Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
' 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 hpa...@fredhutch.org wrote:
Hi,
On 11/02/2014 10:58 PM, Dan Tenenbaum wrote:
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
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
kasperdanielhan...@gmail.com 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
lcoll...@jhu.edu
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/Ge
no
meInfoDb_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/downloa
de
d_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
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 lcoll...@jhu.edu
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
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
kasperdanielhan...@gmail.com 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
lcoll...@jhu.edu
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
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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
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[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
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
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 lcoll...@jhu.edu
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
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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
kasperdanielhan...@gmail.com 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 lcoll...@jhu.edu
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
