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

2017-04-04 Thread 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=
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> 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

2017-04-04 Thread 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

2017-04-04 Thread 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]]
>
> ___
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> 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

2017-04-04 Thread 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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+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

2017-04-04 Thread 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

2017-04-04 Thread 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

2017-04-04 Thread 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 
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Re: [Bioc-devel] Build error on tokay2

2017-04-04 Thread 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

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[Bioc-devel] Build error on tokay2

2017-04-04 Thread 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

2017-04-04 Thread 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

2017-04-04 Thread 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

2017-04-04 Thread 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

[[alternative HTML version deleted]]

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Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

2017-04-04 Thread 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