Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
You should not be using R-3.1.2 patched with the current devel version of
Bioconductor; use R-devel.
Best,
Kasper
On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres
wrote:
> Hi,
>
> I can't seem to install devel packages via biocLite() and I wonder if
> something is broken or if I'm missing something. For example, take
> GenomeInfoDb which is at 1.3.6 and is passing all checks.
>
> The usual code using a fresh R 3.1.2-patched install isn't working as
> it downloads the latest release version (1.2.2):
>
> > source("http://bioconductor.org/biocLite.R";)
> Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> ## Was expecting 3.1 here
> > useDevel()
> Error: 'devel' version already in use
> > biocLite('GenomeInfoDb')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2.
> Installing package(s) 'GenomeInfoDb'
> trying URL '
> http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz
> '
> Content type 'application/x-gzip' length 404120 bytes (394 KB)
> opened URL
> ==
> downloaded 394 KB
>
>
> The downloaded binary packages are in
>
> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages
> >
> > sessionInfo()
> R version 3.1.2 Patched (2014-11-01 r66923)
> ## Note that it matches the current R version used by the Bioc-devel
> build machines
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.16.0 colorout_1.0-2
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.2
>
>
>
> For my computer it's not problem because I can download the pkg via
> svn and install locally. But it breaks my tests in TravisCI which
> relies on biocLite().
>
> Cheers,
> Leo
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Thanks, I incorrectly thought that I was using the same R version as
the Bioc-build machines since the "r66923" part matched. Now I realize
that this tag is used in all of the newest R builds at
http://r.research.att.com/.
On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen
wrote:
> You should not be using R-3.1.2 patched with the current devel version of
> Bioconductor; use R-devel.
>
> Best,
> Kasper
>
> On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres
> wrote:
>>
>> Hi,
>>
>> I can't seem to install devel packages via biocLite() and I wonder if
>> something is broken or if I'm missing something. For example, take
>> GenomeInfoDb which is at 1.3.6 and is passing all checks.
>>
>> The usual code using a fresh R 3.1.2-patched install isn't working as
>> it downloads the latest release version (1.2.2):
>>
>> > source("http://bioconductor.org/biocLite.R";)
>> Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
>> ## Was expecting 3.1 here
>> > useDevel()
>> Error: 'devel' version already in use
>> > biocLite('GenomeInfoDb')
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2.
>> Installing package(s) 'GenomeInfoDb'
>> trying URL
>> 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz'
>> Content type 'application/x-gzip' length 404120 bytes (394 KB)
>> opened URL
>> ==
>> downloaded 394 KB
>>
>>
>> The downloaded binary packages are in
>>
>> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages
>> >
>> > sessionInfo()
>> R version 3.1.2 Patched (2014-11-01 r66923)
>> ## Note that it matches the current R version used by the Bioc-devel
>> build machines
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BiocInstaller_1.16.0 colorout_1.0-2
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.1.2
>>
>>
>>
>> For my computer it's not problem because I can download the pkg via
>> svn and install locally. But it breaks my tests in TravisCI which
>> relies on biocLite().
>>
>> Cheers,
>> Leo
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
___
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Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
- Original Message -
> From: "Leonardo Collado Torres"
> To: "Kasper Daniel Hansen"
> Cc: bioc-devel@r-project.org
> Sent: Sunday, November 2, 2014 9:26:25 PM
> Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for
> BioC 3.1
>
> Thanks, I incorrectly thought that I was using the same R version as
> the Bioc-build machines since the "r66923" part matched. Now I
> realize
> that this tag is used in all of the newest R builds at
> http://r.research.att.com/.
>
It's admittedly confusing; the question of whether to use R-devel with
Bioc-devel has a different answer every six months, but the answer can always
be found here:
http://www.bioconductor.org/developers/how-to/useDevel/
Also, when looking at the devel build report, you should probably focus more on
the version portion of the "R version" column than on the SVN revision number.
Dan
> On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen
> wrote:
> > You should not be using R-3.1.2 patched with the current devel
> > version of
> > Bioconductor; use R-devel.
> >
> > Best,
> > Kasper
> >
> > On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres
> >
> > wrote:
> >>
> >> Hi,
> >>
> >> I can't seem to install devel packages via biocLite() and I wonder
> >> if
> >> something is broken or if I'm missing something. For example, take
> >> GenomeInfoDb which is at 1.3.6 and is passing all checks.
> >>
> >> The usual code using a fresh R 3.1.2-patched install isn't working
> >> as
> >> it downloads the latest release version (1.2.2):
> >>
> >> > source("http://bioconductor.org/biocLite.R";)
> >> Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for
> >> help
> >> ## Was expecting 3.1 here
> >> > useDevel()
> >> Error: 'devel' version already in use
> >> > biocLite('GenomeInfoDb')
> >> BioC_mirror: http://bioconductor.org
> >> Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version
> >> 3.1.2.
> >> Installing package(s) 'GenomeInfoDb'
> >> trying URL
> >> 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz'
> >> Content type 'application/x-gzip' length 404120 bytes (394 KB)
> >> opened URL
> >> ==
> >> downloaded 394 KB
> >>
> >>
> >> The downloaded binary packages are in
> >>
> >> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages
> >> >
> >> > sessionInfo()
> >> R version 3.1.2 Patched (2014-11-01 r66923)
> >> ## Note that it matches the current R version used by the
> >> Bioc-devel
> >> build machines
> >> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods
> >> base
> >>
> >> other attached packages:
> >> [1] BiocInstaller_1.16.0 colorout_1.0-2
> >>
> >> loaded via a namespace (and not attached):
> >> [1] tools_3.1.2
> >>
> >>
> >>
> >> For my computer it's not problem because I can download the pkg
> >> via
> >> svn and install locally. But it breaks my tests in TravisCI which
> >> relies on biocLite().
> >>
> >> Cheers,
> >> Leo
> >>
> >> ___
> >> 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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Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Hi,
On 11/02/2014 10:58 PM, Dan Tenenbaum wrote:
- Original Message -
From: "Leonardo Collado Torres"
To: "Kasper Daniel Hansen"
Cc: bioc-devel@r-project.org
Sent: Sunday, November 2, 2014 9:26:25 PM
Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Thanks, I incorrectly thought that I was using the same R version as
the Bioc-build machines since the "r66923" part matched. Now I
realize
that this tag is used in all of the newest R builds at
http://r.research.att.com/.
It's admittedly confusing;
Agreed. But the error message issued by useDevel() in the current
release adds to the confusion:
> library(BiocInstaller)
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> useDevel()
Error: 'devel' version already in use
What about something like:
Error: you need R 3.2 to run BioC 'devel' version
Thanks,
H.
the question of whether to use R-devel with Bioc-devel has a different answer
every six months, but the answer can always be found here:
http://www.bioconductor.org/developers/how-to/useDevel/
Also, when looking at the devel build report, you should probably focus more on the
version portion of the "R version" column than on the SVN revision number.
Dan
On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen
wrote:
You should not be using R-3.1.2 patched with the current devel
version of
Bioconductor; use R-devel.
Best,
Kasper
On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres
wrote:
Hi,
I can't seem to install devel packages via biocLite() and I wonder
if
something is broken or if I'm missing something. For example, take
GenomeInfoDb which is at 1.3.6 and is passing all checks.
The usual code using a fresh R 3.1.2-patched install isn't working
as
it downloads the latest release version (1.2.2):
source("http://bioconductor.org/biocLite.R";)
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for
help
## Was expecting 3.1 here
useDevel()
Error: 'devel' version already in use
biocLite('GenomeInfoDb')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version
3.1.2.
Installing package(s) 'GenomeInfoDb'
trying URL
'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz'
Content type 'application/x-gzip' length 404120 bytes (394 KB)
opened URL
==
downloaded 394 KB
The downloaded binary packages are in
/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages
sessionInfo()
R version 3.1.2 Patched (2014-11-01 r66923)
## Note that it matches the current R version used by the
Bioc-devel
build machines
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] BiocInstaller_1.16.0 colorout_1.0-2
loaded via a namespace (and not attached):
[1] tools_3.1.2
For my computer it's not problem because I can download the pkg
via
svn and install locally. But it breaks my tests in TravisCI which
relies on biocLite().
Cheers,
Leo
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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] Can't seem to use useDevel(); biocLite() for BioC 3.1
I think there is indeed something more fundamentally broken here: > R.version _ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status Under development (unstable) major 3 minor 2.0 year 2014 month 10 day29 svn rev66895 language R version.string R Under development (unstable) (2014-10-29 r66895) nickname Unsuffered Consequences > useDevel(TRUE) Error: 'devel' version already in use But: > biocinstallRepos() BioCsoft "http://bioconductor.org/packages/3.0/bioc"; BioCann "http://bioconductor.org/packages/3.0/data/annotation"; BioCexp "http://bioconductor.org/packages/3.0/data/experiment"; BioCextra "http://bioconductor.org/packages/3.0/extra"; CRAN "http://cran.fhcrc.org"; So I am running R-devel, R thinks that I should already be using the BiocDevel branch, but the repository is still pointing to Bioconductor 3.0 After taking a closer look at useDevel() I did this: assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE) assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", value=TRUE) And behold: > useDevel(TRUE) Installing package into Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹ (as Œlib¹ is unspecified) trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17.1 .tar.gz' Content type 'application/x-gzip' length 14271 bytes (13 KB) opened URL == downloaded 13 KB * installing *source* package ŒBiocInstaller¹ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help * DONE (BiocInstaller) The downloaded source packages are in Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help 'BiocInstaller' changed to version 1.17.1 I couldn't tell how I got my R installation into this seemingly locked state, but maybe there should be a force=TRUE option to useDevel for cases like this. Florian On 04/11/14 20:04, "Hervé Pagès" wrote: >Hi, > >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: >> >> >> - Original Message - >>> From: "Leonardo Collado Torres" >>> To: "Kasper Daniel Hansen" >>> Cc: bioc-devel@r-project.org >>> Sent: Sunday, November 2, 2014 9:26:25 PM >>> Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for >>>BioC 3.1 >>> >>> Thanks, I incorrectly thought that I was using the same R version as >>> the Bioc-build machines since the "r66923" part matched. Now I >>> realize >>> that this tag is used in all of the newest R builds at >>> http://r.research.att.com/. >>> >> >> It's admittedly confusing; > >Agreed. But the error message issued by useDevel() in the current >release adds to the confusion: > > > library(BiocInstaller) > Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help > > useDevel() > Error: 'devel' version already in use > >What about something like: > > Error: you need R 3.2 to run BioC 'devel' version > >Thanks, >H. > >> the question of whether to use R-devel with Bioc-devel has a different >>answer every six months, but the answer can always be found here: >> >> http://www.bioconductor.org/developers/how-to/useDevel/ >> >> Also, when looking at the devel build report, you should probably focus >>more on the version portion of the "R version" column than on the SVN >>revision number. >> >> Dan >> >> >>> On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen >>> wrote: >>>> You should not be using R-3.1.2 patched with the current devel >>>> version of >>>> Bioconductor; use R-devel. >>>> >>>> Best, >>>> Kasper >>>> >>>> On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres >>>> >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I can&#x
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
- Original Message - > From: "Florian Hahne" > To: "Hervé Pagès" , "Dan Tenenbaum" > , "Leonardo Collado Torres" > > Cc: bioc-devel@r-project.org > Sent: Wednesday, November 5, 2014 12:48:23 AM > Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC > 3.1 > > I think there is indeed something more fundamentally broken here: > > R.version >_ > platform x86_64-apple-darwin13.4.0 > arch x86_64 > os darwin13.4.0 > system x86_64, darwin13.4.0 > status Under development (unstable) > major 3 > minor 2.0 > year 2014 > month 10 > day29 > svn rev66895 > language R > version.string R Under development (unstable) (2014-10-29 r66895) > nickname Unsuffered Consequences > > > > useDevel(TRUE) > Error: 'devel' version already in use > > The only problem is that you should not have seen this message, you should instead see a message saying you need a newer version of R to run the devel version of bioconductor. This has been fixed in the release version of BiocInstaller (1.16.1), available later today. > But: > > > biocinstallRepos() > BioCsoft >"http://bioconductor.org/packages/3.0/bioc"; >BioCann > "http://bioconductor.org/packages/3.0/data/annotation"; >BioCexp > "http://bioconductor.org/packages/3.0/data/experiment"; > BioCextra > "http://bioconductor.org/packages/3.0/extra"; > CRAN >"http://cran.fhcrc.org"; > > > So I am running R-devel, R thinks that I should already be using the > BiocDevel branch, but the repository is still pointing to > Bioconductor 3.0 > After taking a closer look at useDevel() I did this: > > assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE) > assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", value=TRUE) > > > > And behold: > > useDevel(TRUE) > Installing package into > Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹ > (as Œlib¹ is unspecified) > trying URL > 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17.1 > .tar.gz' > Content type 'application/x-gzip' length 14271 bytes (13 KB) > opened URL > == > downloaded 13 KB > > * installing *source* package ŒBiocInstaller¹ ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > * DONE (BiocInstaller) > > The downloaded source packages are in > Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > 'BiocInstaller' changed to version 1.17.1 > > > I couldn't tell how I got my R installation into this seemingly > locked > state, but maybe there should be a force=TRUE option to useDevel for > cases > like this. > Florian > > This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc 3.1 is intended to run with R-devel (3.2) only. Dan > > > > On 04/11/14 20:04, "Hervé Pagès" wrote: > > >Hi, > > > >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: > >> > >> > >> - Original Message - > >>> From: "Leonardo Collado Torres" > >>> To: "Kasper Daniel Hansen" > >>> Cc: bioc-devel@r-project.org > >>> Sent: Sunday, November 2, 2014 9:26:25 PM > >>> Subject: Re: [Bioc-devel] Can't seem to use useDevel(); > >>> biocLite() for > >>>BioC 3.1 > >>> > >>> Thanks, I incorrectly thought that I was using the same R version > >>> as > >>> the Bioc-build machines since the "r66923" part matched. Now I > >>> realize > >>> that this tag is used in all of the newest R builds at > >>> http://r.research.att.com/. > >>> > >> > >> It's admittedly confusing; > > > >Agreed. But the error message issued by useDevel() in the current > >rel
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Taking a closer look at your email... > - Original Message - > > From: "Florian Hahne" > > > I think there is indeed something more fundamentally broken here: > > > R.version > >_ > > platform x86_64-apple-darwin13.4.0 > > arch x86_64 > > os darwin13.4.0 > > system x86_64, darwin13.4.0 > > status Under development (unstable) > > major 3 > > minor 2.0 > > year 2014 > > month 10 > > day29 > > svn rev66895 > > language R > > version.string R Under development (unstable) (2014-10-29 r66895) > > nickname Unsuffered Consequences > > Sorry, didn't notice you were already running R-devel. > > > > > useDevel(TRUE) > > Error: 'devel' version already in use > > > > What version of BiocInstaller were you running at this point> > > The only problem is that you should not have seen this message, you > should instead see a message saying you need a newer version of R to > run the devel version of bioconductor. This has been fixed in the > release version of BiocInstaller (1.16.1), available later today. > > > > But: > > > > > biocinstallRepos() > > BioCsoft > >"http://bioconductor.org/packages/3.0/bioc"; > >BioCann > > "http://bioconductor.org/packages/3.0/data/annotation"; > >BioCexp > > "http://bioconductor.org/packages/3.0/data/experiment"; > > BioCextra > > "http://bioconductor.org/packages/3.0/extra"; > > CRAN > >"http://cran.fhcrc.org"; > > > > > > So I am running R-devel, R thinks that I should already be using > > the > > BiocDevel branch, but the repository is still pointing to > > Bioconductor 3.0 > > After taking a closer look at useDevel() I did this: > > > > assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE) > > assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", > > value=TRUE) > > > > > > > > And behold: > > > useDevel(TRUE) > > Installing package into > > Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹ > > (as Œlib¹ is unspecified) > > trying URL > > 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17.1 > > .tar.gz' > > Content type 'application/x-gzip' length 14271 bytes (13 KB) > > opened URL > > == > > downloaded 13 KB > > > > * installing *source* package ŒBiocInstaller¹ ... > > ** R > > ** inst > > ** preparing package for lazy loading > > ** help > > *** installing help indices > > ** building package indices > > ** testing if installed package can be loaded > > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > > * DONE (BiocInstaller) > > > > The downloaded source packages are in > > Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ > > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > > 'BiocInstaller' changed to version 1.17.1 > > > > > > I couldn't tell how I got my R installation into this seemingly > > locked > > state, but maybe there should be a force=TRUE option to useDevel > > for > > cases > > like this. > > Florian > > > > > I think you somehow had the release version of BiocInstaller installed in R-devel. But it's difficult to know now Dan > > This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc > 3.1 is intended to run with R-devel (3.2) only. > Dan > > > > > > > > > > > > On 04/11/14 20:04, "Hervé Pagès" wrote: > > > > >Hi, > > > > > >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: > > >> > > >> > > >> - Original Message - > > >>> From: "Leonardo Collado Torres" > > >>> To: "Kasper Daniel Hansen" > > >>> Cc: bioc-devel@r-project.org > > >>> Sent: Sunday, November 2, 2014 9:26:25 PM > > >>> Subject: Re: [Bioc-dev
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
That might well be. I can't recall doing anything special, but I'll try to uninstall BiocInstaller the next time I run into a similar issue to test this. Florian On 05/11/14 18:02, "Dan Tenenbaum" wrote: >Taking a closer look at your email... > >> - Original Message - >> > From: "Florian Hahne" > > >> > I think there is indeed something more fundamentally broken here: >> > > R.version >> >_ >> > platform x86_64-apple-darwin13.4.0 >> > arch x86_64 >> > os darwin13.4.0 >> > system x86_64, darwin13.4.0 >> > status Under development (unstable) >> > major 3 >> > minor 2.0 >> > year 2014 >> > month 10 >> > day29 >> > svn rev66895 >> > language R >> > version.string R Under development (unstable) (2014-10-29 r66895) >> > nickname Unsuffered Consequences >> > > >Sorry, didn't notice you were already running R-devel. > >> > >> > > useDevel(TRUE) >> > Error: 'devel' version already in use >> > >> > > >What version of BiocInstaller were you running at this point> > >> >> The only problem is that you should not have seen this message, you >> should instead see a message saying you need a newer version of R to >> run the devel version of bioconductor. This has been fixed in the >> release version of BiocInstaller (1.16.1), available later today. >> >> >> > But: >> > >> > > biocinstallRepos() >> > BioCsoft >> >"http://bioconductor.org/packages/3.0/bioc"; >> >BioCann >> > "http://bioconductor.org/packages/3.0/data/annotation"; >> >BioCexp >> > "http://bioconductor.org/packages/3.0/data/experiment"; >> > BioCextra >> > "http://bioconductor.org/packages/3.0/extra"; >> > CRAN >> >"http://cran.fhcrc.org"; >> > >> > >> > So I am running R-devel, R thinks that I should already be using >> > the >> > BiocDevel branch, but the repository is still pointing to >> > Bioconductor 3.0 >> > After taking a closer look at useDevel() I did this: >> > >> > assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE) >> > assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", >> > value=TRUE) >> > >> > >> > >> > And behold: >> > > useDevel(TRUE) >> > Installing package into >> > Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹ >> > (as Œlib¹ is unspecified) >> > trying URL >> > >>'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17 >>.1 >> > .tar.gz' >> > Content type 'application/x-gzip' length 14271 bytes (13 KB) >> > opened URL >> > == >> > downloaded 13 KB >> > >> > * installing *source* package ŒBiocInstaller¹ ... >> > ** R >> > ** inst >> > ** preparing package for lazy loading >> > ** help >> > *** installing help indices >> > ** building package indices >> > ** testing if installed package can be loaded >> > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help >> > * DONE (BiocInstaller) >> > >> > The downloaded source packages are in >> >Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ >> > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help >> > 'BiocInstaller' changed to version 1.17.1 >> > >> > >> > I couldn't tell how I got my R installation into this seemingly >> > locked >> > state, but maybe there should be a force=TRUE option to useDevel >> > for >> > cases >> > like this. >> > Florian >> > >> > >> > >I think you somehow had the release version of BiocInstaller installed in >R-devel. >But it's difficult to know now > >Dan > > > >> >> This
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
BioCann >>> > "http://bioconductor.org/packages/3.0/data/annotation"; >>> >BioCexp >>> > "http://bioconductor.org/packages/3.0/data/experiment"; >>> > BioCextra >>> > "http://bioconductor.org/packages/3.0/extra"; >>> > CRAN >>> >"http://cran.fhcrc.org"; >>> > >>> > >>> > So I am running R-devel, R thinks that I should already be using >>> > the >>> > BiocDevel branch, but the repository is still pointing to >>> > Bioconductor 3.0 >>> > After taking a closer look at useDevel() I did this: >>> > >>> > assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE) >>> > assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", >>> > value=TRUE) >>> > >>> > >>> > >>> > And behold: >>> > > useDevel(TRUE) >>> > Installing package into >>> > Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹ >>> > (as Œlib¹ is unspecified) >>> > trying URL >>> > >>>'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17 >>>.1 >>> > .tar.gz' >>> > Content type 'application/x-gzip' length 14271 bytes (13 KB) >>> > opened URL >>> > == >>> > downloaded 13 KB >>> > >>> > * installing *source* package ŒBiocInstaller¹ ... >>> > ** R >>> > ** inst >>> > ** preparing package for lazy loading >>> > ** help >>> > *** installing help indices >>> > ** building package indices >>> > ** testing if installed package can be loaded >>> > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help >>> > * DONE (BiocInstaller) >>> > >>> > The downloaded source packages are in >>> >Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ >>> > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help >>> > 'BiocInstaller' changed to version 1.17.1 >>> > >>> > >>> > I couldn't tell how I got my R installation into this seemingly >>> > locked >>> > state, but maybe there should be a force=TRUE option to useDevel >>> > for >>> > cases >>> > like this. >>> > Florian >>> > >>> > >>> >> >>I think you somehow had the release version of BiocInstaller installed in >>R-devel. >>But it's difficult to know now >> >>Dan >> >> >> >>> >>> This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc >>> 3.1 is intended to run with R-devel (3.2) only. >>> Dan >>> >>> >>> >>> >>> > >>> > >>> > >>> > On 04/11/14 20:04, "Hervé Pagès" wrote: >>> > >>> > >Hi, >>> > > >>> > >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: >>> > >> >>> > >> >>> > >> - Original Message - >>> > >>> From: "Leonardo Collado Torres" >>> > >>> To: "Kasper Daniel Hansen" >>> > >>> Cc: bioc-devel@r-project.org >>> > >>> Sent: Sunday, November 2, 2014 9:26:25 PM >>> > >>> Subject: Re: [Bioc-devel] Can't seem to use useDevel(); >>> > >>>biocLite() for >>> > >>>BioC 3.1 >>> > >>> >>> > >>> Thanks, I incorrectly thought that I was using the same R >>> > >>> version >>> > >>> as >>> > >>> the Bioc-build machines since the "r66923" part matched. Now I >>> > >>> realize >>> > >>> that this tag is used in all of the newest R builds at >>> > >>> http://r.research.att.com/. >>> > >>> >>> > >> >>> > >> It's admittedly confusing; >>> > > >>> > >Agreed. But the error message issued by useDevel() in the current >
