Ursprüngliche Nachricht-
> Von: Bioc-devel Im Auftrag von Martin
> Morgan
> Gesendet: Donnerstag, 13. Februar 2020 04:46
> An: stefano ; bioc-devel@r-project.org
> Betreff: Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr'
> does not exist and so has been treated as a topic
>
> This warning
>
> * checking whether package 'ttBulk' can be installed ... WARNING Found the
> following significant warnings:
> Rd warning:
> C:/Users/pkgbuild/AppData/Local/Temp/Rtmp6Js8e8/R.INSTALL1ddcdee5581/ttBulk/man/reexports.Rd:19:
> file link '%>%' in package 'magrittr' does not exist and so has been
> treated as a topic See
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1330/8048f88/ttBulk.Rcheck/00install.out'
> for details.
>
> is actually about the documentation for '%>%'. In your previous 'man' page
> you had
>
> \code{\link[magrittr]{\%>\%}}
>
> which from reading 'Writing R Extensions' RShowDoc("R-exts") section 2.5
> 'Cross-references' indicates that you're trying to link to an html page
> named '%>%.html' in the magrittr package, but actually the man page is
> 'pipe.html' (e.g., by using help.start() and browsing manually to the help
> page). While it's possible to link to that help page, you should instead
> just \code{\link{\%>\%}} and R (possibly with the user choosing the
> package) will generate the correct link.
>
> Your package is too deep into the roxygen foo for me to know what you need
> to do to generate the appropriate link (or even where the link is
> generated...); maybe there's a roxygen expert on the mailing list who can
> help (or you can perhaps post here where you generate the reexports.Rd page
> from).
>
> Also, your github repository seems VERY LARGE (I lost patience trying to
> clone it, although my current link is quite slow); this
> http://bioconductor.org/developers/how-to/git/remove-large-data/ might
> provide some hints for removing large commits.
>
> Hope that helps,
>
> Martin
>
>
> On 2/12/20, 9:51 PM, "Bioc-devel on behalf of stefano" <
> bioc-devel-boun...@r-project.org on behalf of mangiolastef...@gmail.com>
> wrote:
>
> Hello Community,
>
> The CHECK Windows server gives me a warning when I try to reexport an
> existing operator magrittr::`%>%`
>
> ```
> #' @importFrom magrittr %>%
>
> #' @export
>
> magrittr::`%>%`
> ```
>
> okay2 Windows Server 2012 R2 Standard/x64
> OK
> WARNINGS
> OK
> OK
>
> malbec2 Linux (Ubuntu 18.04.3 LTS)/x86_64
> OK
> OK
> skipped
> OK
>
>
> Here is the log
>
> http://bioconductor.org/spb_reports/ttBulk_buildreport_20200212081044.html#tokay2_check_anchor
>
> I looked online but I could not find a definitive answer. An advice
> will be
> highly appreciated.
>
> Thanks!
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
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>
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Re: [Bioc-devel] EXTERNAL: Re: warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Thanks a lot I will try.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno ven 14 feb 2020 alle ore 02:49 Marcel Ramos <
marcel.ra...@roswellpark.org> ha scritto:
> Hi Stefano,
>
> I'm no roxygen expert either but you could try using the
> `usethis::use_pipe(export = TRUE)`
> functionality developed by actual roxygen experts ;)
>
> Best,
> Marcel
>
> On 2/13/20 2:28 AM, Felix Ernst wrote:
> > Hi,
> >
> > I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to
> implicit for anyone's taste, \code{\link[magrittr:pipe]{\%>\%}} should also
> work in this case.
> >
> > The case above is used for a package external link. For an internal
> explicit link use \code{\link[=something]{or other}}.
> >
> > Felix
> >
> > -Ursprüngliche Nachricht-
> > Von: Bioc-devel Im Auftrag von
> Martin Morgan
> > Gesendet: Donnerstag, 13. Februar 2020 04:46
> > An: stefano ; bioc-devel@r-project.org
> > Betreff: Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr'
> does not exist and so has been treated as a topic
> >
> > This warning
> >
> > * checking whether package 'ttBulk' can be installed ... WARNING Found
> the following significant warnings:
> > Rd warning:
> C:/Users/pkgbuild/AppData/Local/Temp/Rtmp6Js8e8/R.INSTALL1ddcdee5581/ttBulk/man/reexports.Rd:19:
> file link '%>%' in package 'magrittr' does not exist and so has been
> treated as a topic See
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1330/8048f88/ttBulk.Rcheck/00install.out'
> for details.
> >
> > is actually about the documentation for '%>%'. In your previous 'man'
> page you had
> >
> > \code{\link[magrittr]{\%>\%}}
> >
> > which from reading 'Writing R Extensions' RShowDoc("R-exts") section 2.5
> 'Cross-references' indicates that you're trying to link to an html page
> named '%>%.html' in the magrittr package, but actually the man page is
> 'pipe.html' (e.g., by using help.start() and browsing manually to the help
> page). While it's possible to link to that help page, you should instead
> just \code{\link{\%>\%}} and R (possibly with the user choosing the
> package) will generate the correct link.
> >
> > Your package is too deep into the roxygen foo for me to know what you
> need to do to generate the appropriate link (or even where the link is
> generated...); maybe there's a roxygen expert on the mailing list who can
> help (or you can perhaps post here where you generate the reexports.Rd page
> from).
> >
> > Also, your github repository seems VERY LARGE (I lost patience trying to
> clone it, although my current link is quite slow); this
> http://bioconductor.org/developers/how-to/git/remove-large-data/ might
> provide some hints for removing large commits.
> >
> > Hope that helps,
> >
> > Martin
> >
> >
> > On 2/12/20, 9:51 PM, "Bioc-devel on behalf of stefano" <
> bioc-devel-boun...@r-project.org on behalf of mangiolastef...@gmail.com>
> wrote:
> >
> > Hello Community,
> >
> > The CHECK Windows server gives me a warning when I try to reexport an
> > existing operator magrittr::`%>%`
> >
> > ```
> > #' @importFrom magrittr %>%
> >
> > #' @export
> >
> > magrittr::`%>%`
> > ```
> >
> > okay2 Windows Server 2012 R2 Standard/x64
> > OK
> > WARNINGS
> > OK
> > OK
> >
> > malbec2 Linux (Ubuntu 18.04.3 LTS)/x86_64
> > OK
> > OK
> > skipped
> > OK
> >
> >
> > Here is the log
> >
> http://bioconductor.org/spb_reports/ttBulk_buildreport_20200212081044.html#tokay2_check_anchor
> >
> > I looked online but I could not find a definitive answer. An advice
> will be
> > highly appreciated.
> >
> > Thanks!
> >
> > Best wishes.
> >
> > *Stefano *
> >
> >
> >
> > Stefano Mangiola | Postdoctoral fellow
> >
> > Papenfuss Laboratory
> >
> > The Walter Eliza Hall Institute of Medical Research
> >
> > +61 (0)466452544
> >
> > [[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
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
> ___
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>
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Re: [Bioc-devel] gds nodes dimensions are inconsistent
Hi Xiuwen,
Thank you very much for the prompt response. I'll look at the new functions and
make necessary changes in my packages.
Best,
Qian
From: Xiuwen Zheng
Sent: Tuesday, February 11, 2020 3:58 PM
To: Liu, Qian
Cc: bioc-devel@r-project.org
Subject: Re: gds nodes dimensions are inconsistent
Hi Qian,
I have modified the GDS file in the SeqArray package.
"annotation/info/AA" should have fewer values than "annotation/info/AC", since
it is a variable-length vector in the new GDS file.
VCF format allows storing variable-length data, so SeqArray also allows
variable-length data.
seqGetData() has been updated in SeqArray_1.27.8, with a new option '.padNA'
for padding array with NA if possible.
Please revise your package according to the new function in SeqArray.
Best wishes,
Xiuwen
On Tue, Feb 11, 2020 at 12:45 PM Liu, Qian
mailto:qian@roswellpark.org>> wrote:
Dear Dr. Zheng & SeqArray maintainer,
I have a Bioconductor package called "GDSArray" that interfaces GDS file nodes
as DelayedArray instances. In this new Bioc devel version of 3.11, this package
failed all platforms. The debugging shows inconsistent dimensions calculated
from different SeqArray / gdsfmt functions. Following is some reproducible code
showing that the "annotation/info/AA" node has different dimension from "AC"
and the overall "num.variant" calculated from "SeqSummary". It works fine in
the Bioc 3.10 (dimension of AA is 1348).Thanks!
Best,
Qian
```{r}
library(SeqArray)
file <- seqExampleFileName("gds")
f <- seqOpen(file)
objdesp.gdsn(index.gdsn(f, "annotation/info/AA"))$dim
## [1] 1328
objdesp.gdsn(index.gdsn(f, "annotation/info/AC"))$dim
## [1] 1348
seqSummary(f, verbose=FALSE)$num.variant
## [1] 1348
seqClose(f)
!> sessionInfo()
R Under development (unstable) (2020-01-07 r77631)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /home/qian/miniconda3/envs/r-devel/lib/R/lib/libRblas.so
LAPACK: /home/qian/miniconda3/envs/r-devel/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeqArray_1.27.8 gdsfmt_1.23.5
loaded via a namespace (and not attached):
[1] IRanges_2.21.2 Biostrings_2.55.4 crayon_1.3.4
[4] bitops_1.0-6 GenomeInfoDb_1.23.1stats4_4.0.0
[7] zlibbioc_1.33.1XVector_0.27.0 S4Vectors_0.25.11
[10] tools_4.0.0RCurl_1.95-4.12parallel_4.0.0
[13] compiler_4.0.0 BiocGenerics_0.33.0GenomicRanges_1.39.1
[16] GenomeInfoDbData_1.2.2
```
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Re: [Bioc-devel] EXTERNAL: Re: warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Hi Stefano,
I'm no roxygen expert either but you could try using the
`usethis::use_pipe(export = TRUE)`
functionality developed by actual roxygen experts ;)
Best,
Marcel
On 2/13/20 2:28 AM, Felix Ernst wrote:
> Hi,
>
> I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to
> implicit for anyone's taste, \code{\link[magrittr:pipe]{\%>\%}} should also
> work in this case.
>
> The case above is used for a package external link. For an internal explicit
> link use \code{\link[=something]{or other}}.
>
> Felix
>
> -Ursprüngliche Nachricht-
> Von: Bioc-devel Im Auftrag von Martin
> Morgan
> Gesendet: Donnerstag, 13. Februar 2020 04:46
> An: stefano ; bioc-devel@r-project.org
> Betreff: Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr' does
> not exist and so has been treated as a topic
>
> This warning
>
> * checking whether package 'ttBulk' can be installed ... WARNING Found the
> following significant warnings:
> Rd warning:
> C:/Users/pkgbuild/AppData/Local/Temp/Rtmp6Js8e8/R.INSTALL1ddcdee5581/ttBulk/man/reexports.Rd:19:
> file link '%>%' in package 'magrittr' does not exist and so has been treated
> as a topic See
> 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1330/8048f88/ttBulk.Rcheck/00install.out'
> for details.
>
> is actually about the documentation for '%>%'. In your previous 'man' page
> you had
>
> \code{\link[magrittr]{\%>\%}}
>
> which from reading 'Writing R Extensions' RShowDoc("R-exts") section 2.5
> 'Cross-references' indicates that you're trying to link to an html page named
> '%>%.html' in the magrittr package, but actually the man page is 'pipe.html'
> (e.g., by using help.start() and browsing manually to the help page). While
> it's possible to link to that help page, you should instead just
> \code{\link{\%>\%}} and R (possibly with the user choosing the package) will
> generate the correct link.
>
> Your package is too deep into the roxygen foo for me to know what you need to
> do to generate the appropriate link (or even where the link is generated...);
> maybe there's a roxygen expert on the mailing list who can help (or you can
> perhaps post here where you generate the reexports.Rd page from).
>
> Also, your github repository seems VERY LARGE (I lost patience trying to
> clone it, although my current link is quite slow); this
> http://bioconductor.org/developers/how-to/git/remove-large-data/ might
> provide some hints for removing large commits.
>
> Hope that helps,
>
> Martin
>
>
> On 2/12/20, 9:51 PM, "Bioc-devel on behalf of stefano"
>
> wrote:
>
> Hello Community,
>
> The CHECK Windows server gives me a warning when I try to reexport an
> existing operator magrittr::`%>%`
>
> ```
> #' @importFrom magrittr %>%
>
> #' @export
>
> magrittr::`%>%`
> ```
>
> okay2 Windows Server 2012 R2 Standard/x64
> OK
> WARNINGS
> OK
> OK
>
> malbec2 Linux (Ubuntu 18.04.3 LTS)/x86_64
> OK
> OK
> skipped
> OK
>
>
> Here is the log
>
> http://bioconductor.org/spb_reports/ttBulk_buildreport_20200212081044.html#tokay2_check_anchor
>
> I looked online but I could not find a definitive answer. An advice will
> be
> highly appreciated.
>
> Thanks!
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
> [[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
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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