Add population info using gl2structure?
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Caroline Chong
Oct 19, 2021, 12:55:14 AM10/19/21
to dartR
Hi Luis and all,
I am wondering how to correctly add the population information stored in a genlight to the Structure file generated using gl2structure.
I have a genlight that has gone through basic filtering and removal of some individuals (and recalculation of metrics). Then if
gl2structure(gl.data.filt.struct, indNames = NULL, addcolumns = 1, ploidy = 2,...)
The error returned is
Error in gl2structure(gl.data.filt.struct, indNames = NULL, addcolumns = 1, :
Fatal Error: No. of individuals in user-specified addColumns and no. of individuals in supplied genlight object x does not match
Can you suggest what I need to do to the genlight object, or what needs to happen in the gl2structure function, so that we can add the population info automatically to the Structure file? Running gl2structure with addcolumns = NULL works fine and produces a .str file as expected (without population info).
Many thanks!
Regards, Caroline.
Jose Luis Mijangos
Oct 19, 2021, 2:10:35 AM10/19/21
to dartR
Hi Caroline,
The description of what should be the input for "addcolumns" is not very clear. The input should be a vector with as many elements as there are individuals. in the case of population information (PopData) should be an integer as described in Structure Manual.
So, to add the population information you can use:
> gl2structure(gl.data.filt.struct, indNames = NULL, addcolumns = as.numeric(gl.data.filt.struct$pop), ploidy = 2,outpath = getwd())
Also, if you want to set the
PopFlag to active the option
USEPOPINFO, you can use:
> gl2structure(gl.data.filt.struct, indNames = NULL, addcolumns = cbind(as.numeric(gl.data.filt.struct$pop),1), ploidy = 2,outpath = getwd())
Cheers,
Luis
Caroline Chong
Oct 19, 2021, 2:17:32 AM10/19/21
to dartR
Hi Luis,
Ah, that's perfect. Thank you!
Regards, Caroline.
Rajneesh Paliwal
Jan 13, 2022, 10:40:12 AM1/13/22
to da...@googlegroups.com
Dear Jose,
I have update my R version 4.1.2 and R studio today. Now my dart R is not working and showing following issue, please help me to load it successfully.
It looks rgdal library issue in new mac version. Could you help me.
Best regards
Rajneesh
I used following script after update and issue are below
> library(dartR)
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Registered S3 method overwritten by 'genetics':
method from
[.haplotype pegas
Error: package or namespace load failed for ‘dartR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so
Reason: image not found
> install.packages("dartR")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dartR_1.9.9.1.tgz'
Content type 'application/x-gzip' length 3002929 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
The downloaded binary packages are in
/var/folders/w0/sk8d6yzx1z179g8zxbh6vtj40000gn/T//Rtmpc5qgQo/downloaded_packages
> library(dartR)
Error: package or namespace load failed for ‘dartR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so
Reason: image not found
> remove.packages("rgdal")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
(as ‘lib’ is unspecified)
> install.packages("rgdal", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.5-28.tar.gz'
Content type 'application/x-gzip' length 4511100 bytes (4.3 MB)
==================================================
downloaded 4.3 MB
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /Library/Frameworks/R.framework/Resources
configure: CC: clang -mmacosx-version-min=10.13
configure: CXX: clang++ -mmacosx-version-min=10.13 -std=gnu++14
configure: CFLAGS: -Wall -g -O2
configure: CPPFLAGS: -I/usr/local/include
configure: CXXFLAGS: -Wall -g -O2
configure: LDFLAGS: -L/usr/local/lib
configure: LDFLAGS: -L/usr/local/lib
configure: CXX11 is: clang++ -mmacosx-version-min=10.13, CXX11STD is: -std=gnu++11
configure: CXX is: clang++ -mmacosx-version-min=10.13 -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.5-28
checking for /usr/bin/svnversion... no
configure: svn revision: 1158
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal’
Warning in install.packages :
installation of package ‘rgdal’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/w0/sk8d6yzx1z179g8zxbh6vtj40000gn/T/Rtmpc5qgQo/downloaded_packages’
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
> devtools::install_github("CRAN/rgdal")
Downloading GitHub repo CRAN/rgdal@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/CRAN/rgdal/tarball/HEAD' failed
> install.packages("rgdal", repos="http://R-Forge.R-project.org")
Warning in install.packages :
unable to access index for repository http://R-Forge.R-project.org/bin/macosx/contrib/4.1:
cannot open URL 'http://R-Forge.R-project.org/bin/macosx/contrib/4.1/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘rgdal’
Do you want to attempt to install these from sources? (Yes/no/cancel) nstall.packages(c("rgdal","sf"),,"https://mac.R-project.org")
Error in install.packages : Unrecognized response “nstall.packages(c("rgdal","sf"),,"https://mac.R-project.org")”
> install.packages(c("rgdal","sf"),,"https://mac.R-project.org")
Warning in install.packages :
unable to access index for repository https://mac.R-project.org/src/contrib:
download from 'https://mac.R-project.org/src/contrib/PACKAGES' failed
Warning in install.packages :
packages ‘rgdal’, ‘sf’ are not available for this version of R
Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> install.packages(c("rgdal","sf"),,"https://r-forge.r-project.org/projects/rgdal/")
Warning in install.packages :
unable to access index for repository https://r-forge.r-project.org/projects/rgdal/src/contrib:
Line starting '<?xml version="1.0" ...' is malformed!
Warning in install.packages :
packages ‘rgdal’, ‘sf’ are not available for this version of R
Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Warning in install.packages :
unable to access index for repository https://r-forge.r-project.org/projects/rgdal/bin/macosx/contrib/4.1:
Line starting '<?xml version="1.0" ...' is malformed!
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Registered S3 method overwritten by 'genetics':
method from
[.haplotype pegas
Error: package or namespace load failed for ‘dartR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so
Reason: image not found
> install.packages("dartR")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dartR_1.9.9.1.tgz'
Content type 'application/x-gzip' length 3002929 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
The downloaded binary packages are in
/var/folders/w0/sk8d6yzx1z179g8zxbh6vtj40000gn/T//Rtmpc5qgQo/downloaded_packages
> library(dartR)
Error: package or namespace load failed for ‘dartR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal/libs/rgdal.so
Reason: image not found
> remove.packages("rgdal")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
(as ‘lib’ is unspecified)
> install.packages("rgdal", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.5-28.tar.gz'
Content type 'application/x-gzip' length 4511100 bytes (4.3 MB)
==================================================
downloaded 4.3 MB
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /Library/Frameworks/R.framework/Resources
configure: CC: clang -mmacosx-version-min=10.13
configure: CXX: clang++ -mmacosx-version-min=10.13 -std=gnu++14
configure: CFLAGS: -Wall -g -O2
configure: CPPFLAGS: -I/usr/local/include
configure: CXXFLAGS: -Wall -g -O2
configure: LDFLAGS: -L/usr/local/lib
configure: LDFLAGS: -L/usr/local/lib
configure: CXX11 is: clang++ -mmacosx-version-min=10.13, CXX11STD is: -std=gnu++11
configure: CXX is: clang++ -mmacosx-version-min=10.13 -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.5-28
checking for /usr/bin/svnversion... no
configure: svn revision: 1158
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rgdal’
Warning in install.packages :
installation of package ‘rgdal’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/w0/sk8d6yzx1z179g8zxbh6vtj40000gn/T/Rtmpc5qgQo/downloaded_packages’
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
> devtools::install_github("CRAN/rgdal")
Downloading GitHub repo CRAN/rgdal@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/CRAN/rgdal/tarball/HEAD' failed
> install.packages("rgdal", repos="http://R-Forge.R-project.org")
Warning in install.packages :
unable to access index for repository http://R-Forge.R-project.org/bin/macosx/contrib/4.1:
cannot open URL 'http://R-Forge.R-project.org/bin/macosx/contrib/4.1/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘rgdal’
Do you want to attempt to install these from sources? (Yes/no/cancel) nstall.packages(c("rgdal","sf"),,"https://mac.R-project.org")
Error in install.packages : Unrecognized response “nstall.packages(c("rgdal","sf"),,"https://mac.R-project.org")”
> install.packages(c("rgdal","sf"),,"https://mac.R-project.org")
Warning in install.packages :
unable to access index for repository https://mac.R-project.org/src/contrib:
download from 'https://mac.R-project.org/src/contrib/PACKAGES' failed
Warning in install.packages :
packages ‘rgdal’, ‘sf’ are not available for this version of R
Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> install.packages(c("rgdal","sf"),,"https://r-forge.r-project.org/projects/rgdal/")
Warning in install.packages :
unable to access index for repository https://r-forge.r-project.org/projects/rgdal/src/contrib:
Line starting '<?xml version="1.0" ...' is malformed!
Warning in install.packages :
packages ‘rgdal’, ‘sf’ are not available for this version of R
Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Warning in install.packages :
unable to access index for repository https://r-forge.r-project.org/projects/rgdal/bin/macosx/contrib/4.1:
Line starting '<?xml version="1.0" ...' is malformed!
Rajneesh Paliwal, PhD (DAAD Fellow)
Associate Scientist
Genetic Resources Center
International Inst. for Tropical Agriculture
Oyo Road PMB-5320, Ibadan, Nigeria
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Rajneesh Paliwal
Jan 13, 2022, 11:34:58 AM1/13/22
to da...@googlegroups.com
Dear Jose,
I tried it again but same issue
install_github("green-striped-gecko/dartR")
Downloading GitHub repo green-striped-gecko/dartR@HEAD
Downloading GitHub repo green-striped-gecko/dartR@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/green-striped-gecko/dartR/tarball/HEAD' failed
> install.packages("dartR")
Warning in install.packages :
dependency ‘SNPRelate’ is not available
also installing the dependencies ‘base64enc’, ‘sass’, ‘jquerylib’, ‘colorspace’, ‘hms’, ‘backports’, ‘pixmap’, ‘httpuv’, ‘fontawesome’, ‘htmltools’, ‘sourcetools’, ‘later’, ‘promises’, ‘bslib’, ‘segmented’, ‘farver’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘viridisLite’, ‘png’, ‘terra’, ‘R.oo’, ‘R.methodsS3’, ‘combinat’, ‘gdata’, ‘mvtnorm’, ‘forcats’, ‘progress’, ‘RcppParallel’, ‘RcppEigen’, ‘broom’, ‘truncnorm’, ‘ade4’, ‘igraph’, ‘shiny’, ‘seqinr’, ‘reshape2’, ‘gtable’, ‘isoband’, ‘scales’, ‘Rcpp’, ‘tidyselect’, ‘permute’, ‘pegas’, ‘doParallel’, ‘RgoogleMaps’, ‘gap’, ‘calibrate’, ‘xtable’, ‘dismo’, ‘reshape’, ‘R.utils’, ‘genetics’, ‘rgdal’, ‘gdistance’, ‘mmod’, ‘GGally’, ‘data.table’, ‘raster’, ‘gaston’, ‘gtools’, ‘DEoptimR’, ‘mice’, ‘Rsolnp’, ‘iterators’, ‘generics’, ‘adegenet’, ‘ggplot2’, ‘plyr’, ‘tidyr’, ‘ape’, ‘vegan’, ‘StAMPP’, ‘sp’, ‘PopGenReport’, ‘hierfstat’, ‘robustbase’, ‘gridExtra’, ‘HardyWeinberg’, ‘foreach’, ‘dplyr’
There is a binary version available but the source version is later:
binary source needs_compilation
terra 1.4-22 1.5-12 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/base64enc_0.1-3.tgz'
Content type 'application/x-gzip' length 31642 bytes (30 KB)
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downloaded 30 KB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sass_0.4.0.tgz'
Content type 'application/x-gzip' length 2388256 bytes (2.3 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jquerylib_0.1.4.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/colorspace_2.0-2.tgz'
Content type 'application/x-gzip' length 2618801 bytes (2.5 MB)
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downloaded 2.5 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/hms_1.1.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/httpuv_1.6.5.tgz'
Content type 'application/x-gzip' length 2746719 bytes (2.6 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fontawesome_0.2.2.tgz'
Content type 'application/x-gzip' length 1530165 bytes (1.5 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/htmltools_0.5.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sourcetools_0.1.7.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/later_1.3.0.tgz'
Content type 'application/x-gzip' length 623693 bytes (609 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/promises_1.2.0.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/labeling_0.4.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/munsell_0.5.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RColorBrewer_1.1-2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/viridisLite_0.4.0.tgz'
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> install.packages("dartR")
Warning in install.packages :
dependency ‘SNPRelate’ is not available
also installing the dependencies ‘base64enc’, ‘sass’, ‘jquerylib’, ‘colorspace’, ‘hms’, ‘backports’, ‘pixmap’, ‘httpuv’, ‘fontawesome’, ‘htmltools’, ‘sourcetools’, ‘later’, ‘promises’, ‘bslib’, ‘segmented’, ‘farver’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘viridisLite’, ‘png’, ‘terra’, ‘R.oo’, ‘R.methodsS3’, ‘combinat’, ‘gdata’, ‘mvtnorm’, ‘forcats’, ‘progress’, ‘RcppParallel’, ‘RcppEigen’, ‘broom’, ‘truncnorm’, ‘ade4’, ‘igraph’, ‘shiny’, ‘seqinr’, ‘reshape2’, ‘gtable’, ‘isoband’, ‘scales’, ‘Rcpp’, ‘tidyselect’, ‘permute’, ‘pegas’, ‘doParallel’, ‘RgoogleMaps’, ‘gap’, ‘calibrate’, ‘xtable’, ‘dismo’, ‘reshape’, ‘R.utils’, ‘genetics’, ‘rgdal’, ‘gdistance’, ‘mmod’, ‘GGally’, ‘data.table’, ‘raster’, ‘gaston’, ‘gtools’, ‘DEoptimR’, ‘mice’, ‘Rsolnp’, ‘iterators’, ‘generics’, ‘adegenet’, ‘ggplot2’, ‘plyr’, ‘tidyr’, ‘ape’, ‘vegan’, ‘StAMPP’, ‘sp’, ‘PopGenReport’, ‘hierfstat’, ‘robustbase’, ‘gridExtra’, ‘HardyWeinberg’, ‘foreach’, ‘dplyr’
There is a binary version available but the source version is later:
binary source needs_compilation
terra 1.4-22 1.5-12 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/iterators_1.0.13.tgz'
Content type 'application/x-gzip' length 334325 bytes (326 KB)
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downloaded 326 KB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/generics_0.1.1.tgz'
Content type 'application/x-gzip' length 74920 bytes (73 KB)
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downloaded 73 KB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/adegenet_2.1.5.tgz'
Content type 'application/x-gzip' length 2830546 bytes (2.7 MB)
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downloaded 2.7 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggplot2_3.3.5.tgz'
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downloaded 3.9 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/plyr_1.8.6.tgz'
Content type 'application/x-gzip' length 1015776 bytes (991 KB)
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downloaded 991 KB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyr_1.1.4.tgz'
Content type 'application/x-gzip' length 964401 bytes (941 KB)
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downloaded 941 KB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ape_5.6-1.tgz'
Content type 'application/x-gzip' length 3631117 bytes (3.5 MB)
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downloaded 3.5 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vegan_2.5-7.tgz'
Content type 'application/x-gzip' length 3636938 bytes (3.5 MB)
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downloaded 3.5 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/StAMPP_1.6.3.tgz'
Content type 'application/x-gzip' length 132678 bytes (129 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sp_1.4-6.tgz'
Content type 'application/x-gzip' length 2224315 bytes (2.1 MB)
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downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/PopGenReport_3.0.4.tgz'
Content type 'application/x-gzip' length 2087708 bytes (2.0 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/hierfstat_0.5-10.tgz'
Content type 'application/x-gzip' length 469080 bytes (458 KB)
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downloaded 458 KB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/robustbase_0.93-9.tgz'
Content type 'application/x-gzip' length 3141126 bytes (3.0 MB)
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downloaded 3.0 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/gridExtra_2.3.tgz'
Content type 'application/x-gzip' length 1102731 bytes (1.1 MB)
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downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/HardyWeinberg_1.7.4.tgz'
Content type 'application/x-gzip' length 1507500 bytes (1.4 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/foreach_1.5.1.tgz'
Content type 'application/x-gzip' length 133610 bytes (130 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dplyr_1.0.7.tgz'
Content type 'application/x-gzip' length 1263555 bytes (1.2 MB)
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downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dartR_1.9.9.1.tgz'
Content type 'application/x-gzip' length 3002929 bytes (2.9 MB)
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downloaded 2.9 MB
The downloaded binary packages are in
/var/folders/w0/sk8d6yzx1z179g8zxbh6vtj40000gn/T//RtmpEf4Jrp/downloaded_packages
installing the source package ‘terra’
trying URL 'https://cran.rstudio.com/src/contrib/terra_1.5-12.tar.gz'
Content type 'application/x-gzip' length 624884 bytes (610 KB)
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downloaded 610 KB
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: clang -mmacosx-version-min=10.13
configure: CXX: clang++ -mmacosx-version-min=10.13 -std=gnu++11
installing the source package ‘terra’
trying URL 'https://cran.rstudio.com/src/contrib/terra_1.5-12.tar.gz'
Content type 'application/x-gzip' length 624884 bytes (610 KB)
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downloaded 610 KB
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: clang -mmacosx-version-min=10.13
configure: CXX: clang++ -mmacosx-version-min=10.13 -std=gnu++11
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘terra’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/terra’
Warning in install.packages :
installation of package ‘terra’ had non-zero exit status
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/terra’
Warning in install.packages :
installation of package ‘terra’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/w0/sk8d6yzx1z179g8zxbh6vtj40000gn/T/RtmpEf4Jrp/downloaded_packages’
Rajneesh Paliwal, PhD (DAAD Fellow)
Associate Scientist
Genetic Resources Center
International Inst. for Tropical Agriculture
Oyo Road PMB-5320, Ibadan, Nigeria
Jose Luis Mijangos
Jan 13, 2022, 7:54:02 PM1/13/22
to dartR
Hi Rajneesh,
Can you try:
> install.packages("rgdal")
# restart your Rstudio session and then
> devtools::install_github("green-striped-gecko/dartR@beta")
# restart your Rstudio session
> library(dartR)
Cheers,
Luis
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