Re: [Rd] Very hard to reproduce bug (?) in R-devel

[Winston Chang]

>
>
>>
I've done some more investigation into the problem, and it is very
difficult to pin down. What it looks like is happening is roughly like this:
- `p` is an environment and `p$e` is also an environment.
- There is a loop. In each iteration, it looks for one item in `p$e`, saves
it in a variable `x`, then removes that item from `p$e`. Then it invokes
`x()`. The loop runs again, until there are no more items in `p$e`.

The problem is that `ls(p$e)` sometimes returns the wrong values -- it
returns the values that it had in previous iterations of the loop. The
behavior is very touchy. Almost any change to the code will slightly change
the behavior; sometimes the `ls()` returns values from a different
iteration of the loop, and sometimes the problem doesn't happen at all.

I've put a  Dockerfile and instructions for reproducing the problem here:
  https://gist.github.com/wch/2596a1c9f1bcdee91bb210c782141c88

I think that I've gotten about as far with this as I can, though I'd be
happy to provide more information if anyone wants to take look at the
problem.

-Winston

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

[Michael Lawrence]

Sorry I have been traveling. Will get to it soon.

On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
wrote:

> Hi Herve,
>
> sorry for all the reds - actually I provided the patches to biovizBase and
> ggbio, but it did not work out that smoothly that I hoped. For the other
> packages that depend on ensembldb there's no problem or only small changes
> required (did contact the developers).
> Fingers crossed that Michael can patch biovizBase and ggbio soon.
>
> cheers, jo
>
> > On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:
> >
> > Hi Johannes,
> >
> > This move is generating a lot of red today on the build report.
> > Hopefully biovizBase and ggbio can be fixed quickly. Note that
> > maybe a smoother path would have been to notify the maintainers
> > of these packages first and wait that they make the required
> > changes (i.e. to import the filters from AnnotationFilter)
> > before modifying ensembldb. Maybe for next time ;-)
> >
> > Cheers,
> > H.
> >
> > On 04/04/2017 04:02 AM, Rainer Johannes wrote:
> >>
> >>
> >> On 4 Apr 2017, at 10:59, Stian Lågstad > wrote:
> >>
> >> Hi,
> >>
> >> Thanks again for notifying me about the changes needed in chimeraviz.
> Right now I'm having problems installing Gviz - I get these errors:
> >>
> >> """
> >> No methods found in "GenomicAlignments" for requests:
> pmapFromTranscripts
> >> Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
> >> ERROR: lazy loading failed for package 'Gviz'
> >> """
> >>
> >> Are these errors caused by the change in ensembldb? If so: Do you know
> how I can keep developing without having to wait for Gviz?
> >>
> >>
> >> These come from biovizBase which Gviz imports. I've sent Micheal the
> fixes for biovizBase and ggbio that should fix this.
> >> We need to wait for the changes to be propagated, since also for
> ensembldb I get today still version 1.99.12 but not the new 1.99.13.
> >>
> >> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
> johannes.rai...@eurac.edu> wrote:
> >> Dear all,
> >>
> >> I've just committed a change in ensembldb (version 1.99.13) that
> removes all filter classes from it and imports them from the
> AnnotationFilter package. This change will break biovizBase and ggbio (and
> all packages downstream of them, e.g. Gviz). I've already sent Michael
> Lawrence patches to fix both packages, but  there might still be some
> problems in the upcoming build reports I guess.
> >>
> >> I've also contacted the developers of the TVTB and chimeraviz packages
> and made them aware of the change. Could be that there are other packages
> out there possibly affected by the change. If so, let me know and I'll
> assist fixing the problems (if needed).
> >>
> >> cheers, jo
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=
> BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> >>
> >>
> >>
> >> --
> >> Stian Lågstad
> >> +47 41 80 80 25
> >>
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=
> BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> >>
> >
> > --
> > 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...@fredhutch.org
> > Phone:  (206) 667-5791
> > Fax:(206) 667-1319
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

[Rainer Johannes]

Hi Herve,

sorry for all the reds - actually I provided the patches to biovizBase and 
ggbio, but it did not work out that smoothly that I hoped. For the other 
packages that depend on ensembldb there's no problem or only small changes 
required (did contact the developers).
Fingers crossed that Michael can patch biovizBase and ggbio soon.

cheers, jo

> On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:
> 
> Hi Johannes,
> 
> This move is generating a lot of red today on the build report.
> Hopefully biovizBase and ggbio can be fixed quickly. Note that
> maybe a smoother path would have been to notify the maintainers
> of these packages first and wait that they make the required
> changes (i.e. to import the filters from AnnotationFilter)
> before modifying ensembldb. Maybe for next time ;-)
> 
> Cheers,
> H.
> 
> On 04/04/2017 04:02 AM, Rainer Johannes wrote:
>> 
>> 
>> On 4 Apr 2017, at 10:59, Stian Lågstad 
>> > wrote:
>> 
>> Hi,
>> 
>> Thanks again for notifying me about the changes needed in chimeraviz. Right 
>> now I'm having problems installing Gviz - I get these errors:
>> 
>> """
>> No methods found in "GenomicAlignments" for requests: pmapFromTranscripts
>> Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
>> ERROR: lazy loading failed for package 'Gviz'
>> """
>> 
>> Are these errors caused by the change in ensembldb? If so: Do you know how I 
>> can keep developing without having to wait for Gviz?
>> 
>> 
>> These come from biovizBase which Gviz imports. I've sent Micheal the fixes 
>> for biovizBase and ggbio that should fix this.
>> We need to wait for the changes to be propagated, since also for ensembldb I 
>> get today still version 1.99.12 but not the new 1.99.13.
>> 
>> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes 
>> > wrote:
>> Dear all,
>> 
>> I've just committed a change in ensembldb (version 1.99.13) that removes all 
>> filter classes from it and imports them from the AnnotationFilter package. 
>> This change will break biovizBase and ggbio (and all packages downstream of 
>> them, e.g. Gviz). I've already sent Michael Lawrence patches to fix both 
>> packages, but  there might still be some problems in the upcoming build 
>> reports I guess.
>> 
>> I've also contacted the developers of the TVTB and chimeraviz packages and 
>> made them aware of the change. Could be that there are other packages out 
>> there possibly affected by the change. If so, let me know and I'll assist 
>> fixing the problems (if needed).
>> 
>> cheers, jo
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
>> 
>> 
>> 
>> --
>> Stian Lågstad
>> +47 41 80 80 25
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
>> 
> 
> -- 
> 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...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

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Re: [Bioc-devel] Check error on malbec2

[Aimin Yan]

Thank you, I changed to use tempdir(), and it works now.
One more question is how to locate those outputs in temporary directory since
I want users to use those outputs.

Aimin

On Tue, Apr 4, 2017 at 2:00 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Write and access your output to a temporary directory instead using
> tempdir().
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of Aimin
> Yan 
> *Sent:* Tuesday, April 4, 2017 1:45:28 PM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] Check error on malbec2
>
> In the package I am trying ti submit to bioconductor, I got the following
> error for check.
>
> Warning in dir.create(output.file.dir) :
>   cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission
> denied'
> Warning in file(file, ifelse(append, "a", "w")) :
>   cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such
> file or directory
> Error in file(file, ifelse(append, "a", "w")) :
>   cannot open the connection
> Calls: enrichmentmap -> write.table -> file
>
> It seems I do not have permission to create a directory.
> Does anyone know how to fix this check error?
>
>
> Thanks,
> Aimin
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

[Hervé Pagès]

Hi Johannes,

This move is generating a lot of red today on the build report.
Hopefully biovizBase and ggbio can be fixed quickly. Note that
maybe a smoother path would have been to notify the maintainers
of these packages first and wait that they make the required
changes (i.e. to import the filters from AnnotationFilter)
before modifying ensembldb. Maybe for next time ;-)

Cheers,
H.

On 04/04/2017 04:02 AM, Rainer Johannes wrote:



On 4 Apr 2017, at 10:59, Stian Lågstad 
> wrote:

Hi,

Thanks again for notifying me about the changes needed in chimeraviz. Right now 
I'm having problems installing Gviz - I get these errors:

"""
No methods found in "GenomicAlignments" for requests: pmapFromTranscripts
Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know how I 
can keep developing without having to wait for Gviz?


These come from biovizBase which Gviz imports. I've sent Micheal the fixes for 
biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for ensembldb I 
get today still version 1.99.12 but not the new 1.99.13.

On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes 
> wrote:
Dear all,

I've just committed a change in ensembldb (version 1.99.13) that removes all 
filter classes from it and imports them from the AnnotationFilter package. This 
change will break biovizBase and ggbio (and all packages downstream of them, 
e.g. Gviz). I've already sent Michael Lawrence patches to fix both packages, 
but  there might still be some problems in the upcoming build reports I guess.

I've also contacted the developers of the TVTB and chimeraviz packages and made 
them aware of the change. Could be that there are other packages out there 
possibly affected by the change. If so, let me know and I'll assist fixing the 
problems (if needed).

cheers, jo

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--
Stian Lågstad
+47 41 80 80 25


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--
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...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Check error on malbec2

[Shepherd, Lori]

Write and access your output to a temporary directory instead using tempdir().



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Aimin Yan 

Sent: Tuesday, April 4, 2017 1:45:28 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Check error on malbec2

In the package I am trying ti submit to bioconductor, I got the following
error for check.

Warning in dir.create(output.file.dir) :
  cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such
file or directory
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: enrichmentmap -> write.table -> file

It seems I do not have permission to create a directory.
Does anyone know how to fix this check error?


Thanks,
Aimin

[[alternative HTML version deleted]]

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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Check error on malbec2

[Aimin Yan]

In the package I am trying ti submit to bioconductor, I got the following
error for check.

Warning in dir.create(output.file.dir) :
  cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such
file or directory
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: enrichmentmap -> write.table -> file

It seems I do not have permission to create a directory.
Does anyone know how to fix this check error?


Thanks,
Aimin

[[alternative HTML version deleted]]

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[Bioc-devel] ensembl 87 and 88 added to AnnotationHub

[Shepherd, Lori]

Hello all,

The ensembl 87 and 88 gtfs (converted to GRanges on the fly) have been added to 
AnnotationHub and are currently available:

> library(AnnotationHub)
> hub = AnnotationHub()
updating metadata: retrieving 1 resource

|==|
100%
snapshotDate(): 2017-04-04

> length(query(hub, c("ensembl", "gtf", "release-87")))
[1] 218
> length(query(hub, c("ensembl", "gtf", "release-88")))
[1] 218


The fasta (twobit files) are not yet available but will be added before the 
upcoming release.

Thank you.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Build error on tokay2

[Shepherd, Lori]

This is an ERROR on our tokay2 builder and we are in the process of resolving.  
You do not need to take any actions at this time and when it is resolved this 
should clear up automatically on the next build.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Alina Selega 

Sent: Tuesday, April 4, 2017 7:24:07 AM
To: bioc-devel
Subject: [Bioc-devel] Build error on tokay2

Hi,

My package BUMHMM fails to build on tokay2 with the following error
message:
" there is no package called 'Biobase' ".

http://bioconductor.org/checkResults/3.5/bioc-LATEST/
BUMHMM/tokay2-buildsrc.html

There are no problems with other platforms.

It seems that many packages are encountering this problem since the last
snapshot on the 2nd April.

Could anyone provide any advice?

Thanks,
Alina

[[alternative HTML version deleted]]

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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Build error on tokay2

[Alina Selega]

Hi,

My package BUMHMM fails to build on tokay2 with the following error
message:
" there is no package called 'Biobase' ".

http://bioconductor.org/checkResults/3.5/bioc-LATEST/
BUMHMM/tokay2-buildsrc.html

There are no problems with other platforms.

It seems that many packages are encountering this problem since the last
snapshot on the 2nd April.

Could anyone provide any advice?

Thanks,
Alina

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

[Rainer Johannes]

On 4 Apr 2017, at 10:59, Stian Lågstad 
> wrote:

Hi,

Thanks again for notifying me about the changes needed in chimeraviz. Right now 
I'm having problems installing Gviz - I get these errors:

"""
No methods found in "GenomicAlignments" for requests: pmapFromTranscripts
Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know how I 
can keep developing without having to wait for Gviz?


These come from biovizBase which Gviz imports. I've sent Micheal the fixes for 
biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for ensembldb I 
get today still version 1.99.12 but not the new 1.99.13.

On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes 
> wrote:
Dear all,

I've just committed a change in ensembldb (version 1.99.13) that removes all 
filter classes from it and imports them from the AnnotationFilter package. This 
change will break biovizBase and ggbio (and all packages downstream of them, 
e.g. Gviz). I've already sent Michael Lawrence patches to fix both packages, 
but  there might still be some problems in the upcoming build reports I guess.

I've also contacted the developers of the TVTB and chimeraviz packages and made 
them aware of the change. Could be that there are other packages out there 
possibly affected by the change. If so, let me know and I'll assist fixing the 
problems (if needed).

cheers, jo

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+47 41 80 80 25


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[Bioc-devel] Error when building on tokay2 for BioC 3.5

[Alina Selega]

## I am resending this email as I it got rejected from posting due to "a
message with identical text being posted to the list recently" (for reasons
unknown to me). ##

Hi,

My package BUMHMM is giving an error when building on tokay2, with the
error message: "there is no package called 'Biobase'". The package is built
and checked with no problems on other platforms.

The build report is here:
http://bioconductor.org/checkResults/3.5/bioc-LATEST/
BUMHMM/tokay2-buildsrc.html

This seems like a problem that many packages are encountering since the
last snapshot on the 2nd April.

Could anyone provide any advice?

Thanks,
Alina

[[alternative HTML version deleted]]

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[Bioc-devel] Error when building on tokay2 for BioC 3.5

[Alina Selega]

Hi,

My package BUMHMM is failing to build on tokay2, with the error: "there is
no package called 'Biobase'". The package is built and checked with no
problems on other platforms.

The build report is here:
http://bioconductor.org/checkResults/3.5/bioc-LATEST/BUMHMM/tokay2-buildsrc.html

This seems like a problem that many packages are encountering since the
last snapshot on the 2nd April.

Could anyone provide any advice?

Thanks,
Alina

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Re: [Rd] Potential bug in utils::citation()

[Martin Maechler]

> Martin Maechler 
> on Mon, 3 Apr 2017 10:22:52 +0200 writes:

> Zhian Kamvar 
> on Sun, 2 Apr 2017 16:26:37 -0500 writes:

>> Hi, I believe the function utils::citation() will fail if
>> the package specified has two or more citation entries in
>> the current R-devel. The following error is issued:

>> 'missing' can only be used for arguments

>> I have created a working example on github [0] that is
>> build using R-devel on travis-ci [1]. Jim Hester has
>> potentially identified [2] the source of the problem as
>> being from a commit on the 27th [3, 4]. I do not have
>> R-devel built on my machine, but I believe this error can
>> be reproduced on the current R-devel with:

>> if (require("boot") & require("utils"))
>> utils::citation("boot")

> Correct: it does reproduce the new bug 
> and that is due to a change by me, and I had started investigation
> on Friday (but not with your package and not having seen a
> straighforward example yet).

> This will be fixed ASAP, i.e., within hours.

In the end, it took two dozens of hours. The change is
r72478 | maechler | 2017-04-04 11:41:51 +0200 

Martin


>> Background:

>> My package poppr suddenly started failing check on R-devel
>> during a weekly travis-ci job [5] due to the error
>> above. Another package of mine, ezec, passed [6]. Both
>> contain calls to utils::citation() within the vignettes,
>> but poppr has two citations and ezec only has one (called
>> from another package).

>> Thanks, Zhian

>> [0]: https://github.com/zkamvar/citest [1]:
>> https://travis-ci.org/zkamvar/citest/jobs/217874351 [2]:
>> 
https://github.com/wch/r-source/commit/7890e9e87d44f85ab76c0e786036a191eacd71d1
>> [3]: https://svn.r-project.org/R/trunk@72419 [4]:
>> 
https://github.com/wch/r-source/commit/7890e9e87d44f85ab76c0e786036a191eacd71d1
>> [5]:
>> https://travis-ci.org/grunwaldlab/poppr/jobs/216452458
>> [6]: https://travis-ci.org/grunwaldlab/ezec/jobs/216452916

>> -
>> Zhian N. Kamvar, Ph. D.  Postdoctoral Researcher (Everhart
>> Lab) Department of Plant Pathology University of
>> Nebraska-Lincoln

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[Rd] Bug report: POSIX regular expression doesn't match for somewhat higher values of upper bound

[dietmar.schindler]

Dear Sirs,

while

> regexpr('(.{1,2})\\1', 'foo')
[1] 2
attr(,"match.length")
[1] 2
attr(,"useBytes")
[1] TRUE

yields the correct match, an incremented upper bound in

> regexpr('(.{1,3})\\1', 'foo')
[1] -1
attr(,"match.length")
[1] -1
attr(,"useBytes")
[1] TRUE

incorrectly yields no match.

R versions tested:
2.11.1 on i486-pc-linux-gnu
2.15.1 on x86_64-pc-linux-gnu
3.2.1 on i386-w64-mingw32
3.2.1 on x86_64-w64-mingw32
3.3.3 on x86_64-w64-mingw32
--
Best regards,
Dietmar Schindler

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Registered Office: Augsburg -- Trade Register: AG Augsburg -- HRB-No.: 26816 -- 
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[Rd] Some "lm" methods give wrong results when applied to "mlm" objects

[Jari Oksanen]

I had a look at some influence measures, and it seems to me that currently 
several methods handle multiple lm (mlm) objects wrongly in R. In some cases 
there are separate "mlm" methods, but usually "mlm" objects are handled by the 
same methods as univariate "lm" methods, and in some cases this fails.

There are two general patterns of problems in influence measures:

1) The univariate methods assume that overall standard deviation (sd) is of 
length one, but for "mlm" models we have a multivariate response with a 
multicolumn residual matrix. The functions also get correctly the sd vector 
corresponding to the columns, but it is not applied to these, but recycled for 
rows. This influences rstandard.lm and cooks.distance.lm. For instance, in 
cooks.distance.lm we have ((res/(sd * (1 - hat)))^2 * hat)/p, where res is a n 
x m matrix, sd is a m-vector and hat is a n-vector).  Both of these functions 
are very easily fixed.

2) Another problem is that several functions are based on lm.influence 
function, and it seems that it returns elements sigma and coefficients that are 
only based on the first variable (first column of the residual matrix wt.res) 
and give wrong results for other variables. This will influence functions 
dfbeta.lm (coefficients), dfbetas.lm (coefficients, sigma), dffits (sigma), 
rstudent.lm (sigma) and covratio (sigma). lm.influence finds these elements in 
compiled code and this is harder to fix. MASS (the book & the package) avoid 
using compiled code in their (univariate) studentized residuals, and instead 
use a clever short-cut.

In addition to these, there are a couple of other cases which seem to fail with 
"mlm" models: 

confint.lm gives empty result, because the length of the results is defined by 
names(coef(object)) which is NULL because "mlm" objects return a matrix of 
coefficients instead of a vector with names.

dummy.coef fails because "mlm" objects do not have xlevels item.

extractAIC.lm returns only one value instead of a vector, and edf is 
misleading. Separate deviance.mlm returns a vector of deviances, and logLik.lm 
returns "'logLik.lm' does not support multiple responses". Probably 
extractAIC.lm should work like logLik.lm.

Several methods already handle "mlm" methods by returning message "  is not 
yet implemented for multivariate lm()" which of course is a natural and correct 
solution to the problems.

Cheers, Jari Oksanen
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Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

[Maarten van Iterson]

Thanks for looking into this!

Maarten

On Mon, Apr 3, 2017 at 7:00 PM, Hervé Pagès  wrote:

> Hi Maarten,
>
> identical() is not reliable on DNAStringSet objects or other objects
> that contain external pointers as it can return false negatives as well
> as false positives. We'll fix the "cbind" and "rbind" methods for
> SummarizedExperiment to work around this problem.
>
> Thanks for the report.
>
> H.
>
>
> On 04/03/2017 12:58 AM, Maarten van Iterson wrote:
>
>> Dear list,
>>
>> Combining SummarizedExperiment object, containing a DNAStringSet in the
>> rowData seems not to work properly. If I cbind two SummarizedExperiment
>> objects, which I know are identical, an error is reported:
>>
>> Error in FUN(X[[i]], ...) (from #2) :
>>   column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not
>> match
>>
>> I think I traced the problem existing in `SummarizedExperiment:::.compa
>> re`
>> in that `identical` is used to compare DNAStringSets which is not behaving
>> as expected. Whereas it should return all identical it returns it is not!
>>
>> Here is a counter example (which was easier to construct) showing that
>> `identical` returns FALSE where it should return TRUE.
>>
>> library(Biostrings)
>>> seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>>> seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>>>
>>> seq1
>>>
>> [1] "GACTC"
>>
>>> seq2
>>>
>> [1] "GAATG"
>>
>>>
>>> s1 <- DNAStringSet(seq1)
>>> s2 <- DNAStringSet(seq2)
>>>
>>> str(s1)
>>>
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
>> with 2 slots
>>   .. .. ..@ xp_list:List of 1
>>   .. .. .. ..$ :
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :
>>   ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
>> with 7 slots
>>   .. .. ..@ group  : int 1
>>   .. .. ..@ start  : int 1
>>   .. .. ..@ width  : int 5
>>   .. .. ..@ NAMES  : NULL
>>   .. .. ..@ elementType: chr "integer"
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ metadata   : list()
>>   ..@ elementType: chr "DNAString"
>>   ..@ elementMetadata: NULL
>>   ..@ metadata   : list()
>>
>>> str(s2)
>>>
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
>> with 2 slots
>>   .. .. ..@ xp_list:List of 1
>>   .. .. .. ..$ :
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :
>>
>>   ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
>> with 7 slots
>>   .. .. ..@ group  : int 1
>>   .. .. ..@ start  : int 1
>>   .. .. ..@ width  : int 5
>>   .. .. ..@ NAMES  : NULL
>>   .. .. ..@ elementType: chr "integer"
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ metadata   : list()
>>   ..@ elementType: chr "DNAString"
>>   ..@ elementMetadata: NULL
>>   ..@ metadata   : list()
>>
>>>
>>> identical(seq1, seq2)
>>>
>> [1] FALSE
>>
>>> identical(s1, s2)
>>>
>> [1] TRUE
>>
>>> seq1 == seq2
>>>
>> [1] FALSE
>>
>>> s1 == s2
>>>
>> [1] FALSE
>>
>>>
>>> sessionInfo()
>>>
>> R version 3.3.2 (2016-10-31)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.2 LTS
>>
>> locale:
>>  [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
>>  [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
>>  [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
>>  [7] LC_PAPER=en_US.utf8   LC_NAME=C
>>  [9] LC_ADDRESS=C  LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats4stats graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] Biostrings_2.42.1  XVector_0.14.1
>>  [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4.0
>>  [5] Biobase_2.34.0 GenomicRanges_1.26.4
>>  [7] GenomeInfoDb_1.10.3IRanges_2.8.2
>>  [9] S4Vectors_0.12.2   BiocGenerics_0.20.0
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.10 AnnotationDbi_1.36.2
>> hms_0.3
>>  [4] GenomicAlignments_1.10.1 zlibbioc_1.20.0
>> BiocParallel_1.8.1
>>  [7] BSgenome_1.42.0  lattice_0.20-35
>> R6_2.2.0
>> [10] httr_1.2.1   tools_3.3.2
>> grid_3.3.2
>> [13] DBI_0.6  assertthat_0.1
>> digest_0.6.12
>> [16] tibble_1.2   Matrix_1.2-8
>> readr_1.1.0
>> [19] rtracklayer_1.34.2   bitops_1.0-6
>> biomaRt_2.30.0
>> [22] RCurl_1.95-4.8   memoise_1.0.0
>> RSQLite_1.1-2
>> [25] compiler_3.3.2   GenomicFeatures_1.26.3
>> Rsamtools_1.26.1
>> [28] XML_3.98-1.5 jsonlite_1.3
>> VariantAnnotation_1.20.3
>>
>>>
>>>
>> I don't completely understand understand why `identical` is not working
>> properly is it comparing the environment address