Closed Sunnylee78 closed 5 years ago
martinamorris
commented
5 years ago If ergm is the package you're interested in, you'll need to install that using:
install.packages("ergm")
If you're not familiar with installing packages in R, you might want to review our intro tutorial. All of our tutorials are online here:
statnet.github.io/Workshops
best, Martina
On Sun, 30 Jun 2019, Sunnylee78 wrote:
Sunnylee78
commented
5 years ago Thanks for your quick response. I am somewhat familiar with statnet as I have used it for my research and published it a while ago. That's why I'm bummed to find out my statnet package is not working properly in R studio, and install.packages("ergm") got me this message: There is a binary version available but the source version is later: binary source needs_compilation ergm 3.9.4 3.10.4 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package ‘ergm’
downloaded 2.0 MB
The downloaded source packages are in ‘/private/var/folders/05/gclpw8_j7zsc2ksx_9ts6s000000gn/T/RtmpAswsOH/downloaded_packages’
Something seems wrong, right?
martinamorris
commented
5 years ago I'm not sure when you got this message, but we released a new version of ergm a couple weeks back (3.10.4) and it takes a week or so for the binaries to build on CRAN.
I've just checked, and the binaries are now all available, so you should be able to install the binaries directly.
Sunnylee78
commented
5 years ago Thanks for the information! I will certainly try it.
Sunnylee78
commented
5 years ago Hi Martina,
I tried to install statnet again, and got this message. Another person I know also has the same trouble installing statnet and ergm:
install.packages('statnet') also installing the dependencies ‘tergm’, ‘ergm.count’, ‘ergm’
There are binary versions available but the source versions are later: binary source needs_compilation tergm 3.5.2 3.6.1 TRUE ergm.count 3.3.0 3.4.0 TRUE ergm 3.9.4 3.10.4 TRUE statnet 2018.10 2019.6 FALSE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes installing the source packages ‘tergm’, ‘ergm.count’, ‘ergm’, ‘statnet’
downloaded 729 KB
downloaded 15 KB
downloaded 2.0 MB
downloaded 7589 bytes
The downloaded source packages are in ‘/private/var/folders/05/gclpw8_j7zsc2ksx_9ts6s000000gn/T/RtmpTOgxHE/downloaded_packages’
Could you suggest how I could install "binary" version?
Is this an issue of compatibility between R and statnet versions?
Sunny
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
martinamorris
commented
5 years ago Hi Sunny,
This is very strange, as all of these packages have the updated binary versions available on CRAN.
Can you please send me:
thx, mm
Sunnylee78
commented
5 years ago Hi Martina,
My OS is Mac, and here's the info you asked for:
sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.5
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
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] sna_2.4 statnet.common_4.3.0 network_1.15
loaded via a namespace (and not attached): [1] lattice_0.20-38 crayon_1.3.4 grid_3.5.0 stats4_3.5.0 [5] magrittr_1.5 coda_0.19-2 pillar_1.4.2 rlang_0.4.0 [9] rstudioapi_0.10 pbivnorm_0.6.0 tools_3.5.0 compiler_3.5.0 [13] pkgconfig_2.0.2 mnormt_1.5-5 lavaan_0.6-3 tibble_2.1.3
getOption("repos") CRAN "https://cran.rstudio.com/" attr(,"RStudio") [1] TRUE
martinamorris
commented
5 years ago Try updating to ergm 3.6 and let me know if that fixes it.
Sunnylee78
commented
5 years ago Ok, but I'm not sure how to update it when I can't seem to install ergm at all? ergm is not found in my library or packages. Can you tell me which codes I should use in R?
Sunny
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
martinamorris
commented
5 years ago Sorry! Update your copy of R, not ergm.
Sunnylee78
commented
5 years ago Hi Martina,
I finally figured it out! It seems R studio's latest version is only R 3.5, but regular R has 3.6 and I downloaded that one. Now I can run ergm!
Thanks so much for being patient with me!
Sunny
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
martinamorris
commented
5 years ago Rstudio just uses the version of R you have installed on your machine. Updating Rstudio is also a good idea (it doesn't update R -- that's always a separate process). In general, it's a good idea to keep both R and Rstudio up to date :)
Sunnylee78
commented
5 years ago Aha! Thanks a lot again for the tips and help!!
Sun Kyong (Sunny) Lee, Ph.D. Associate Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
From: Martina Morris notifications@github.com Sent: Friday, July 12, 2019 3:40 PM To: statnet/statnetWeb Cc: Lee, Sunny; Author Subject: Re: [statnet/statnetWeb] ERGM not found in R studio (#74)
Rstudio just uses the version of R you have installed on your machine. Updating Rstudio is also a good idea (it doesn't update R -- that's always a separate process). In general, it's a good idea to keep both R and Rstudio up to date :)
On Fri, 12 Jul 2019, Sunnylee78 wrote:
Hi Martina,
I finally figured it out! It seems R studio's latest version is only R 3.5, but regular R has 3.6 and I downloaded that one. Now I can run ergm!
Thanks so much for being patient with me!
Sunny
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
From: Martina Morris notifications@github.com Sent: Friday, July 12, 2019 3:00 PM To: statnet/statnetWeb Cc: Lee, Sunny; Author Subject: Re: [statnet/statnetWeb] ERGM not found in R studio (#74)
Update your copy of R, not ergm.
On Fri, 12 Jul 2019, Sunnylee78 wrote:
Ok, but I'm not sure how to update it when I can't seem to install ergm at all? ergm is not found in my library or packages. Can you tell me which codes I should use in R?
Sunny
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
From: Martina Morris notifications@github.com Sent: Friday, July 12, 2019 1:19 PM To: statnet/statnetWeb Cc: Lee, Sunny; Author Subject: Re: [statnet/statnetWeb] ERGM not found in R studio (#74)
Try updating to ergm 3.6 and let me know if that fixes it.
On Fri, 12 Jul 2019, Sunnylee78 wrote:
Hi Martina,
My OS is Mac, and here's the info you asked for:
sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.5
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
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] sna_2.4 statnet.common_4.3.0 network_1.15
loaded via a namespace (and not attached): [1] lattice_0.20-38 crayon_1.3.4 grid_3.5.0 stats4_3.5.0 [5] magrittr_1.5 coda_0.19-2 pillar_1.4.2 rlang_0.4.0 [9] rstudioapi_0.10 pbivnorm_0.6.0 tools_3.5.0 compiler_3.5.0 [13] pkgconfig_2.0.2 mnormt_1.5-5 lavaan_0.6-3 tibble_2.1.3
getOption("repos") CRAN "https://cran.rstudio.com/" attr(,"RStudio") [1] TRUE
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
From: Martina Morris notifications@github.com Sent: Thursday, July 11, 2019 2:36:31 PM To: statnet/statnetWeb Cc: Lee, Sunny; Author Subject: Re: [statnet/statnetWeb] ERGM not found in R studio (#74)
Hi Sunny,
This is very strange, as all of these packages have the updated binary versions available on CRAN.
Can you please send me:
- output from: sessionInfo()
- the OS you are working on (mac/windows/linux)
- output from: getOption("repos")
thx, mm
On Tue, 9 Jul 2019, Sunnylee78 wrote:
Hi Martina,
I tried to install statnet again, and got this message. Another person I know also has the same trouble installing statnet and ergm:
install.packages('statnet') also installing the dependencies ‘tergm’, ‘ergm.count’, ‘ergm’
There are binary versions available but the source versions are later: binary source needs_compilation tergm 3.5.2 3.6.1 TRUE ergm.count 3.3.0 3.4.0 TRUE ergm 3.9.4 3.10.4 TRUE statnet 2018.10 2019.6 FALSE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes installing the source packages ‘tergm’, ‘ergm.count’, ‘ergm’, ‘statnet’
trying URL 'https://cran.rstudio.com/src/contrib/tergm_3.6.1.tar.gz' Content type 'application/x-gzip' length 746918 bytes (729 KB)
downloaded 729 KB
trying URL 'https://cran.rstudio.com/src/contrib/ergm.count_3.4.0.tar.gz' Content type 'application/x-gzip' length 16203 bytes (15 KB)
downloaded 15 KB
trying URL 'https://cran.rstudio.com/src/contrib/ergm_3.10.4.tar.gz' Content type 'application/x-gzip' length 2130579 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/statnet_2019.6.tar.gz' Content type 'application/x-gzip' length 7589 bytes
downloaded 7589 bytes
- installing source package ‘ergm’ ... package ‘ergm’ successfully unpacked and MD5 sums checked libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘ergm’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ergm’ Warning in install.packages : installation of package ‘ergm’ had non-zero exit status ERROR: dependency ‘ergm’ is not available for package ‘tergm’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tergm’ Warning in install.packages : installation of package ‘tergm’ had non-zero exit status ERROR: dependency ‘ergm’ is not available for package ‘ergm.count’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ergm.count’ Warning in install.packages : installation of package ‘ergm.count’ had non-zero exit status ERROR: dependencies ‘tergm’, ‘ergm.count’, ‘ergm’ are not available for package ‘statnet’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/statnet’ Warning in install.packages : installation of package ‘statnet’ had non-zero exit status
The downloaded source packages are in ‘/private/var/folders/05/gclpw8_j7zsc2ksx_9ts6s000000gn/T/RtmpTOgxHE/downloaded_packages’
Could you suggest how I could install "binary" version?
Is this an issue of compatibility between R and statnet versions?
Sunny
Sun Kyong (Sunny) Lee, Ph.D. Assistant Professor Department of Communication The University of Oklahoma 610 Elm Ave., Norman, OK 73019
From: Martina Morris notifications@github.com Sent: Thursday, July 4, 2019 7:12:09 PM To: statnet/statnetWeb Cc: Lee, Sunny; Author Subject: Re: [statnet/statnetWeb] ERGM not found in R studio (#74)
I'm not sure when you got this message, but we released a new version of ergm a couple weeks back (3.10.4) and it takes a week or so for the binaries to build on CRAN.
I've just checked, and the binaries are now all available, so you should be able to install the binaries directly.
On Mon, 1 Jul 2019, Sunnylee78 wrote:
Thanks for your quick response. I am somewhat familiar with statnet as I have used it for my research and published it a while ago. That's why I'm bummed to find out my statnet package is not working properly in R studio, and install.packages("ergm") got me this message: There is a binary version available but the source version is later: binary source needs_compilation ergm 3.9.4 3.10.4 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package ‘ergm’
trying URL 'https://cran.rstudio.com/src/contrib/ergm_3.10.4.tar.gz' Content type 'application/x-gzip' length 2130579 bytes (2.0 MB)
downloaded 2.0 MB
- installing source package ‘ergm’ ... package ‘ergm’ successfully unpacked and MD5 sums checked libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘ergm’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ergm’ Warning in install.packages : installation of package ‘ergm’ had non-zero exit status
The downloaded source packages are in ‘/private/var/folders/05/gclpw8_j7zsc2ksx_9ts6s000000gn/T/RtmpAswsOH/downloaded_packages’
Something seems wrong, right?
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Professor of Sociology and Statistics Box 354322 University of Washington Seattle, WA 98195-4322
Office: (206) 685-3402 Dept Office: (206) 543-5882, 543-7237 Fax: (206) 685-7419
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Professor of Sociology and Statistics Box 354322 University of Washington Seattle, WA 98195-4322
Office: (206) 685-3402 Dept Office: (206) 543-5882, 543-7237 Fax: (206) 685-7419
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skhan890
commented
5 years ago Closing this issue, as it was resolved by updating the underlying R to the current version.
Hi my Rstudio is the most recent version, but it won't load ergm on it. I installed, statnet.common packages. I tried statnetWeb, too, but it does not work, either. Can anyone help?