Re: [R] system command to a specific shell (bash)
On 17.04.2012 01:26, MacQueen, Don wrote:
I believe that shell() was superceded by system(), quite a long time ago.
Not really, under Windows, shell() will start a shell while system() won't.
Uwe Ligges
However, I get this:
foo- system('printenv',intern=TRUE) ; foo[grepl('SHELL',foo)]
[1] SHELL=/bin/tcsh XTERM_SHELL=/bin/tcsh
And tcsh is my login shell, i.e., as specified for my account at the OS
level. To me, this implies that you should get bash by default if your
account is configured for bash, but I can't know for certain.
-Don
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[R] system command to a specific shell (bash)
I need to run a bash command, but when you call system() the default shell
is sh (see my sessionInfo below).
I found the shell command (
http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/base/html/shell.html)
but it seems to be disappeared in current versions of R?
I am running all this from R CMD BATCH with system calls to other R
scripts.
For a little more info, I'm generating sphinx documents (a python
documentation library) through R and need to use a python virtual
environment.
So I need to call system('source bin/activate'), but source isn't a
recognized command in the sh shell...
Any help is appreciated,
Justin
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8LC_PAPER=C
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] graphics grDevices utils datasets stats grid methods
base
other attached packages:
[1] ggplot2_0.9.0 reshape2_1.2.1 plyr_1.7.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4digest_0.5.1 MASS_7.3-16
memoise_0.1munsell_0.3
[7] proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.0 stringr_0.6
tools_2.15.0
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] system command to a specific shell (bash)
You could make a hash bang bash script that sources the file and then proceeds
to do whatever you want. Bourne shell should have no problems invoking another
shell.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
Justin Haynes jto...@gmail.com wrote:
I need to run a bash command, but when you call system() the default
shell
is sh (see my sessionInfo below).
I found the shell command (
http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/base/html/shell.html)
but it seems to be disappeared in current versions of R?
I am running all this from R CMD BATCH with system calls to other R
scripts.
For a little more info, I'm generating sphinx documents (a python
documentation library) through R and need to use a python virtual
environment.
So I need to call system('source bin/activate'), but source isn't a
recognized command in the sh shell...
Any help is appreciated,
Justin
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8LC_PAPER=C
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] graphics grDevices utils datasets stats grid methods
base
other attached packages:
[1] ggplot2_0.9.0 reshape2_1.2.1 plyr_1.7.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4digest_0.5.1
MASS_7.3-16
memoise_0.1munsell_0.3
[7] proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.0
stringr_0.6
tools_2.15.0
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] system command to a specific shell (bash)
Thanks Jeff, but I'm running a python program that expects certain
functionality that bash provides and sh doesn't... I can just stop using
github checkouts and use system packages though and fix this.
I'm mostly wondering where the shell command went in base R... it sounds
like it completely solves this issue but doesn't exist in my R
On Mon, Apr 16, 2012 at 10:58 AM, Jeff Newmiller
jdnew...@dcn.davis.ca.uswrote:
You could make a hash bang bash script that sources the file and then
proceeds to do whatever you want. Bourne shell should have no problems
invoking another shell.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
Justin Haynes jto...@gmail.com wrote:
I need to run a bash command, but when you call system() the default
shell
is sh (see my sessionInfo below).
I found the shell command (
http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/base/html/shell.html
)
but it seems to be disappeared in current versions of R?
I am running all this from R CMD BATCH with system calls to other R
scripts.
For a little more info, I'm generating sphinx documents (a python
documentation library) through R and need to use a python virtual
environment.
So I need to call system('source bin/activate'), but source isn't a
recognized command in the sh shell...
Any help is appreciated,
Justin
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8LC_PAPER=C
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] graphics grDevices utils datasets stats grid methods
base
other attached packages:
[1] ggplot2_0.9.0 reshape2_1.2.1 plyr_1.7.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4digest_0.5.1
MASS_7.3-16
memoise_0.1munsell_0.3
[7] proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.0
stringr_0.6
tools_2.15.0
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] system command to a specific shell (bash)
I believe that shell() was superceded by system(), quite a long time ago.
However, I get this:
foo - system('printenv',intern=TRUE) ; foo[grepl('SHELL',foo)]
[1] SHELL=/bin/tcsh XTERM_SHELL=/bin/tcsh
And tcsh is my login shell, i.e., as specified for my account at the OS
level. To me, this implies that you should get bash by default if your
account is configured for bash, but I can't know for certain.
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 4/16/12 12:05 PM, Justin Haynes jto...@gmail.com wrote:
Thanks Jeff, but I'm running a python program that expects certain
functionality that bash provides and sh doesn't... I can just stop using
github checkouts and use system packages though and fix this.
I'm mostly wondering where the shell command went in base R... it sounds
like it completely solves this issue but doesn't exist in my R
On Mon, Apr 16, 2012 at 10:58 AM, Jeff Newmiller
jdnew...@dcn.davis.ca.uswrote:
You could make a hash bang bash script that sources the file and then
proceeds to do whatever you want. Bourne shell should have no problems
invoking another shell.
-
--
Jeff NewmillerThe . . Go
Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#.
rocks...1k
-
--
Sent from my phone. Please excuse my brevity.
Justin Haynes jto...@gmail.com wrote:
I need to run a bash command, but when you call system() the default
shell
is sh (see my sessionInfo below).
I found the shell command (
http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/base/html/shell.htm
l
)
but it seems to be disappeared in current versions of R?
I am running all this from R CMD BATCH with system calls to other R
scripts.
For a little more info, I'm generating sphinx documents (a python
documentation library) through R and need to use a python virtual
environment.
So I need to call system('source bin/activate'), but source isn't a
recognized command in the sh shell...
Any help is appreciated,
Justin
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8LC_PAPER=C
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] graphics grDevices utils datasets stats grid methods
base
other attached packages:
[1] ggplot2_0.9.0 reshape2_1.2.1 plyr_1.7.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4digest_0.5.1
MASS_7.3-16
memoise_0.1munsell_0.3
[7] proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.0
stringr_0.6
tools_2.15.0
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
