[Bioc-devel] 2 candidates for BiocGenerics

2015-03-10 Thread Laurent Gatto 

Dear all,

Two possible candidates for BiocGenerics:

> GenomeInfoDb::species
standardGeneric for "species" defined from package "GenomeInfoDb"

function (x) 
standardGeneric("species")

Methods may be defined for arguments: x
Use  showMethods("species")  for currently available ones.
> AnnotationDbi::species
standardGeneric for "species" defined from package "AnnotationDbi"

function (x) 
standardGeneric("species")

Methods may be defined for arguments: x
Use  showMethods("species")  for currently available ones.


and

> annotate::organism
standardGeneric for "organism" defined from package "annotate"

function (object) 
standardGeneric("organism")

Methods may be defined for arguments: object
Use  showMethods("organism")  for currently available ones.
> GenomeInfoDb::organism
standardGeneric for "organism" defined from package "GenomeInfoDb"

function (x) 
standardGeneric("organism")

Methods may be defined for arguments: x
Use  showMethods("organism")  for currently available ones.


Best wishes,

Laurent

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Re: [Bioc-devel] using devel bug

2015-03-10 Thread Kasper Daniel Hansen 
Ok, I had to manually remove the BiocInstaller package, restart R and then
run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0

Clearly, there is some issue with the IS_UPGRADEABLE variable which (I
guess) is initialized at install time.

On Tue, Mar 10, 2015 at 2:01 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> Using R-devel, I get
>
> R-devel
>
> R Under development (unstable) (2015-03-09 r67969) -- "Unsuffered
> Consequences"
> Copyright (C) 2015 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> 
> ** Hopkins NEWS and Notes **
> 
>
> News and updates for the R installation will be sent to bit-help, so
> consider subscribing
>
> An automatic user library has been created (in case it did not already
> exist) as
> ~/R/x86_64-unknown-linux-gnu-library/3.2
> install.packages and R CMD INSTALL will automatically install to this
> directory, so there is no need for a -l or a lib argument to these
> functions.
>
> Loading required package: utils
>   none
> > source("http://www.bioconductor.org/biocLite.R";)
> Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
>
>
> Why?  In the past it would auto-detect my R version and automatically use
> Bioc devel.  Also, I get
>
> > useDevel(TRUE)
> Error: 'devel' version requires a more recent R
>
> Enter a frame number, or 0 to exit
>
> 1: useDevel(TRUE)
> 2: .stop("'devel' version requires a more recent R")
>
> Best,
> Kasper
>
>

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Re: [Bioc-devel] using devel bug

2015-03-10 Thread Vincent Carey 
FWIW I encountered a similar situation a couple of weeks ago.  I should
have said something, I guess.

On Tue, Mar 10, 2015 at 2:08 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> Ok, I had to manually remove the BiocInstaller package, restart R and then
> run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0
>
> Clearly, there is some issue with the IS_UPGRADEABLE variable which (I
> guess) is initialized at install time.
>
> On Tue, Mar 10, 2015 at 2:01 PM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
> > Using R-devel, I get
> >
> > R-devel
> >
> > R Under development (unstable) (2015-03-09 r67969) -- "Unsuffered
> > Consequences"
> > Copyright (C) 2015 The R Foundation for Statistical Computing
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> >   Natural language support but running in an English locale
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> > 
> > ** Hopkins NEWS and Notes **
> > 
> >
> > News and updates for the R installation will be sent to bit-help, so
> > consider subscribing
> >
> > An automatic user library has been created (in case it did not already
> > exist) as
> > ~/R/x86_64-unknown-linux-gnu-library/3.2
> > install.packages and R CMD INSTALL will automatically install to this
> > directory, so there is no need for a -l or a lib argument to these
> > functions.
> >
> > Loading required package: utils
> >   none
> > > source("http://www.bioconductor.org/biocLite.R";)
> > Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> >
> >
> > Why?  In the past it would auto-detect my R version and automatically use
> > Bioc devel.  Also, I get
> >
> > > useDevel(TRUE)
> > Error: 'devel' version requires a more recent R
> >
> > Enter a frame number, or 0 to exit
> >
> > 1: useDevel(TRUE)
> > 2: .stop("'devel' version requires a more recent R")
> >
> > Best,
> > Kasper
> >
> >
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] using devel bug

2015-03-10 Thread Martin Morgan 

On 03/10/2015 11:08 AM, Kasper Daniel Hansen wrote:

Ok, I had to manually remove the BiocInstaller package, restart R and then
run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0


any idea how BiocInstaller 1.16.x was installed in the R-3.2 library? I think 
install.packages() will actually currently do the wrong thing...




Clearly, there is some issue with the IS_UPGRADEABLE variable which (I
guess) is initialized at install time.

On Tue, Mar 10, 2015 at 2:01 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:


Using R-devel, I get

R-devel

R Under development (unstable) (2015-03-09 r67969) -- "Unsuffered
Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


** Hopkins NEWS and Notes **


News and updates for the R installation will be sent to bit-help, so
consider subscribing

An automatic user library has been created (in case it did not already
exist) as
 ~/R/x86_64-unknown-linux-gnu-library/3.2
install.packages and R CMD INSTALL will automatically install to this
directory, so there is no need for a -l or a lib argument to these
functions.

Loading required package: utils
   none

source("http://www.bioconductor.org/biocLite.R";)

Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help


Why?  In the past it would auto-detect my R version and automatically use
Bioc devel.  Also, I get


useDevel(TRUE)

Error: 'devel' version requires a more recent R

Enter a frame number, or 0 to exit

1: useDevel(TRUE)
2: .stop("'devel' version requires a more recent R")

Best,
Kasper




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Phone: (206) 667-2793

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Re: [Bioc-devel] using devel bug

2015-03-10 Thread Henrik Bengtsson 
On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan  wrote:
> On 03/10/2015 11:08 AM, Kasper Daniel Hansen wrote:
>>
>> Ok, I had to manually remove the BiocInstaller package, restart R and then
>> run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0
>
>
> any idea how BiocInstaller 1.16.x was installed in the R-3.2 library? I
> think install.packages() will actually currently do the wrong thing...

I think *when* could also be an important lead. See my troubleshooting
on this in Bioc devel thread '[Bioc-devel] Can't seem to use
useDevel(); biocLite() for BioC 3.1' on Nov 17, 2014:

  https://stat.ethz.ch/pipermail/bioc-devel/2014-November/006670.html

Maybe related?

/Henrik

>
>
>>
>> Clearly, there is some issue with the IS_UPGRADEABLE variable which (I
>> guess) is initialized at install time.
>>
>> On Tue, Mar 10, 2015 at 2:01 PM, Kasper Daniel Hansen <
>> kasperdanielhan...@gmail.com> wrote:
>>
>>> Using R-devel, I get
>>>
>>> R-devel
>>>
>>> R Under development (unstable) (2015-03-09 r67969) -- "Unsuffered
>>> Consequences"
>>> Copyright (C) 2015 The R Foundation for Statistical Computing
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>> 
>>> ** Hopkins NEWS and Notes **
>>> 
>>>
>>> News and updates for the R installation will be sent to bit-help, so
>>> consider subscribing
>>>
>>> An automatic user library has been created (in case it did not already
>>> exist) as
>>>  ~/R/x86_64-unknown-linux-gnu-library/3.2
>>> install.packages and R CMD INSTALL will automatically install to this
>>> directory, so there is no need for a -l or a lib argument to these
>>> functions.
>>>
>>> Loading required package: utils
>>>none

 source("http://www.bioconductor.org/biocLite.R";)
>>>
>>> Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
>>>
>>>
>>> Why?  In the past it would auto-detect my R version and automatically use
>>> Bioc devel.  Also, I get
>>>
 useDevel(TRUE)
>>>
>>> Error: 'devel' version requires a more recent R
>>>
>>> Enter a frame number, or 0 to exit
>>>
>>> 1: useDevel(TRUE)
>>> 2: .stop("'devel' version requires a more recent R")
>>>
>>> Best,
>>> Kasper
>>>
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] using devel bug

2015-03-10 Thread Martin Morgan 

On 03/10/2015 01:01 PM, Kasper Daniel Hansen wrote:

Yeah, I basically have one version of R devel which is re-compiled every morning
and then all packages are updated.  This is probably happening around the
transition from R-devel using one version of BiocInstaller to another.  Reading
the code, it seems weird to me that IS_UPGRADABLE gets set at install time; this
is something that will depend on query time, at least for R-devel.


IS_UPGRADEABLE (also useDevel()) is meant to key off the version of 
BiocInstaller, under the assumption that BiocInstaller is correct for the 
version of R in use. Each release is accompanied by version bumps in 
end-of-life, devel-to-release, and new-devel branches of BiocInstaller, so (a) 
you'll be told BiocInstaller is out-of-date and (b) the current devel 
IS_UPGRADEABLE=FALSE will become IS_UPGRADEABLE=TRUE and you'll be able to upgrade.


It isn't really simpler to think in terms of the version of R in use, either, 
e.g., BiocInstaller under R-3.1 was initially (Bioc version 2.15) not 
upgradeable, until our Bioc 3.0 came out.


BiocInstaller could / should detect that it was running on the wrong version of 
R for Kasper's and Henrik's case.


Martin



Best,
Kasper

On Tue, Mar 10, 2015 at 3:50 PM, Henrik Bengtsson mailto:henrik.bengts...@ucsf.edu>> wrote:

On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan mailto:mtmor...@fredhutch.org>> wrote:
> On 03/10/2015 11:08 AM, Kasper Daniel Hansen wrote:
>>
>> Ok, I had to manually remove the BiocInstaller package, restart R and 
then
>> run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0
>
>
> any idea how BiocInstaller 1.16.x was installed in the R-3.2 library? I
> think install.packages() will actually currently do the wrong thing...

I think *when* could also be an important lead. See my troubleshooting
on this in Bioc devel thread '[Bioc-devel] Can't seem to use
useDevel(); biocLite() for BioC 3.1' on Nov 17, 2014:

https://stat.ethz.ch/pipermail/bioc-devel/2014-November/006670.html

Maybe related?

/Henrik

 >
 >
 >>
 >> Clearly, there is some issue with the IS_UPGRADEABLE variable which (I
 >> guess) is initialized at install time.
 >>
 >> On Tue, Mar 10, 2015 at 2:01 PM, Kasper Daniel Hansen <
 >> kasperdanielhan...@gmail.com > 
wrote:
 >>
 >>> Using R-devel, I get
 >>>
 >>> R-devel
 >>>
 >>> R Under development (unstable) (2015-03-09 r67969) -- "Unsuffered
 >>> Consequences"
 >>> Copyright (C) 2015 The R Foundation for Statistical Computing
 >>> Platform: x86_64-unknown-linux-gnu (64-bit)
 >>>
 >>> R is free software and comes with ABSOLUTELY NO WARRANTY.
 >>> You are welcome to redistribute it under certain conditions.
 >>> Type 'license()' or 'licence()' for distribution details.
 >>>
 >>>Natural language support but running in an English locale
 >>>
 >>> R is a collaborative project with many contributors.
 >>> Type 'contributors()' for more information and
 >>> 'citation()' on how to cite R or R packages in publications.
 >>>
 >>> Type 'demo()' for some demos, 'help()' for on-line help, or
 >>> 'help.start()' for an HTML browser interface to help.
 >>> Type 'q()' to quit R.
 >>>
 >>> 
 >>> ** Hopkins NEWS and Notes **
 >>> 
 >>>
 >>> News and updates for the R installation will be sent to bit-help, so
 >>> consider subscribing
 >>>
 >>> An automatic user library has been created (in case it did not already
 >>> exist) as
 >>>  ~/R/x86_64-unknown-linux-gnu-library/3.2
 >>> install.packages and R CMD INSTALL will automatically install to this
 >>> directory, so there is no need for a -l or a lib argument to these
 >>> functions.
 >>>
 >>> Loading required package: utils
 >>>none
 
  source("http://www.bioconductor.org/biocLite.R";)
 >>>
 >>> Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
 >>>
 >>>
 >>> Why?  In the past it would auto-detect my R version and automatically 
use
 >>> Bioc devel.  Also, I get
 >>>
  useDevel(TRUE)
 >>>
 >>> Error: 'devel' version requires a more recent R
 >>>
 >>> Enter a frame number, or 0 to exit
 >>>
 >>> 1: useDevel(TRUE)
 >>> 2: .stop("'devel' version requires a more recent R")
 >>>
 >>> Best,
 >>> Kasper
 >>>
 >>>
 >>
 >> [[alternative HTML version deleted]]
 >>
 >> ___
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 >>
 >
 >
 > --
 > Computational Biology / Fred Hutchinson Cancer Research Center
 > 1100 Fairview Av

Re: [Bioc-devel] Package build error for windows system

2015-03-10 Thread Hervé Pagès 

Hi Liu,

On 03/10/2015 10:08 AM, Liu, Yuanhang wrote:

Hello, everyone,


I recently submitted my first R package. Everything checks fine on my
local machine. However, when I upload the tarball to the single package
builder at bioconductor.org, it gave me the following error on windows
system:


* creating vignettes ...Warning: running command
'"E:/packagebuilder/R/bin/x64/Rscript" --vanilla --default-packages= -e
"tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 5
ERROR
Error in withCallingHandlers(tryCatch(evalq((function (i) :
object '.rcpp_warning_recorder' not found


Don't worry about this one. The problem is probably on the build machine
side (in the R it uses). Please ignore.




The name of the windows build system is :


moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit)/x64​


What does this mean? I would really appreciate it if someone can help me
with this.


I also got a warning on one linux system (morelia Mac OS X Mavericks
(10.9.5)/x86_64):


* checking loading without being on the library search path ... WARNING

Loading required package: IRanges
Error: package BiocGenerics 0.13.4 is loaded, but >= 0.13.6 is required by 
IRanges
In addition: Warning message:
version 0.13.6 of BiocGenerics masked by 0.13.4 in 
/private/tmp/Rtmp8nLYMq/RLIBS_9d027c2fae3
Execution halted


mmh... again something doesn't look quite right on this build machine. 
Please ignore.




Then I checked my version of BiocGenerics, which is 0.12.1, the latest version.


This is the current release version. However remember that for testing
before package submission you should be using BioC devel (BioC 3.1, 
which requires R 3.2), not BioC release (BioC 3.0). That's what the

automatic single package builder uses.
The latest version of BiocGenerics in devel is 0.13.6.

Cheers,
H.


How come the system require 0.13.6? I also checked IRanges manual, which it says 
it depends on BiocGenerics(>= 0.11.3). Would anybody tell me what does this 
mean? Thanks in advance!

Regards
Yuanhang Liu
PhD Candidate
Bioinformatics and Computational Biology laboratory
Cellular & Structural Biology, Department of Epidemiology & Biostatistics
UT Health Science Center at San Antonio
email: liu...@uthscsa.educel: 210-784-082​8


--
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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