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wpeterman / ResistanceGA

Optimize resistance surfaces using Genetic Algorithms
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ResistanceGA Install Error #21

Closed cmu002 closed 3 years ago

cmu002 commented 3 years ago

G'day, I've been trying to install the ResistanceGA package through the standard installation process, however, I keep running into errors with 'rlang' and 'nloptr'. It looks as though there's an issue with the configuration, but I could be mistaken. I've tried both the following installation commands but returned the same issue. Any advice would be appreciated!

Installation Code devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev') & devtools::install_github("wpeterman/ResistanceGA", build_vignettes = TRUE)

Returned Output `> 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: rlang (0.4.11 -> 0.4.12 ) [CRAN] 5: nloptr (1.2.2.2 -> 1.2.2.3) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 rlang (0.4.11 -> 0.4.12 ) [CRAN] nloptr (1.2.2.2 -> 1.2.2.3) [CRAN] Installing 2 packages: rlang, nloptr Installing packages into ‘C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation nloptr 1.2.2.2 1.2.2.3 TRUE

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/rlang_0.4.12.zip' Content type 'application/zip' length 1202691 bytes (1.1 MB) downloaded 1.1 MB

package ‘rlang’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘rlang’ Warning: restored ‘rlang’

The downloaded binary packages are in C:\Users\User\AppData\Local\Temp\RtmpKgUxrQ\downloaded_packages installing the source package ‘nloptr’

trying URL 'https://cran.rstudio.com/src/contrib/nloptr_1.2.2.3.tar.gz' Content type 'application/x-gzip' length 2456474 bytes (2.3 MB) downloaded 2.3 MB

** libs

*** arch - i386 /mingw32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-41~1.1/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o /mingw32/bin/gcc -I"C:/PROGRA~1/R/R-41~1.1/include" -DNDEBUG -I"/i386/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_nloptr.c -o init_nloptr.o init_nloptr.c:35:10: fatal error: nlopt.h: No such file or directory

include "nlopt.h"

      ^~~~~~~~~

compilation terminated. make: *** [C:/PROGRA~1/R/R-41~1.1/etc/i386/Makeconf:238: init_nloptr.o] Error 1 ERROR: compilation failed for package 'nloptr'

The downloaded source packages are in ‘C:\Users\User\AppData\Local\Temp\RtmpKgUxrQ\downloaded_packages’ √ checking for file 'C:\Users\User\AppData\Local\Temp\RtmpKgUxrQ\remotes35e87e292427\wpeterman-ResistanceGA-5b30f1c/DESCRIPTION' ...

Installing package into ‘C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified)

wpeterman commented 3 years ago

The julia branch is no longer supported as it has been merged with the main branch. To install, use:

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

The errors you are receiving are prone to happen when updating packages within the current R/RStudio session. You can manually delete these packages, restart your session, then manually install them to the most recent version. This may be an iterative process to get all necessary packages updated. Once they are, everything should install as expected using devtools.

On Thu, Nov 4, 2021 at 4:20 AM cmu002 @.***> wrote:

G'day, I've been trying to install the ResistanceGA package through the standard installation process, however, I keep running into errors with 'rlang' and 'nloptr'. It looks as though there's an issue with the configuration, but I could be mistaken. I've tried both the following installation commands but returned the same issue. Any advice would be appreciated!

Installation Code devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev') & devtools::install_github("wpeterman/ResistanceGA", build_vignettes = TRUE)

Returned Output `> devtools::install_github("wpeterman/ResistanceGA", ref = 'julia_dev') Downloading GitHub repo @.***_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: rlang (0.4.11 -> 0.4.12 ) [CRAN] 5: nloptr (1.2.2.2 -> 1.2.2.3) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 rlang (0.4.11 -> 0.4.12 ) [CRAN] nloptr (1.2.2.2 -> 1.2.2.3) [CRAN] Installing 2 packages: rlang, nloptr Installing packages into ‘C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified)

There is a binary version available but the source version is later: binary source needs_compilation nloptr 1.2.2.2 1.2.2.3 TRUE

trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.1/rlang_0.4.12.zip' Content type 'application/zip' length 1202691 bytes (1.1 MB) downloaded 1.1 MB

package ‘rlang’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘rlang’ Warning: restored ‘rlang’

The downloaded binary packages are in C:\Users\User\AppData\Local\Temp\RtmpKgUxrQ\downloaded_packages installing the source package ‘nloptr’

trying URL 'https://cran.rstudio.com/src/contrib/nloptr_1.2.2.3.tar.gz' Content type 'application/x-gzip' length 2456474 bytes (2.3 MB) downloaded 2.3 MB

-

installing source package 'nloptr' ... package 'nloptr' successfully unpacked and MD5 sums checked using staged installation

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 /mingw32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-411.1/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o /mingw32/bin/gcc -I"C:/PROGRA1/R/R-411.1/include" -DNDEBUG -I"/i386/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_nloptr.c -o init_nloptr.o init_nloptr.c:35:10: fatal error: nlopt.h: No such file or directory

include "nlopt.h"

^~~~~ compilation terminated. make: *** [C:/PROGRA1/R/R-411.1/etc/i386/Makeconf:238: init_nloptr.o] Error 1 ERROR: compilation failed for package 'nloptr'

  • removing 'C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1/nloptr'
  • restoring previous 'C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1/nloptr'

The downloaded source packages are in ‘C:\Users\User\AppData\Local\Temp\RtmpKgUxrQ\downloaded_packages’ √ checking for file 'C:\Users\User\AppData\Local\Temp\RtmpKgUxrQ\remotes35e87e292427\wpeterman-ResistanceGA-5b30f1c/DESCRIPTION' ...

  • preparing 'ResistanceGA': (376ms) √ 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 package into ‘C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1’ (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: object 'as.im' is not exported by 'namespace:spatstat' Execution halted ERROR: lazy loading failed for package 'ResistanceGA'
  • removing 'C:/Users/User/OneDrive-UniversityoftheSunshineCoast/Documents/R/win-library/4.1/ResistanceGA' Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\User\OneDrive-UniversityoftheSunshineCoast\Documents\R\win-library\4.1\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\User\OneDrive-UniversityoftheSunshineCoast\Documents\R\win-library\4.1\rlang\libs\x64\rlang.dll: Permission denied 2: In i.p(...) : installation of package ‘nloptr’ had non-zero exit status 3: In i.p(...) : installation of package ‘C:/Users/User/AppData/Local/Temp/RtmpKgUxrQ/file35e84e734507/ResistanceGA_4.1-0.40.tar.gz’ had non-zero exit status`

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--

-Bill-

cmu002 commented 3 years ago

G'day,

Thanks so much for your timely response, that means a lot. When I first tried installing the package I used the main branch through devtools, however ran into the same issue. I'll try the iterative process of manually updating each of those packages. I attempted that earlier, yet was running into issues with the binaries. I'll give it a another crack later today to see if I can troubleshoot 👍

Cheers, Chris

julian-wittische commented 3 years ago

Hello,

Similar error with nloptr here. The 1.2.2.3 source version fails, however, the 1.2.2.2 binary version works for me.

cmu002 commented 3 years ago

I ended up installing the binaries for the 'nloptr' package and it ended up working fine for me!

install.packages("nloptr", type = "binary")