[R-sig-ME] Problem-installing-package-GlmmADMB

Discussion:

C. AMAL D. GLELE

2018-06-27 12:42:13 UTC

Hi, dear all.
neither
install.packages("glmmADMB", repos="http://R-Forge.R-project.org")
nor
install.packages("R2admb")
install.packages("glmmADMB",
repos=c("http://glmmadmb.r-forge.r-project.org/repos",
getOption("repos")),
type="source")
,
helps me to intall this package.
In advance, many thanks for any help.
Kind regards,
Amal

[[alternative HTML version deleted]]

Mollie Brooks

2018-06-27 12:45:21 UTC

Permalink

Hi Amal,

Maybe installing from GitHub could work. See instructions here https://github.com/bbolker/glmmadmb

If that doesn’t work, please give us more information, like error messages.

Mollie

Post by C. AMAL D. GLELE
Hi, dear all.
neither
install.packages("glmmADMB", repos="http://R-Forge.R-project.org")
nor
install.packages("R2admb")
install.packages("glmmADMB",
repos=c("http://glmmadmb.r-forge.r-project.org/repos",
getOption("repos")),
type="source")
,
helps me to intall this package.
In advance, many thanks for any help.
Kind regards,
Amal
[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

C. AMAL D. GLELE

2018-06-27 13:11:15 UTC

Permalink

Mollie,
many thanks for your reply.
These instructions do not work and I get the message below:

Downloading GitHub repo bbolker/***@master
from URL https://api.github.com/repos/bbolker/glmmadmb/zipball/masterInstalling
glmmADMB"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ
--no-save --no-restore \
--quiet CMD INSTALL \
"C:/Users/Coliasso/AppData/Local/Temp/Rtmpopho7h/devtools20ec3a7135b9/bbolker-glmmadmb-ac75f73"
\
--library="C:/Users/Coliasso/Documents/R/win-library/3.4"
--install-tests Installation failed: cannot change working directory

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error messages.
Mollie

[[alternative HTML version deleted]]

romunov

2018-06-27 13:24:53 UTC

Permalink

Please include a bit more information in your problem report. At which step
the problem occurs?

Cheers,
Roman

Post by C. AMAL D. GLELE
Mollie,
many thanks for your reply.
from URL
https://api.github.com/repos/bbolker/glmmadmb/zipball/masterInstalling
glmmADMB"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ
--no-save --no-restore \
--quiet CMD INSTALL \
"C:/Users/Coliasso/AppData/Local/Temp/Rtmpopho7h/devtools20ec3a7135b9/bbolker-glmmadmb-ac75f73"
\
--library="C:/Users/Coliasso/Documents/R/win-library/3.4"
--install-tests Installation failed: cannot change working directory

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error

messages.

Post by Mollie Brooks
Mollie

[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

--
In God we trust, all others bring data.

[[alternative HTML version deleted]]

C. AMAL D. GLELE

2018-06-27 13:41:58 UTC

Permalink

Hi, Roman.
The problem occurs at the third of the installation steps here:
https://github.com/bbolker/glmmadmb
My 64 bits pc is running under windows 8.1.
Kind regards,
Amal

Post by romunov
Please include a bit more information in your problem report. At which
step the problem occurs?
Cheers,
Roman

Post by C. AMAL D. GLELE
Mollie,
many thanks for your reply.
from URL https://api.github.com/repos/bbolker/glmmadmb/zipball/
masterInstalling
glmmADMB"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ
--no-save --no-restore \
--quiet CMD INSTALL \
"C:/Users/Coliasso/AppData/Local/Temp/Rtmpopho7h/
devtools20ec3a7135b9/bbolker-glmmadmb-ac75f73"
\
--library="C:/Users/Coliasso/Documents/R/win-library/3.4"
--install-tests Installation failed: cannot change working directory

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error

messages.

Post by Mollie Brooks
Mollie

[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

--
In God we trust, all others bring data.

[[alternative HTML version deleted]]

romunov

2018-06-27 13:55:15 UTC

Permalink

A shotgun approach to solving this would be to have all R instances closed
and make sure you have permission to write. Forgive me if I have not
followed this thread from the beginning, but do you have appropriate
Windows toolchain installed?

Cheers,
Roman

Post by C. AMAL D. GLELE
Hi, Roman.
https://github.com/bbolker/glmmadmb
My 64 bits pc is running under windows 8.1.
Kind regards,
Amal

Post by romunov
Please include a bit more information in your problem report. At which
step the problem occurs?
Cheers,
Roman

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error

messages.

Post by Mollie Brooks
Mollie

[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

--
In God we trust, all others bring data.

--
In God we trust, all others bring data.

[[alternative HTML version deleted]]

C. AMAL D. GLELE

2018-06-27 13:59:24 UTC

Permalink

Please, Roman,
which Windows toolchain do you mean?

Post by romunov
A shotgun approach to solving this would be to have all R instances closed
and make sure you have permission to write. Forgive me if I have not
followed this thread from the beginning, but do you have appropriate
Windows toolchain installed?
Cheers,
Roman

Post by C. AMAL D. GLELE
Hi, Roman.
https://github.com/bbolker/glmmadmb
My 64 bits pc is running under windows 8.1.
Kind regards,
Amal

Post by romunov
Please include a bit more information in your problem report. At which
step the problem occurs?
Cheers,
Roman

Post by C. AMAL D. GLELE
Mollie,
many thanks for your reply.
from URL https://api.github.com/repos/bbolker/glmmadmb/zipball/
masterInstalling
glmmADMB"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ
--no-save --no-restore \
--quiet CMD INSTALL \
"C:/Users/Coliasso/AppData/Local/Temp/Rtmpopho7h/
devtools20ec3a7135b9/bbolker-glmmadmb-ac75f73"
\
--library="C:/Users/Coliasso/Documents/R/win-library/3.4"
--install-tests Installation failed: cannot change working directory

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error

messages.

Post by Mollie Brooks
Mollie

[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

--
In God we trust, all others bring data.

[[alternative HTML version deleted]]

Ben Bolker

2018-06-27 14:05:02 UTC

Permalink

A few quick points:

(1) I don't think you should need the windows toolchain to install
glmmADMB; it doesn't have any compiled components (it has a
pre-compiled binary "blob" that prevents it from being posted to
CRAN). But try devtools::dr_devtools()
(2) The fact that your error report ends with " --install-tests
Installation failed: cannot change working directory" strongly
suggests that you may have other problems with file permissions, as
romunov suggests
(3) It might be worth trying glmmTMB instead. glmmADMB is still
supported (sort of), but glmmTMB is newer, nearly drop-in compatible
with glmmADMB, faster, and better supported/under more rapid
development.

Post by C. AMAL D. GLELE
Please, Roman,
which Windows toolchain do you mean?

Post by C. AMAL D. GLELE
Hi, Roman.
https://github.com/bbolker/glmmadmb
My 64 bits pc is running under windows 8.1.
Kind regards,
Amal

Post by romunov
Please include a bit more information in your problem report. At which
step the problem occurs?
Cheers,
Roman

Post by C. AMAL D. GLELE
Mollie,
many thanks for your reply.
from URL https://api.github.com/repos/bbolker/glmmadmb/zipball/
masterInstalling
glmmADMB"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ
--no-save --no-restore \
--quiet CMD INSTALL \
"C:/Users/Coliasso/AppData/Local/Temp/Rtmpopho7h/
devtools20ec3a7135b9/bbolker-glmmadmb-ac75f73"
\
--library="C:/Users/Coliasso/Documents/R/win-library/3.4"
--install-tests Installation failed: cannot change working directory

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error

messages.

Post by Mollie Brooks
Mollie

[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

--
In God we trust, all others bring data.

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_______________________________________________
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Phillip Alday

2018-06-27 14:01:13 UTC

Permalink

I've run into this issue with rstan when using RStudio (from a conda
installation, but I think RStudio is the relevant bit). As part of its
support of project-based workflows, RStudio does some managing of the
working directory and I think that's what blocks changing the working
directory. In my case, I was unable to install the rstan examples from
RStudio, but was able to do so from the standalone R.

Best,
Phillip

Post by C. AMAL D. GLELE
Hi, Roman.
https://github.com/bbolker/glmmadmb
My 64 bits pc is running under windows 8.1.
Kind regards,
Amal

Post by romunov
Please include a bit more information in your problem report. At which
step the problem occurs?
Cheers,
Roman

Post by Mollie Brooks
Hi Amal,
Maybe installing from GitHub could work. See instructions here
https://github.com/bbolker/glmmadmb
If that doesn’t work, please give us more information, like error

messages.

Post by Mollie Brooks
Mollie

[[alternative HTML version deleted]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

--
In God we trust, all others bring data.