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wpeterman / ResistanceGA

Optimize resistance surfaces using Genetic Algorithms
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ResistanceGA package can not be install in R #9

Closed leefusi closed 4 years ago

leefusi commented 5 years ago

I used the code below to install ResistanceGA , but I have been getting errors. The following picture is the code I used and the problem that occurred. I hope I can get an answer, thank you.

QQ截图20191017224545

wpeterman commented 5 years ago

Try:

devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev')

This is the most up to date development version.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 10:47 AM leefusi notifications@github.com wrote:

I used the code below to install ResistanceGA , but I have been getting errors. The following picture is the code I used and the problem that occurred. I hope I can get an answer, thank you.

[image: QQ截图20191017224545] https://user-images.githubusercontent.com/49238081/67019921-f94f6e00-f12f-11e9-991f-88ccafebc6a4.jpg

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leefusi commented 5 years ago

Hi Bill Peterman: Thank you for your reply. I have tried the R code you sent,but it still appears "Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) cannot remove prior installation of package ‘backports" "Enter one or more Numbers, or an empty line to skip updates:" appeared in the install process, and then I entered "1". I don't know if there was a mistake in my input.(fig.1) Sincerely Lee

fig.1

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-18 01:44:35, "Bill Peterman" notifications@github.com wrote: Try:

devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev')

This is the most up to date development version.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 10:47 AM leefusi notifications@github.com wrote:

I used the code below to install ResistanceGA , but I have been getting errors. The following picture is the code I used and the problem that occurred. I hope I can get an answer, thank you.

[image: QQ截图20191017224545] https://user-images.githubusercontent.com/49238081/67019921-f94f6e00-f12f-11e9-991f-88ccafebc6a4.jpg

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wpeterman commented 5 years ago

That's isn't a ResistanceGA issue.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 9:46 PM leefusi notifications@github.com wrote:

Hi Bill Peterman: Thank you for your reply. I have tried the R code you sent,but it still appears "Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) cannot remove prior installation of package ‘backports" "Enter one or more Numbers, or an empty line to skip updates:" appeared in the install process, and then I entered "1". I don't know if there was a mistake in my input.(fig.1) Sincerely Lee

fig.1

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-18 01:44:35, "Bill Peterman" notifications@github.com wrote: Try:

devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev')

This is the most up to date development version.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 10:47 AM leefusi notifications@github.com wrote:

I used the code below to install ResistanceGA , but I have been getting errors. The following picture is the code I used and the problem that occurred. I hope I can get an answer, thank you.

[image: QQ截图20191017224545] < https://user-images.githubusercontent.com/49238081/67019921-f94f6e00-f12f-11e9-991f-88ccafebc6a4.jpg

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/wpeterman/ResistanceGA/issues/9?email_source=notifications&email_token=ABDLQUK54IFNW4HUVJQ4EBLQPB3G7A5CNFSM4JB2YB3KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSPQTSA , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABDLQUL5ONZW7HSD5BE36PLQPB3G7ANCNFSM4JB2YB3A

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leefusi commented 5 years ago

Hi Bill Peterman: Thank you very much for your answer. Maybe it's my R problem.Let me try downloading R again. Lee

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-18 10:01:21, "Bill Peterman" notifications@github.com wrote: That's isn't a ResistanceGA issue.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 9:46 PM leefusi notifications@github.com wrote:

Hi Bill Peterman: Thank you for your reply. I have tried the R code you sent,but it still appears "Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) cannot remove prior installation of package ‘backports" "Enter one or more Numbers, or an empty line to skip updates:" appeared in the install process, and then I entered "1". I don't know if there was a mistake in my input.(fig.1) Sincerely Lee

fig.1

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-18 01:44:35, "Bill Peterman" notifications@github.com wrote: Try:

devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev')

This is the most up to date development version.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 10:47 AM leefusi notifications@github.com wrote:

I used the code below to install ResistanceGA , but I have been getting errors. The following picture is the code I used and the problem that occurred. I hope I can get an answer, thank you.

[image: QQ截图20191017224545] < https://user-images.githubusercontent.com/49238081/67019921-f94f6e00-f12f-11e9-991f-88ccafebc6a4.jpg

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/wpeterman/ResistanceGA/issues/9?email_source=notifications&email_token=ABDLQUK54IFNW4HUVJQ4EBLQPB3G7A5CNFSM4JB2YB3KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSPQTSA , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABDLQUL5ONZW7HSD5BE36PLQPB3G7ANCNFSM4JB2YB3A

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leefusi commented 5 years ago

Hi Bill Peterman: The "ResistanceGA" package is install successful. But I got an error "Error in mkRespMod(fr, REML = REMLpass) : response must be numeric"when using the mlpe_rga function.

I don't know what went wrong. Figure 1 is my operation in R. Sinecrely Lee

fig.1

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-18 10:01:21, "Bill Peterman" notifications@github.com wrote: That's isn't a ResistanceGA issue.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 9:46 PM leefusi notifications@github.com wrote:

Hi Bill Peterman: Thank you for your reply. I have tried the R code you sent,but it still appears "Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) cannot remove prior installation of package ‘backports" "Enter one or more Numbers, or an empty line to skip updates:" appeared in the install process, and then I entered "1". I don't know if there was a mistake in my input.(fig.1) Sincerely Lee

fig.1

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-18 01:44:35, "Bill Peterman" notifications@github.com wrote: Try:

devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev')

This is the most up to date development version.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Oct 17, 2019 at 10:47 AM leefusi notifications@github.com wrote:

I used the code below to install ResistanceGA , but I have been getting errors. The following picture is the code I used and the problem that occurred. I hope I can get an answer, thank you.

[image: QQ截图20191017224545] < https://user-images.githubusercontent.com/49238081/67019921-f94f6e00-f12f-11e9-991f-88ccafebc6a4.jpg

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/wpeterman/ResistanceGA/issues/9?email_source=notifications&email_token=ABDLQUK54IFNW4HUVJQ4EBLQPB3G7A5CNFSM4JB2YB3KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSPQTSA , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABDLQUL5ONZW7HSD5BE36PLQPB3G7ANCNFSM4JB2YB3A

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wpeterman commented 5 years ago

I don’t see any figure. I can’t really diagnose issues without seeing the code you’re using.

leefusi commented 5 years ago

Dear Bill Peterman:

Thank you very much for your reply.

I am sorry that my operation made you unable to see the picture.

My problem has been solved.

Thank you again.

Lee

--

李叶晨 福建农林大学 福州，中国 电话：+86-17746073673 邮箱：yechenlee@163.com

Yechen Lee Fujian Agriculture and Foresty University Fuzhou，China Tel：+86-17746073673 Email：yechenlee@163.com

At 2019-10-20 00:54:15, "Bill Peterman" notifications@github.com wrote: I don’t see any figure. I can’t really diagnose issues without seeing the code you’re using.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

Fabrina-Ferraz commented 4 years ago

Hi Bill Peterman,

I'm having trouble installing ResistanceGA. When I use the command "devtools :: install_github (" wpeterman / ResistanceGA ", ref = 'julia_dev')", I get the following error message:

"Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) cannot remove prior installation of package ‘rlang’ ".

However, each time I try it, it happens with a different package, not just with 'rlang'.

What could be happening?

Additionally, when I use the command "install.packages (" wpeterman / ResistanceGA ")", I get the following error message as well:

"Warning in install.packages: package ‘wpeterman / ResistanceGA’ is not available (for R version 3.6.1) "

Are there any other specifications regarding the version of R that I must use in order to install ResistanceGA?

I hope I can get an answer, thank you.

wpeterman commented 4 years ago

ResistanceGA is not available through CRAN, so install.packages will not work. You need to use devtools, as you've tried. I'd suggest closing and restarting R, then update all of your packages, then try to install ResistanceGA via devtools.

Bill Peterman Assistant Professor School of Environment and Natural Resources The Ohio State University 2021 Coffey Road Columbus, OH 43210-1085 Phone: 614.292.9795 Web Page https://goo.gl/4Gc15W Terrestrial Wildlife Ecology Lab http://www.twel.osu.edu

Bill Peterman

On Thu, Mar 19, 2020 at 1:32 PM Fabrina-Ferraz notifications@github.com wrote:

Hi Bill Peterman,

I'm having trouble installing ResistanceGA. When I use the command "devtools :: install_github (" wpeterman / ResistanceGA ", ref = 'julia_dev')", I get the following error message:

"Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) cannot remove prior installation of package ‘rlang’ ".

However, each time I try it, it happens with a different package, not just with 'rlang'.

What could be happening?

Additionally, when I use the command "install.packages (" wpeterman / ResistanceGA ")", I get the following error message as well:

"Warning in install.packages: package ‘wpeterman / ResistanceGA’ is not available (for R version 3.6.1) "

Are there any other specifications regarding the version of R that I must use in order to install ResistanceGA?

I hope I can get an answer, thank you.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/wpeterman/ResistanceGA/issues/9#issuecomment-601315572, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDLQUINMXZMENYZEATZ4KLRIJJKBANCNFSM4JB2YB3A .

Fabrina-Ferraz commented 4 years ago

Hi Bill Peterman,

Thank you for the suggestion to update the packages. I took advantage and also updated the version of R and Rstudio to the latest releases.

I couldn't update one of the packages and it was always giving me an error, but after I updated the software I managed to install ResistanceGA anyway. It worked.

Thank you!

AsadiMarziehAF commented 3 years ago

Hey, I used the code below to install ResistanceGA , but I have been getting errors. The following image is the code I used and the problem that occurred. I hope I can get an answer, (R version 4.0.3 (2020-10-10)). Does anybody how can I fix that? Thank you so much 1

devtools::install_github("wpeterman/ResistanceGA", ref = "julia_dev") Downloading GitHub repo wpeterman/ResistanceGA@julia_dev √ checking for file 'C:\Users\A\AppData\Local\Temp\RtmpyMbiam\remotesb50212711c6\wpeterman-ResistanceGA-5b30f1c/DESCRIPTION' (794ms)

  • preparing 'ResistanceGA': (1.1s) √ checking DESCRIPTION meta-information ...
  • checking for LF line-endings in source and make files and shell scripts (469ms)
  • checking for empty or unneeded directories
  • building 'ResistanceGA_4.1-0.40.tar.gz'

Installing package into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

Fabrina-Ferraz commented 3 years ago

Hi, AsadiMarziehAF

I used this code (below) and it worked. Also, try to update all packages already installed in R before installing ResistanceGA.

devtools::install_github("wpeterman/ResistanceGA", build_vignettes = TRUE)

AsadiMarziehAF commented 3 years ago

Hi Fabrina-Ferraz, Thank you so much for your reply. All of the packages are up to date. I have tried the R code you sent, but it still appears Error. Thanks

devtools::install_github("wpeterman/ResistanceGA", build_vignettes = TRUE) Downloading GitHub repo wpeterman/ResistanceGA@HEAD √ checking for file 'C:\Users\A\AppData\Local\Temp\RtmpYFed3C\remotesdc1ab84b0c\wpeterman-ResistanceGA-f4c1b44/DESCRIPTION' (412ms)

  • preparing 'ResistanceGA': (1.8s) √ checking DESCRIPTION meta-information ...

  • installing the package to build vignettes (1.4s)

  • installing source package 'ResistanceGA' ... using staged installation R ** data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'lme4::getData' by 'raster::getData' when loading 'ResistanceGA' Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'spdep' Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package 'ResistanceGA'

  • removing 'C:/Users/A/AppData/Local/Temp/Rtmpmun0qg/Rinst16b842af1395/ResistanceGA'

    ERROR: package installation failed Error: Failed to install 'ResistanceGA' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> * byte-compile and prepare package for lazy loading E> Warning: replacing previous import 'lme4::getData' by 'raster::getData' when loading 'ResistanceGA' E> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : E> there is no package called 'spdep' E> Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart E> Execution halted E> ERROR: lazy loading failed for package 'ResistanceGA' E> removing 'C:/Users/A/AppData/Local/Temp/Rtmpmun0qg/Rinst16b842af1395/ResistanceGA' E> ----------------------------------- E> ERROR: package installation failed

wpeterman commented 3 years ago

It looks like you still need to install the 'spdep' package. Try restarting your R session, installing 'spdep', then install ResistanceGA.

On Mon, Jan 25, 2021 at 1:10 PM AsadiMarziehAF notifications@github.com wrote:

Hi Fabrina-Ferraz, Thank you so much for your reply. All of the packages are up to date. I have tried the R code you sent, but it still appears Error. Thanks

devtools::install_github("wpeterman/ResistanceGA", build_vignettes = TRUE) Downloading GitHub repo wpeterman/ResistanceGA@HEAD √ checking for file 'C:\Users\A\AppData\Local\Temp\RtmpYFed3C\remotesdc1ab84b0c\wpeterman-ResistanceGA-f4c1b44/DESCRIPTION' (412ms)

  • preparing 'ResistanceGA': (1.8s) √ checking DESCRIPTION meta-information ...

  • installing the package to build vignettes (1.4s)

  • installing source package 'ResistanceGA' ... using staged installation R ** data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'lme4::getData' by 'raster::getData' when loading 'ResistanceGA' Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'spdep' Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package 'ResistanceGA'

  • removing 'C:/Users/A/AppData/Local/Temp/Rtmpmun0qg/Rinst16b842af1395/ResistanceGA'

    ERROR: package installation failed Error: Failed to install 'ResistanceGA' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> * byte-compile and prepare package for lazy loading E> Warning: replacing previous import 'lme4::getData' by 'raster::getData' when loading 'ResistanceGA' E> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : E> there is no package called 'spdep' E> Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart E> Execution halted E> ERROR: lazy loading failed for package 'ResistanceGA' E> removing 'C:/Users/A/AppData/Local/Temp/Rtmpmun0qg/Rinst16b842af1395/ResistanceGA' E> ----------------------------------- E> ERROR: package installation failed

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AsadiMarziehAF commented 3 years ago

Hey, Bill Peterman Thank you so much for your reply. I installed the 'spdep' package, but it still appears Error. Thanks

install.packages("C:/Users/A/Desktop/spdep_1.1-5.zip", repos = NULL, type = "win.binary") Installing package into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) package ‘spdep’ successfully unpacked and MD5 sums checked devtools::install_github("wpeterman/ResistanceGA", ref = "julia_dev") Downloading GitHub repo wpeterman/ResistanceGA@julia_dev These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: fastmap (1.0.1 -> 1.1.0) [CRAN] 5: shiny (1.5.0 -> 1.6.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: Installing 5 packages: rappdirs, jquerylib, sass, cachem, bslib Installing packages into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation sass 0.3.0 0.3.1 TRUE

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rappdirs_0.3.1.zip' Content type 'application/zip' length 147871 bytes (144 KB) downloaded 144 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/jquerylib_0.1.3.zip' Content type 'application/zip' length 524799 bytes (512 KB) downloaded 512 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cachem_1.0.1.zip' Content type 'application/zip' length 70505 bytes (68 KB) downloaded 68 KB

package ‘rappdirs’ successfully unpacked and MD5 sums checked package ‘jquerylib’ successfully unpacked and MD5 sums checked package ‘cachem’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\A\AppData\Local\Temp\RtmpoLDypS\downloaded_packages installing the source packages ‘sass’, ‘bslib’

trying URL 'https://cran.rstudio.com/src/contrib/sass_0.3.1.tar.gz' Content type 'application/x-gzip' length 1837396 bytes (1.8 MB) downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/src/contrib/bslib_0.2.4.tar.gz' Content type 'application/x-gzip' length 3481982 bytes (3.3 MB) downloaded 3.3 MB

*** arch - i386 C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk:28: warning: overriding recipe for target 'shlib-clean' Makevars.win:12: warning: ignoring old recipe for target 'shlib-clean' "C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c compile.c -o compile.o "C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o MAKEFLAGS= CC=""C:/rtools40/mingw32/bin/"gcc " CFLAGS="-O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign" CXX=""C:/rtools40/mingw32/bin/"g++ -std=gnu++11 " AR=""C:/rtools40/mingw32/bin/"ar" LDFLAGS="" /usr/bin/make -C libsass make[1]: Entering directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-i386/libsass' C:/rtools40/mingw32/bin/gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -O2 -I ./include -c -o src/cencode.o src/cencode.c C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast.o src/ast.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_values.o src/ast_values.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_supports.o src/ast_supports.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_super.o src/ast_sel_super.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_selectors.o src/ast_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/context.o src/context.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/constants.o src/constants.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_utils.o src/fn_utils.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_miscs.o src/fn_miscs.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_maps.o src/fn_maps.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_lists.o src/fn_lists.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_colors.o src/fn_colors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_numbers.o src/fn_numbers.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_strings.o src/fn_strings.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_selectors.o src/fn_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/color_maps.o src/color_maps.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/environment.o src/environment.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/bind.o src/bind.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/file.o src/file.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util.o src/util.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util_string.o src/util_string.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/json.o src/json.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/units.o src/units.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/values.o src/values.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/plugins.o src/plugins.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source.o src/source.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/position.o src/position.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/lexer.o src/lexer.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser.o src/parser.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser_selectors.o src/parser_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/prelexer.o src/prelexer.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval.o src/eval.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval_selectors.o src/eval_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/expand.o src/expand.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/listize.o src/listize.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/cssize.o src/cssize.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extender.o src/extender.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extension.o src/extension.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/stylesheet.o src/stylesheet.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/output.o src/output.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/inspect.o src/inspect.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/emitter.o src/emitter.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/check_nesting.o src/check_nesting.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/remove_placeholders.o src/remove_placeholders.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass.o src/sass.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_values.o src/sass_values.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_context.o src/sass_context.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_functions.o src/sass_functions.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass2scss.o src/sass2scss.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/backtrace.o src/backtrace.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/operators.o src/operators.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast2c.o src/ast2c.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/c2ast.o src/c2ast.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/to_value.o src/to_value.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source_map.o src/source_map.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/error_handling.o src/error_handling.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/allocator.o src/memory/allocator.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/utf8_string.o src/utf8_string.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib C:/rtools40/mingw32/bin/ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-i386/libsass' C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o sass.dll tmp.def compile.o init.o ./libsass/lib/libsass.a -lstdc++ -LC:/PROGRA~1/R/R-40~1.3/bin/i386 -lR installing to C:/Users/A/Documents/R/win-library/4.0/00LOCK-sass/00new/sass/libs/i386

* arch - x64 C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk:28: warning: overriding recipe for target 'shlib-clean' Makevars.win:12: warning: ignoring old recipe for target 'shlib-clean' "C:/rtools40/mingw64/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c compile.c -o compile.o "C:/rtools40/mingw64/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o MAKEFLAGS= CC=""C:/rtools40/mingw64/bin/"gcc " CFLAGS="-O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign" CXX=""C:/rtools40/mingw64/bin/"g++ -std=gnu++11 " AR=""C:/rtools40/mingw64/bin/"ar" LDFLAGS="" /usr/bin/make -C libsass make[1]: Entering directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-x64/libsass' C:/rtools40/mingw64/bin/gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -O2 -I ./include -c -o src/cencode.o src/cencode.c C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast.o src/ast.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_values.o src/ast_values.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_supports.o src/ast_supports.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_super.o src/ast_sel_super.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_selectors.o src/ast_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/context.o src/context.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/constants.o src/constants.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_utils.o src/fn_utils.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_miscs.o src/fn_miscs.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_maps.o src/fn_maps.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_lists.o src/fn_lists.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_colors.o src/fn_colors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_numbers.o src/fn_numbers.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_strings.o src/fn_strings.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_selectors.o src/fn_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/color_maps.o src/color_maps.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/environment.o src/environment.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/bind.o src/bind.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/file.o src/file.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util.o src/util.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util_string.o src/util_string.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/json.o src/json.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/units.o src/units.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/values.o src/values.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/plugins.o src/plugins.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source.o src/source.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/position.o src/position.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/lexer.o src/lexer.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser.o src/parser.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser_selectors.o src/parser_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/prelexer.o src/prelexer.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval.o src/eval.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval_selectors.o src/eval_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/expand.o src/expand.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/listize.o src/listize.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/cssize.o src/cssize.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extender.o src/extender.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extension.o src/extension.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/stylesheet.o src/stylesheet.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/output.o src/output.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/inspect.o src/inspect.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/emitter.o src/emitter.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/check_nesting.o src/check_nesting.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/remove_placeholders.o src/remove_placeholders.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass.o src/sass.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_values.o src/sass_values.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_context.o src/sass_context.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_functions.o src/sass_functions.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass2scss.o src/sass2scss.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/backtrace.o src/backtrace.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/operators.o src/operators.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast2c.o src/ast2c.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/c2ast.o src/c2ast.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/to_value.o src/to_value.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source_map.o src/source_map.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/error_handling.o src/error_handling.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/allocator.o src/memory/allocator.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/utf8_string.o src/utf8_string.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib C:/rtools40/mingw64/bin/ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-x64/libsass' C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o sass.dll tmp.def compile.o init.o ./libsass/lib/libsass.a -lstdc++ -LC:/PROGRA~1/R/R-40~1.3/bin/x64 -lR installing to C:/Users/A/Documents/R/win-library/4.0/00LOCK-sass/00new/sass/libs/x64 R inst byte-compile and prepare package for lazy loading help * installing help indices converting help for package 'sass' finding HTML links ... done FileCache html
as_sass html
as_sass_layer html
output_template html
sass-deprecated html
sass html
sass_cache_context_dir html
sass_cache_get html
sass_cache_get_dir html
sass_cache_options html
sass_file_cache html
sass_import html
sass_layer html
sass_options html
sass_partial html
write_file_attachments html
* copying figures building package indices installing vignettes * testing if installed package can be loaded from temporary location arch - i386 * arch - x64 * testing if installed package can be loaded from final location arch - i386 * arch - x64 testing if installed package keeps a record of temporary installation path

The downloaded source packages are in ‘C:\Users\A\AppData\Local\Temp\RtmpoLDypS\downloaded_packages’ √ checking for file 'C:\Users\A\AppData\Local\Temp\RtmpoLDypS\remotes1be81cb4686f\wpeterman-ResistanceGA-5b30f1c/DESCRIPTION' (744ms)

Installing package into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

wpeterman commented 3 years ago

You need to look at the warning generated when trying to install ResistanceGA. This is telling you what the issue is.

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'spData'

Install 'spData'

There may be many rounds of this, unfortunately, until you have all the required packages and dependencies installed.

On Tue, Jan 26, 2021 at 9:21 AM AsadiMarziehAF notifications@github.com wrote:

Hey, Bill Peterman Thank you so much for your reply. I installed the 'spdep' package, but it still appears Error. Thanks

install.packages("C:/Users/A/Desktop/spdep_1.1-5.zip", repos = NULL, type = "win.binary") Installing package into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) package ‘spdep’ successfully unpacked and MD5 sums checked devtools::install_github("wpeterman/ResistanceGA", ref = "julia_dev") Downloading GitHub repo wpeterman/ResistanceGA@julia_dev These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All 2: CRAN packages only 3: None 4: fastmap (1.0.1 -> 1.1.0) [CRAN] 5: shiny (1.5.0 -> 1.6.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: Installing 5 packages: rappdirs, jquerylib, sass, cachem, bslib Installing packages into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation sass 0.3.0 0.3.1 TRUE

trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.0/rappdirs_0.3.1.zip' Content type 'application/zip' length 147871 bytes (144 KB) downloaded 144 KB

trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.0/jquerylib_0.1.3.zip' Content type 'application/zip' length 524799 bytes (512 KB) downloaded 512 KB

trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.0/cachem_1.0.1.zip' Content type 'application/zip' length 70505 bytes (68 KB) downloaded 68 KB

package ‘rappdirs’ successfully unpacked and MD5 sums checked package ‘jquerylib’ successfully unpacked and MD5 sums checked package ‘cachem’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\A\AppData\Local\Temp\RtmpoLDypS\downloaded_packages installing the source packages ‘sass’, ‘bslib’

trying URL 'https://cran.rstudio.com/src/contrib/sass_0.3.1.tar.gz' Content type 'application/x-gzip' length 1837396 bytes (1.8 MB) downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/src/contrib/bslib_0.2.4.tar.gz' Content type 'application/x-gzip' length 3481982 bytes (3.3 MB) downloaded 3.3 MB

  • installing source package 'sass' ... package 'sass' successfully unpacked and MD5 sums checked using staged installation ** libs

*** arch - i386 C:/PROGRA1/R/R-401.3/share/make/winshlib.mk:28: warning: overriding recipe for target 'shlib-clean' Makevars.win:12: warning: ignoring old recipe for target 'shlib-clean' "C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA1/R/R-401.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c compile.c -o compile.o "C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA1/R/R-401.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o MAKEFLAGS= CC=""C:/rtools40/mingw32/bin/"gcc " CFLAGS="-O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign" CXX=""C:/rtools40/mingw32/bin/"g++ -std=gnu++11 " AR=""C:/rtools40/mingw32/bin/"ar" LDFLAGS="" /usr/bin/make -C libsass make[1]: Entering directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-i386/libsass' C:/rtools40/mingw32/bin/gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -O2 -I ./include -c -o src/cencode.o src/cencode.c C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast.o src/ast.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_values.o src/ast_values.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_supports.o src/ast_supports.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_super.o src/ast_sel_super.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_selectors.o src/ast_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/context.o src/context.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/constants.o src/constants.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_utils.o src/fn_utils.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_miscs.o src/fn_miscs.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_maps.o src/fn_maps.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_lists.o src/fn_lists.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_colors.o src/fn_colors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_numbers.o src/fn_numbers.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_strings.o src/fn_strings.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_selectors.o src/fn_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/color_maps.o src/color_maps.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/environment.o src/environment.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/bind.o src/bind.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/file.o src/file.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util.o src/util.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util_string.o src/util_string.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/json.o src/json.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/units.o src/units.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/values.o src/values.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/plugins.o src/plugins.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source.o src/source.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/position.o src/position.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/lexer.o src/lexer.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser.o src/parser.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser_selectors.o src/parser_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/prelexer.o src/prelexer.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval.o src/eval.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval_selectors.o src/eval_selectors.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/expand.o src/expand.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/listize.o src/listize.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/cssize.o src/cssize.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extender.o src/extender.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extension.o src/extension.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/stylesheet.o src/stylesheet.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/output.o src/output.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/inspect.o src/inspect.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/emitter.o src/emitter.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/check_nesting.o src/check_nesting.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/remove_placeholders.o src/remove_placeholders.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass.o src/sass.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_values.o src/sass_values.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_context.o src/sass_context.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_functions.o src/sass_functions.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass2scss.o src/sass2scss.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/backtrace.o src/backtrace.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/operators.o src/operators.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast2c.o src/ast2c.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/c2ast.o src/c2ast.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/to_value.o src/to_value.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source_map.o src/source_map.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/error_handling.o src/error_handling.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/allocator.o src/memory/allocator.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/utf8_string.o src/utf8_string.cpp C:/rtools40/mingw32/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib C:/rtools40/mingw32/bin/ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-i386/libsass' C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o sass.dll tmp.def compile.o init.o ./libsass/lib/libsass.a -lstdc++ -LC:/PROGRA1/R/R-401.3/bin/i386 -lR installing to C:/Users/A/Documents/R/win-library/4.0/00LOCK-sass/00new/sass/libs/i386

* arch - x64 C:/PROGRA1/R/R-401.3/share/make/winshlib.mk:28: warning: overriding recipe for target 'shlib-clean' Makevars.win:12: warning: ignoring old recipe for target 'shlib-clean' "C:/rtools40/mingw64/bin/"gcc -I"C:/PROGRA1/R/R-401.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c compile.c -o compile.o "C:/rtools40/mingw64/bin/"gcc -I"C:/PROGRA1/R/R-401.3/include" -DNDEBUG -I./libsass/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o MAKEFLAGS= CC=""C:/rtools40/mingw64/bin/"gcc " CFLAGS="-O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign" CXX=""C:/rtools40/mingw64/bin/"g++ -std=gnu++11 " AR=""C:/rtools40/mingw64/bin/"ar" LDFLAGS="" /usr/bin/make -C libsass make[1]: Entering directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-x64/libsass' C:/rtools40/mingw64/bin/gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -O2 -I ./include -c -o src/cencode.o src/cencode.c C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast.o src/ast.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_values.o src/ast_values.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_supports.o src/ast_supports.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_super.o src/ast_sel_super.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_selectors.o src/ast_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/context.o src/context.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/constants.o src/constants.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_utils.o src/fn_utils.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_miscs.o src/fn_miscs.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_maps.o src/fn_maps.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_lists.o src/fn_lists.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_colors.o src/fn_colors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_numbers.o src/fn_numbers.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_strings.o src/fn_strings.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/fn_selectors.o src/fn_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/color_maps.o src/color_maps.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/environment.o src/environment.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/bind.o src/bind.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/file.o src/file.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util.o src/util.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/util_string.o src/util_string.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/json.o src/json.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/units.o src/units.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/values.o src/values.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/plugins.o src/plugins.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source.o src/source.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/position.o src/position.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/lexer.o src/lexer.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser.o src/parser.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/parser_selectors.o src/parser_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/prelexer.o src/prelexer.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval.o src/eval.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/eval_selectors.o src/eval_selectors.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/expand.o src/expand.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/listize.o src/listize.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/cssize.o src/cssize.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extender.o src/extender.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/extension.o src/extension.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/stylesheet.o src/stylesheet.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/output.o src/output.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/inspect.o src/inspect.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/emitter.o src/emitter.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/check_nesting.o src/check_nesting.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/remove_placeholders.o src/remove_placeholders.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass.o src/sass.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_values.o src/sass_values.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_context.o src/sass_context.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass_functions.o src/sass_functions.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/sass2scss.o src/sass2scss.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/backtrace.o src/backtrace.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/operators.o src/operators.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/ast2c.o src/ast2c.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/c2ast.o src/c2ast.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/to_value.o src/to_value.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/source_map.o src/source_map.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/error_handling.o src/error_handling.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/allocator.o src/memory/allocator.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/utf8_string.o src/utf8_string.cpp C:/rtools40/mingw64/bin/g++ -std=gnu++11 -Wall -O2 -std=c++11 -I ./include -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib C:/rtools40/mingw64/bin/ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/c/Users/A/AppData/Local/Temp/RtmpYxxYyo/R.INSTALL189070b65737/sass/src-x64/libsass' C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o sass.dll tmp.def compile.o init.o ./libsass/lib/libsass.a -lstdc++ -LC:/PROGRA1/R/R-401.3/bin/x64 -lR installing to C:/Users/A/Documents/R/win-library/4.0/00LOCK-sass/00new/sass/libs/x64 R inst byte-compile and prepare package for lazy loading help * installing help indices converting help for package 'sass' finding HTML links ... done FileCache html as_sass html as_sass_layer html output_template html sass-deprecated html sass html sass_cache_context_dir html sass_cache_get html sass_cache_get_dir html sass_cache_options html sass_file_cache html sass_import html sass_layer html sass_options html sass_partial html write_file_attachments html * copying figures building package indices installing vignettes * testing if installed package can be loaded from temporary location arch - i386 * arch - x64 * testing if installed package can be loaded from final location arch - i386 * arch - x64 testing if installed package keeps a record of temporary installation path

-

DONE (sass)

installing source package 'bslib' ... package 'bslib' successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading help *** installing help indices converting help for package 'bslib' finding HTML links ... done bootswatch_themes html bs_bundle html bs_current_theme html bs_dependency html finding level-2 HTML links ... done

bs_get_variables html bs_global_theme html bs_remove html bs_theme html bs_theme_dependencies html bs_theme_preview html deprecated html font_face html pipe html precompiled_css_path html run_with_themer html theme_bootswatch html theme_version html versions html building package indices testing if installed package can be loaded from temporary location arch - i386 arch - x64 testing if installed package can be loaded from final location ** arch - i386 arch - x64 ** testing if installed package keeps a record of temporary installation path

DONE (bslib)

The downloaded source packages are in ‘C:\Users\A\AppData\Local\Temp\RtmpoLDypS\downloaded_packages’ √ checking for file 'C:\Users\A\AppData\Local\Temp\RtmpoLDypS\remotes1be81cb4686f\wpeterman-ResistanceGA-5b30f1c/DESCRIPTION' (744ms)

  • preparing 'ResistanceGA': (3.5s) √ checking DESCRIPTION meta-information ...
  • checking for LF line-endings in source and make files and shell scripts (439ms)
  • checking for empty or unneeded directories
  • building 'ResistanceGA_4.1-0.40.tar.gz'

Installing package into ‘C:/Users/A/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

  • installing source package 'ResistanceGA' ... using staged installation R ** data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'lme4::getData' by 'raster::getData' when loading 'ResistanceGA' Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'spData' Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package 'ResistanceGA'
  • removing 'C:/Users/A/Documents/R/win-library/4.0/ResistanceGA' Error: Failed to install 'ResistanceGA' from GitHub: (converted from warning) installation of package ‘C:/Users/A/AppData/Local/Temp/RtmpoLDypS/file1be8234d4aee/ResistanceGA_4.1-0.40.tar.gz’ had non-zero exit status

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AsadiMarziehAF commented 3 years ago

Hi Bill Peterman: The "ResistanceGA" package is installed successfully. Thank you again Best Wishes Marzieh

AsadiMarziehAF commented 3 years ago

Hey, I used the code below to execute the command jl.inputs <- jl.prep, but I have been getting errors. The following text is the code I used and the problem that occurred. I hope I can get an answer, (R version 4.0.3 (2020-10-10)). Does anybody how can I fix that? Thank you so much Step: 1) I did execute the command in Julia 1.3.1: using Pkg Pkg.add("Circuitscape") Pkg.test("Circuitscape") 2) I did install "JuliaCall_0.17.2.zip" in RStudio. 3) I used the code below to execute the command jl.inputs <- jl.prep: 1

setwd("C:/Users/A/Desktop/R") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ sp.dat <- sample_pops$sample_cont cont.rast <- raster_orig$cont_orig plot(cont.rast) plot(sp.dat, add = T, pch = 19) JULIA_HOME <- "C:/Users/peterman.73/AppData/Local/Julia-1.3.1/bin/" JuliaCall::julia_setup(JULIA_HOME) Error in JuliaCall::julia_setup(JULIA_HOME) : Julia is not found.

jl.prep function (n.Pops, response = NULL, CS_Point.File, covariates = NULL, formula = NULL, JULIA_HOME = NULL, Neighbor.Connect = 8, pairs_to_include = NULL, pop2ind = NULL, nb = NULL, parallel = FALSE, cores = NULL, cholmod = TRUE, precision = FALSE, run_test = TRUE, write.files = NULL, write.criteria = NULL, silent = TRUE, Julia_link = "JuliaCall", scratch = NULL, rm.files = TRUE) { if (!is.null(covariates) && !is.data.frame(covariates)) { stop("Please provide a data frame when specifying additional covariates") } if (!is.null(covariates) && nrow(covariates) != length(response)) { stop("Response and covariates must have the same number of observations") } if (Julia_link == "XRJulia") { JULIA_HOME <- findJulia() } if (!is.null(write.files)) { write.files <- paste0(normalizePath(write.files, winslash = "/"), "/") if (!dir.exists(write.files)) stop("write.files directory does not exist") } if (Julia_link != "XRJulia") { if (!is.null(JULIA_HOME)) { if (isTRUE(dir.exists(JULIA_HOME))) { julia_setup(JULIA_HOME = JULIA_HOME) } else { stop("Specified JULIA_HOME directory does not exist") } } else { jl.setup <- try(julia_setup(), TRUE) JULIA_HOME <- XRJulia::findJulia() JULIA_HOME <- paste0(dirname(JULIA_HOME), "/") if (class(jl.setup) == "try-error") stop("Specified JULIA_HOME directory does not exist") } } JULIA_HOME <- normalizePath(JULIA_HOME) jl.cs <- julia_installed_package("Circuitscape") if (jl.cs == "nothing") { stop(cat(paste("You must install the Julia CIRCUITSCAPE package!!!", "https://github.com/Circuitscape/Circuitscape.jl", sep = "\n"))) } try(JuliaCall::julia_library("Circuitscape"), silent = T) JuliaCall::julia_library("Circuitscape") wd <- getwd() if (run_test == TRUE) { print("Test: Run Circuitscape from Julia") if (Sys.info()[["sysname"]] == "Windows") { td <- paste0(normalizePath(tempdir(), winslash = "/"), "/") setwd(JULIA_HOME) } else { td <- paste0(tempdir(), "/") } if (!is.null(scratch)) { if (Sys.info()[["sysname"]] == "Linux") { scratch <- td <- paste0(normalizePath(scratch), "/") } else { scratch <- td <- normalizePath(scratch, winslash = "/") } } write.table(samples[1:5, ], paste0(td, "samples.txt"), quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE) temp.ini <- tempfile(pattern = "", tmpdir = tempdir(), fileext = ".ini") if (!is.null(scratch)) { temp.ini <- paste0(scratch, basename(temp.ini)) } tmp.name <- basename(temp.ini) %>% strsplit(., ".ini") %>% unlist() writeRaster(resistance_surfaces$continuous, paste0(td, tmp.name, ".asc"), overwirte = TRUE) write.CS_4.0(BATCH = paste0(td, tmp.name, ".ini"), OUT = paste0("output_file = ", td, tmp.name, ".out"), HABITAT = paste0("habitat_file = ", td, tmp.name, ".asc"), LOCATION.FILE = paste0("point_file = ", td, "samples.txt"), PARALLELIZE = FALSE, CORES = NULL, solver = "cholmod", precision = FALSE, silent = silent) if (Julia_link == "JuliaCall") { out <- julia_call("compute", temp.ini)[-1, -1] } else { cs.jl <- RJulia() cs.jl$Using("Circuitscape") cs.out <- cs.jl$Call("compute", temp.ini) out <- as.matrix(read.table(paste0(scratch, "//", tmp.name, "_resistances.out"), quote = "\"", comment.char = ""))[-1, -1] } if (wd != getwd()) { setwd(wd) } if (dim(out)[1] == 5) { cat("\n") cat("\n") cat("Test Passed") cat("\n") cat("\n") } else { stop("Test Failed") } if (isTRUE(rm.files)) { unlink.list <- list.files(td, pattern = tmp.name, all.files = TRUE, full.names = TRUE) del.files <- sapply(unlink.list, unlink, force = TRUE) } if (!is.null(scratch)) { unlink.list2 <- list.files(scratch, pattern = tmp.name, all.files = TRUE, full.names = TRUE) del.files <- sapply(unlink.list2, unlink, force = TRUE) } } if (isTRUE(precision)) { precision <- "single" } if (isTRUE(cholmod) && (precision == "single")) { stop(cat(paste0("\n", "jl.prep ERROR:", "\n", "CHOLMOD solver only works when using double precision. Set either cholmod = FALSE OR precision = FALSE to proceed", "\n", "\n"))) } if (isTRUE(cholmod)) { solver <- "cholmod" } else { solver <- NULL } if (class(CS_Point.File) == "SpatialPoints") { td <- paste0(tempdir(), "//") if (!is.null(scratch)) { if (Sys.info()[["sysname"]] == "Windows") { td <- normalizePath(scratch) } else { td <- scratch } } site <- c(1:length(CS_Point.File)) cs.txt <- data.frame(site, CS_Point.File) write.table(cs.txt, file = paste0(td, "sample_pts.txt"), col.names = F, row.names = F) CS_Point.File <- paste0(td, "sample_pts.txt") } if (grepl(".asc", x = CS_Point.File)) { CS_grid <- raster <- raster(CS_Point.File) CS_Point.txt <- rasterToPoints(x = CS_grid) site <- CS_Point.txt[, 3] CS_Point.txt <- data.frame(site, CS_Point.txt[, c(1, 2)]) CS_Point.txt <- CS_Point.txt[order(site), ] CS_Point.File <- sub(".asc", ".txt", x = CS_Point.File) write.table(CS_Point.txt, file = CS_Point.File, col.names = F, row.names = F) } if (!is.null(response)) { TEST.response <- ((is.vector(response)) || (ncol(response) == 1)) if (TEST.response == FALSE) { stop("The object 'response' is not in the form of a single column vector") } } if (!exists(x = "ID")) { if (!is.null(nb)) { ID <- To.From.ID(sampled_pops = n.Pops, pop_n = pop2ind, spLoc = CS_Point.File, nb = nb) } else { ID <- To.From.ID(sampled_pops = n.Pops, pop_n = pop2ind, spLoc = NULL, nb = nb) } } suppressWarnings(ZZ <- ZZ.mat(ID)) fmla <- formula df <- NULL if (!is.null(response)) { if (!is.null(covariates)) { if (!is.null(pop2ind)) { keep.vec <- expand.keep(pop2ind) gd.mat <- matrix(0, n.Pops, n.Pops) cov.list <- vector("list", length(names(covariates))) for (i in 1:length(cov.list)) { mat <- gd.mat mat[lower.tri(mat)] <- covariates[, i] cov.list[[i]] <- expand.mat(mat, pop2ind) } names(cov.list) <- names(covariates) cov.df <- as.data.frame(cov.list) covariates <- cov.df response <- response[keep.vec == 1] if (!is.null(nb)) { df <- data.frame(gd = response, cov.df, pop = ID$pop, grp = ID$pop1.pop, cor.grp = ID$cor.grp) } else { df <- data.frame(gd = response, cov.df, pop = ID$pop, grp = ID$pop1.pop) } } else { if (!is.null(nb)) { df <- data.frame(gd = response, covariates, pop = ID$pop1, cor.grp = ID$cor.grp) } else { df <- data.frame(gd = response, covariates, pop = ID$pop1) } } } else { if (!is.null(pop2ind)) { keep.vec <- expand.keep(pop2ind) gd.mat <- matrix(0, n.Pops, n.Pops) response <- response[keep.vec == 1] if (!is.null(nb)) { df <- data.frame(gd = response, pop = ID$pop, grp = ID$pop1.pop, cor.grp = ID$cor.grp) } else { df <- data.frame(gd = response, pop = ID$pop, grp = ID$pop1.pop) } } else { if (!is.null(nb)) { df <- data.frame(gd = response, pop = ID$pop1, cor.grp = ID$cor.grp) } else { df <- data.frame(gd = response, pop = ID$pop1) } } } } if (!is.null(fmla)) { if (!is.null(pop2ind)) { if (!is.null(nb)) { fmla <- update(fmla, gd ~ . + cd + (1 | pop) + (1 | grp) + (1 | cor.grp)) } else { fmla <- update(fmla, gd ~ . + cd + (1 | pop) + (1 | grp)) } } else { if (!is.null(nb)) { fmla <- update(fmla, gd ~ . + cd + (1 | pop) + (1 | cor.grp)) } else { fmla <- update(fmla, gd ~ . + cd + (1 | pop)) } } } else { if (!is.null(pop2ind)) { if (!is.null(nb)) { fmla <- gd ~ cd + (1 | pop) + (1 | grp) + (1 | cor.grp) } else { fmla <- gd ~ cd + (1 | pop) + (1 | grp) } } else { if (!is.null(nb)) { fmla <- gd ~ cd + (1 | pop) + (1 | cor.grp) } else { fmla <- gd ~ cd + (1 | pop) } } } pairs_to_include.file <- NULL keep <- pairs_to_include if (is.null(keep)) { keep <- rep(1, nrow(ID)) } ID.keep <- ID covariates.keep <- covariates ZZ.keep <- ZZ response.keep <- response if (!is.null(pairs_to_include)) { keep <- pairs_to_include df <- df[keep == 1, ] ZZ.keep <- ZZ[, keep == 1] pop <- ID$pop1[keep == 1] miss.pops <- as.character(pop) ZZ.keep <- ZZ.keep[rownames(ZZ.keep) %in% unique(miss.pops), ] response.keep <- response[keep == 1] covariates.keep <- covariates[keep == 1, ] keep.id <- ID[keep == 1, ] names(keep.id) <- c("mode", "include") write.table(keep.id, file = paste0(td, "include_pairs.txt"), col.names = TRUE, row.names = FALSE, quote = FALSE) pairs_to_include.file <- paste0(td, "include_pairs.txt") ID.keep <- ID[keep == 1, ] } list(ID = ID.keep, ZZ = ZZ.keep, df = df, response = response.keep, covariates = covariates.keep, formula = fmla, CS_Point.File = CS_Point.File, Neighbor.Connect = Neighbor.Connect, n.Pops = n.Pops, pairs_to_include = pairs_to_include.file, pop2ind = pop2ind, nb = nb, parallel = parallel, cores = cores, solver = solver, precision = precision, JULIA_HOME = JULIA_HOME, write.files = write.files, write.criteria = write.criteria, silent = silent, Julia_link = Julia_link, scratch = scratch, keep = keep, response.all = response, ID.all = ID, ZZ.all = ZZ, covariates.all = covariates, rm.files = rm.files, opt.input = "jl") } <bytecode: 0x000000001d390d58>

GA.inputs <- GA.prep(ASCII.dir = raster_orig.raster.object <- raster("raster_orig.tif"), + Results.dir = "C:/Users/A/Desktop/R/", + max.cat = 500, + parallel = 5) jl.inputs <- jl.prep(n.Pops = length(sample_pops$sample_cat), + response = lower(Dc_list$Dc_cat), + CS_Point.File = sample_pops$sample_cat, + JULIA_HOME = "C:/Users/A/AppData/Local/Julia-1.3.1/bin/", + cholmod = T) Julia version 1.3.1 at location C:\Users\A\AppData\Local\JULIA-~1.1\bin will be used. Loading setup script for JuliaCall... Error in .julia$cmd(paste0("Base.include(Main,\"", system.file("julia/setup.jl", : Error happens when you try to execute command Base.include(Main,"C:/Users/A/Documents/R/win-library/4.0/JuliaCall/julia/setup.jl") in Julia. To have more helpful error messages, you could considering running the command in Julia directly In addition: Warning message: In system2(file.path(.julia$bin_dir, "julia"), shQuote(command), : running command '"C:\Users\A\AppData\Local\JULIA-~1.1\bin/julia" "--startup-file=no" "C:/Users/A/Documents/R/win-library/4.0/JuliaCall/julia/install_dependency.jl" "C:/PROGRA~1/R/R-40~1.3"' had status 1
wpeterman commented 3 years ago

You have not changed the JULIA_HOME object to the path where Julia is installed on your computer. You are following example code and some directories need to be updated to match your computer configuration.

AsadiMarziehAF commented 3 years ago

Hey Bill Peterman, Thank you very much for your reply. Marzieh

AsadiMarziehAF commented 3 years ago

Hey, I need to specify the full path to the Julia software on my computer and connect Julia to R. but I have been getting errors. The following text is the code that I used and the problem that occurred. Does anybody know how can I fix that? Thank you so much Marzieh

setwd("C:/Users/ASADI/Desktop/R") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ JULIA_HOME <- "C:/Users/ASADI/AppData/Local/Julia-1.3.1/bin/" JuliaCall::julia_setup(JULIA_HOME) Julia version 1.3.1 at location C:\Users\ASADI\AppData\Local\JULIA-~1.1\bin will be used. Loading setup script for JuliaCall... Error in .julia$cmd(paste0("Base.include(Main,\"", system.file("julia/setup.jl", : Error happens when you try to execute command Base.include(Main,"C:/Users/ASADI/Documents/R/win-library/4.0/JuliaCall/julia/setup.jl") in Julia. To have more helpful error messages, you could considering running the command in Julia directly In addition: Warning message: In system2(file.path(.julia$bin_dir, "julia"), shQuote(command), : running command '"C:\Users\ASADI\AppData\Local\JULIA-~1.1\bin/julia" "--startup-file=no" "C:/Users/ASADI/Documents/R/win-library/4.0/JuliaCall/julia/install_dependency.jl" "C:/PROGRA~1/R/R-40~1.3"' had status 1 Untitled

AsadiMarziehAF commented 3 years ago

Hey, My analysis encountered an issue. For running the analysis, at this step (ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs), the laptop hangs and the laptop screen goes black. Does anybody know how can I fix that?

setwd("C:/Users/ASADI/Desktop/R") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ gen_dist <- lower(Dc_list$Dc_cat) r_stack <- raster_orig sample_locs <- sample_pops$sample_cat library(parallel) parallel::detectCores() [] 4 GA.inputs <- GA.prep(ASCII.dir = raster_orig.raster.object <- raster("raster_orig.tif",) Results.dir = "C:/Users/ASADI/Desktop/R/", max.cat = 500, parallel = 5) jl.inputs <- jl.prep(n.Pops = length(sample_pops$sample_cat), response = lower(Dc_list$Dc_cat), CS_Point.File = sample_pops$sample_cat, JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = FALSE precision = TRUE) Julia version 1.5.3 at location C:\Users\ASADI\AppData\Local\Programs\JULIA1~1.3\bin will be used. Loading setup script for JuliaCall... Finish loading setup script for JuliaCall. ]1 "[Test: Run Circuitscape from Julia" Test Passed ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs) .... The laptop hangs and the laptop screen goes black.....

Thank you so much Marzieh

wpeterman commented 3 years ago

This is occurring when trying to analyze the sample data provided with the package?

On Mon, Apr 5, 2021 at 2:34 PM AsadiMarziehAF @.***> wrote:

Hey, My analysis encountered an issue. For running the analysis, at this step ( ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs), the laptop hangs and the laptop screen goes black. Does anybody know how can I fix that?

setwd("C:/Users/ASADI/Desktop/R") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ gen_dist <- lower(Dc_list$Dc_cat) r_stack <- raster_orig sample_locs <- sample_pops$sample_cat library(parallel) parallel::detectCores() [] 4 GA.inputs <- GA.prep(ASCII.dir = raster_orig.raster.object <- raster("raster_orig.tif",) Results.dir = "C:/Users/ASADI/Desktop/R/", max.cat = 500, parallel = 5) jl.inputs <- jl.prep(n.Pops = length(sample_pops$sample_cat), response = lower(Dc_list$Dc_cat), CS_Point.File = sample_pops$sample_cat, JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = FALSE precision = TRUE) Julia version 1.5.3 at location C:\Users\ASADI\AppData\Local\Programs\JULIA1~1.3\bin will be used. Loading setup script for JuliaCall... Finish loading setup script for JuliaCall. ]1 "[Test: Run Circuitscape from Julia" Test Passed ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs) .... The laptop hangs and the laptop screen goes black.....

Thank you so much Marzieh

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wpeterman/ResistanceGA/issues/9#issuecomment-813563659, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDLQUN7TJHIXVKYEZDQMDLTHH7DFANCNFSM4JB2YB3A .

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AsadiMarziehAF commented 3 years ago

Hey, Bill Peterman Thank you so much for your reply. I did test my codes with the sample data provided with the package and it was successful. But, when I want to analyze my one data the laptop hangs and the laptop screen goes black. I am not sure, I guess my raster file is too large and the laptop doesn't have enough memory. Thanks Marzieh

wpeterman commented 3 years ago

How large (number of cells) is your raster and how many spatial locations are you calculating resistance between?

On Tue, Apr 6, 2021 at 6:05 AM AsadiMarziehAF @.***> wrote:

Hey, Bill Peterman Thank you so much for your reply. I did test my codes with the sample data provided with the package and it was successful. But, when I want to analyze my one data the laptop hangs and the laptop screen goes black. I am not sure, I guess my raster file is too large and the laptop doesn't have enough memory. Thanks Marzieh

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wpeterman/ResistanceGA/issues/9#issuecomment-813998193, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDLQUK24CAPKDVJRQYR2CLTHLMH5ANCNFSM4JB2YB3A .

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AsadiMarziehAF commented 3 years ago

Hey, Bill Peterman Thank you so much for your reply. The raster file has 6387 columns and 13139 rows and there are 50 spatial locations to calculate resistance. Thanks Marzieh

wpeterman commented 3 years ago

This is an extremely large surface for a single solve of Circuitscap (>80 million cells) and certainly not tractable for optimization. ResistanceGA is a computationally intensive approach that requires Circuitscape to run thousands of times to optimize a surface. Most successful optimization analyses have less than 2 million raster cells. To do an analysis on a standard laptop/desktop, rasters will typically need to be <1 million cells.

On Wed, Apr 7, 2021 at 11:16 AM AsadiMarziehAF @.***> wrote:

Hey, Bill Peterman Thank you so much for your reply. The raster file has 6387 columns and 13139 rows and there are 50 spatial locations to calculate resistance. Thanks Marzieh

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wpeterman/ResistanceGA/issues/9#issuecomment-814998704, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDLQUORJDNUNIBFOYM73I3THRZMFANCNFSM4JB2YB3A .

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AsadiMarziehAF commented 3 years ago

Hey, Bill Peterman Thank you for your reply. Yes, the raster file is too large. The cell size of the raster file is 30 * 30, can I increase the cell/grid size (e.g., 60 m x 60 m cells or 5 km x 5km cells)? Thanks Marzieh

wpeterman commented 3 years ago

Adjusting the raster resolution to 300m would make this workable. Coarser (e.g., 510m or 750m) will further reduce optimization time. You just need to balance how much detail is lost in your raster surfaces and take into consideration your focal species and the scale at which they interact with and perceive the landscape. There are no hard and fast rules for this. I'd encourage you to peruse the landscape genetics literature to see how people have handled this in different systems.

On Fri, Apr 9, 2021 at 6:27 AM AsadiMarziehAF @.***> wrote:

Hey, Bill Peterman Thank you for your the reply. Yes, the raster file is too large. The cell size of the raster file is 30 * 30, can I increase the cell/grid size (e.g., 60 m x 60 m cells or 5 km x 5km cells)? Thanks Marzieh

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wpeterman/ResistanceGA/issues/9#issuecomment-816586145, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDLQUNKK6LPPASA2MNCPILTH3JAHANCNFSM4JB2YB3A .

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AsadiMarziehAF commented 3 years ago

Hi, Bill Peterman Thank you so much for helping me. My project is about a mammal species, tree squirrel with high mobility and I think 300 m would make this workable. Thanks Marzieh

AsadiMarziehAF commented 3 years ago

Hi, Bill Peterman Hope you are doing fine. Sorry, I have an issue with my analysis with ResistanceGA, actually, I have a problem with importing my data (raster file, sample points, genetic distance) and running the analysis. I executed codes based on the guideline and at the first step I determined the directory but I can't see my data and I can see example's data. Then I did change the name of my import files but I can't see them and I can see just the example's data. If you have time, please look at the codes and tell me your idea. Thank you so much Marzieh

setwd("C:/Users/ASADI/Desktop/R") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ gen_dist <- lower(Dc_list$Dc_cat) r_stack <- raster_orig sample_locs <- sample_pops$sample_cat library(parallel) parallel::detectCores() 4 GA.inputs <- GA.prep(ASCII.dir = raster_orig.raster.object <- raster("raster_orig.tif"), Results.dir = "C:/Users/ASADI/Desktop/R/", max.cat = 500, parallel = 5) jl.inputs <- jl.prep(n.Pops = length(sample_pops$sample_cat), response = lower(Dc_list$Dc_cat), CS_Point.File = sample_pops$sample_cat, JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = T) Julia version 1.5.3 at location C:\Users\ASADI\AppData\Local\Programs\JULIA1~1.3\bin will be used. Loading setup script for JuliaCall... Finish loading setup script for JuliaCall. [1] "Test: Run Circuitscape from Julia"

Test Passed

ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs) 1 2

wpeterman commented 3 years ago

I'm sorry Marzieh, but I'm not really sure what your issue is. This doesn't sound like a problem with ResistanceGA.

On Mon, Apr 26, 2021 at 8:36 AM AsadiMarziehAF @.***> wrote:

Hi, Bill Peterman Hope you are doing fine. Sorry, I have an issue with my analysis with ResistanceGA, actually, I have a problem with importing my data (raster file, sample points, genetic distance) and running the analysis. I executed codes based on the guideline and at the first step I determined the directory but I can't see my data and I can see example's data. Then I did change the name of my import files but I can't see them and I can see just the example's data. If you have time, please look at the codes and tell me your idea. Thank you so much Marzieh

setwd("C:/Users/ASADI/Desktop/R") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ gen_dist <- lower(Dc_list$Dc_cat) r_stack <- raster_orig sample_locs <- sample_pops$sample_cat library(parallel) parallel::detectCores() 4 GA.inputs <- GA.prep(ASCII.dir = raster_orig.raster.object <- raster("raster_orig.tif"), Results.dir = "C:/Users/ASADI/Desktop/R/", max.cat = 500, parallel = 5) jl.inputs <- jl.prep(n.Pops = length(sample_pops$sample_cat), response = lower(Dc_list$Dc_cat), CS_Point.File = sample_pops$sample_cat, JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = T) Julia version 1.5.3 at location C:\Users\ASADI\AppData\Local\Programs\JULIA1~1.3\bin will be used. Loading setup script for JuliaCall... Finish loading setup script for JuliaCall. [1] "Test: Run Circuitscape from Julia"

Test Passed

ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs) [image: 1] https://user-images.githubusercontent.com/57016053/116083081-7490c900-a6b1-11eb-95cb-66f9882b5966.png [image: 2] https://user-images.githubusercontent.com/57016053/116083102-7a86aa00-a6b1-11eb-9780-d854f3c23ec9.png

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AsadiMarziehAF commented 3 years ago

Hi, Bill Peterman Thank you so much for your reply. I have fixed the issue but I have another issue. I think my analysis goes wrong, because after execute the code: ss.cat <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs, there is a weird value (GA | iter = 1 | Mean = -99999 | Best = -99999). I am not sure but I think the value -9999, it's not true. If you have time, please look at the codes and tell me your idea. Thank you very much Marzieh

setwd("C:/Users/ASADI/Desktop/R/T") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ library(parallel) parallel::detectCores() [1] 4 GA.inputs <- GA.prep(ASCII.dir = raster_orig.raster.object <- raster("raster_orig.tif"),

  • Results.dir = "C:/Users/ASADI/Desktop/R/T/",
  • max.cat = 500,
  • parallel = 4) jl.inputs <- jl.prep(n.Pops = length(sample_pops$sample_cat),
  • response = lower(Dc_list$Dc_cat),
  • CS_Point.File = sample_pops$sample_cat,
  • JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/",
  • cholmod = T) Julia version 1.5.3 at location C:\Users\ASADI\AppData\Local\Programs\JULIA1~1.3\bin will be used. Loading setup script for JuliaCall... Finish loading setup script for JuliaCall. [1] "Test: Run Circuitscape from Julia"

Test Passed

ss.cat <- SS_optim(jl.inputs = jl.inputs,

  • GA.inputs = GA.inputs) GA | iter = 1 | Mean = -99999 | Best = -99999 GA | iter = 2 | Mean = -99999 | Best = -99999 GA | iter = 3 | Mean = -99999 | Best = -99999 GA | iter = 4 | Mean = -99999 | Best = -99999 GA | iter = 5 | Mean = -99999 | Best = -99999 GA | iter = 6 | Mean = -99999 | Best = -99999 GA | iter = 7 | Mean = -99999 | Best = -99999 GA | iter = 8 | Mean = -99999 | Best = -99999
AsadiMarziehAF commented 3 years ago

Hi Bill Peterman I work ResistanceGA 4.0.3 with Julia 1.5.3. It worked well until "SS_optim" The following text is the code I used and the problem that occurred. Do you know how can I fix that? Thank you so much (The name of input files: GD= genetic distance, SL= sample location, raster_r= raster map)

setwd("C:/Users/ASADI/Desktop/R/T") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ GD <- read.delim("C:/Users/ASADI/Desktop/R/T/GD.txt", header=FALSE) View(GD) SL <- read.delim("C:/Users/ASADI/Desktop/R/T/SL.txt", header=FALSE) View(SL) GA.inputs <- GA.prep(ASCII.dir = raster_r <- raster("raster_r.tif"), Results.dir = "C:/Users/ASADI/Desktop/R/T/", max.cat = 500, parallel = 4) jl.inputs <- jl.prep(n.Pops = length(SL), response = lower(GD), CS_Point.File = paste0("SL.txt"), JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = T) jl.optim <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs)

SS_RESULTS <SS_optim(jl.inputs=jl.inputs, GA.inputs=GA.inputs) GA | iter = 1 | Mean = -99999 | Best = -99999 GA | iter = 2 | Mean = -99999 | Best = -99999 GA | iter = 3 | Mean = -99999 | Best = -99999 GA | iter = 4 | Mean = -99999 | Best = -99999 GA | iter = 5 | Mean = -99999 | Best = -99999

wpeterman commented 3 years ago

This output looks like there are issues with some of your data. If you are able to share the data and code you're trying to use, I can try to debug and troubleshoot.

On Sun, May 16, 2021 at 1:30 PM AsadiMarziehAF @.***> wrote:

Hi Bill Peterman I work ResistanceGA 4.0.3 with Julia 1.5.3. It worked well until "SS_optim" The following text is the code I used and the problem that occurred. Do you know how can I fix that? Thank you so much

setwd("C:/Users/ASADI/Desktop/R/T") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ GD <- read.delim("C:/Users/ASADI/Desktop/R/T/GD.txt", header=FALSE) View(GD) SL <- read.delim("C:/Users/ASADI/Desktop/R/T/SL.txt", header=FALSE) View(SL) GA.inputs <- GA.prep(ASCII.dir = raster_r <- raster("raster_r.tif"), Results.dir = "C:/Users/ASADI/Desktop/R/T/", max.cat = 500, parallel = 4) jl.inputs <- jl.prep(n.Pops = length(SL), response = lower(GD), CS_Point.File = paste0("SL.txt"), JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = T) jl.optim <- SS_optim(jl.inputs = jl.inputs, GA.inputs = GA.inputs)

SS_RESULTS <SS_optim(jl.inputs=CS.inputs, GA.inputs=GA.inputs) GA | iter = 1 | Mean = -99999 | Best = -99999 GA | iter = 2 | Mean = -99999 | Best = -99999 GA | iter = 3 | Mean = -99999 | Best = -99999 GA | iter = 4 | Mean = -99999 | Best = -99999 GA | iter = 5 | Mean = -99999 | Best = -99999

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AsadiMarziehAF commented 3 years ago

Hi, Bill Peterman Thank you so much for your reply. I send my data via email to you. Thank you so much Marzieh

AsadiMarziehAF commented 3 years ago

Hi, Bill Peterman Your solution works, the error messages are gone. But I got new issues, the following text is the code I used and the problem that occurred. Do you know, how do I resolve this issue? Thank you very much

setwd("C:/Users/ASADI/Desktop/R/T") library(ResistanceGA) Loading required package: raster Loading required package: sp Registered S3 method overwritten by 'spatstat': method from print.boxx cli Warning message: replacing previous import ‘lme4::getData’ by ‘raster::getData’ when loading ‘ResistanceGA’ GD <- read.delim("GD.txt", header=T) GD <- as.matrix(GD[,-1]) SL <- read.delim("SL.txt", header=T) sp_pts <- SpatialPoints(SL[,c(2,3)])

raster_r <- raster("raster_r.tif") plot(raster_r, main = 'MR') plot(sp_pts, add = T, pch = 19) extract(raster_r, sp_pts) [1] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 duplicated(cellFromXY(raster_r, sp_pts)) [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [19] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [37] FALSE FALSE GA.inputs <- GA.prep(ASCII.dir = raster_r, Results.dir = "results/", max.cat = 500, maxiter = 1, pop.size = 5, parallel = F) jl.inputs <- jl.prep(n.Pops = length(sp_pts), response = lower(GD), CS_Point.File = sp_pts, JULIA_HOME = "C:/Users/ASADI/AppData/Local/Programs/Julia 1.5.3/bin/", cholmod = T) Julia version 1.5.3 at location C:\Users\ASADI\AppData\Local\Programs\JULIA1~1.3\bin will be used. Loading setup script for JuliaCall... Finish loading setup script for JuliaCall. [1] "Test: Run Circuitscape from Julia"

Test Passed

SS_RESULTS <- SS_optim(jl.inputs=jl.inputs, GA.inputs=GA.inputs) Iteration took 37.26 seconds LL = 428.2174 

Iteration took 43.7 seconds 
LL = 426.7657 

Iteration took 30.86 seconds 
LL = 429.0338 

Iteration took 1.61 seconds 
LL = 427.8649 

Iteration took 2.81 seconds 
LL = 428.4906

GA | iter = 1 | Mean = 428.0745 | Best = 429.0338 Error in file(file, ifelse(append, "a", "w")) : cannot open the connection In addition: Warning messages: 1: In ga(type = "real-valued", fitness = Resistance.Opt_single, Resistance = r, : The population size is less than 10. 2: In file(file, ifelse(append, "a", "w")) : cannot open file 'results/Results/raster_r_jlResistMat.csv': No such file or directory

wpeterman commented 3 years ago

You need to specify the full path to the directory where results will be written.

AsadiMarziehAF commented 3 years ago

Hi, Bill Peterman Thank you so much for your reply

FAmorim81 commented 3 years ago

Hi @wpeterman,

I'm using devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev') to install ResistanceGA, but I have runing into errors related to spatstat.

Downloading GitHub repo wpeterman/ResistanceGA@julia_dev
√  checking for file 'C:\Users\Francisco\AppData\Local\Temp\RtmpAFuAQA\remotes463c5b7a7652\wpeterman-ResistanceGA-5b30f1c/DESCRIPTION' ... 
-  preparing 'ResistanceGA': (1.3s)
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'ResistanceGA_4.1-0.40.tar.gz'

* installing *source* package 'ResistanceGA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'lme4::getData' by 'raster::getData' when loading 'ResistanceGA'
Error: object 'as.im' is not exported by 'namespace:spatstat'
Execution halted
ERROR: lazy loading failed for package 'ResistanceGA'
* removing 'C:/Program Files/R/R-4.1.0/library/ResistanceGA'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/FRANCI~1/AppData/Local/Temp/RtmpAFuAQA/file463c200e6edd/ResistanceGA_4.1-0.40.tar.gz’ had non-zero exit status

This has also been reported here.

Thank you for your help