gl.run.structure output files not saving
32 views
Skip to first unread message
Emily Rush
Jul 31, 2025, 7:26:40 PMJul 31
to dartR
Hello,
I have been running Structure in R and thought everything was running okay (for a few months). I can plot evanno and view the gl.plot.structure plots fine using the below code.
structure_north_noadmix1 <- gl.run.structure(subsampled_north1, k.range = 1:10, num.k.rep = 5, exec = 'C:/Users/errus/Desktop/structure/structure.exe', noadmix=TRUE, burnin = 10000, numreps = 10000)
# Round 1: evanno plots
gl.evanno(structure_north_noadmix1)
# Round 1: view STRUCTURE plot - change k for different results
gl.plot.structure(structure_north_noadmix1, K=10, clumpak = FALSE)
# Round 1: evanno plots
gl.evanno(structure_north_noadmix1)
# Round 1: view STRUCTURE plot - change k for different results
gl.plot.structure(structure_north_noadmix1, K=10, clumpak = FALSE)
It wasn't until yesterday that I wanted to start making plots for publication that I realised I am not getting the correct output files saved on my computer. I only had three saved to the working directory on a rerun yesterday, these were:...structureRun.k1; ...r1_extraparams and ....r1_mainparams.
I read that maybe this was because I should be saving directly into the structure folder (where the executable is) on my desktop, so I changed this but then I got no output at all. I cannot find any more 'gtypes' file folders on my computer, other than those created in March back when I first started using the program.
I read that maybe this was because I should be saving directly into the structure folder (where the executable is) on my desktop, so I changed this but then I got no output at all. I cannot find any more 'gtypes' file folders on my computer, other than those created in March back when I first started using the program.
I do get this error when I looked to see if the program was executing properly:
system("C:/Users/errus/Desktop/structure/structure.exe", intern = TRUE) [1] ""
[2] ""
[3] "----------------------------------------------------"
[4] "STRUCTURE by Pritchard, Stephens and Donnelly (2000)"
[5] " and Falush, Stephens and Pritchard (2003)"
[6] " Code by Pritchard, Falush and Hubisz"
[7] " Version 2.3.4 (Jul 2012)"
[8] "----------------------------------------------------"
[9] ""
[10] ""
[11] "Can't open the file \"mainparams\"."
[12] ""
[13] "Exiting the program due to error(s) listed above."
[14] ""
attr(,"status")
[1] 1Warning message:
In system("C:/Users/errus/Desktop/structure/structure.exe", intern = TRUE) :
running command 'C:/Users/errus/Desktop/structure/structure.exe' had status 1
[2] ""
[3] "----------------------------------------------------"
[4] "STRUCTURE by Pritchard, Stephens and Donnelly (2000)"
[5] " and Falush, Stephens and Pritchard (2003)"
[6] " Code by Pritchard, Falush and Hubisz"
[7] " Version 2.3.4 (Jul 2012)"
[8] "----------------------------------------------------"
[9] ""
[10] ""
[11] "Can't open the file \"mainparams\"."
[12] ""
[13] "Exiting the program due to error(s) listed above."
[14] ""
attr(,"status")
[1] 1Warning message:
In system("C:/Users/errus/Desktop/structure/structure.exe", intern = TRUE) :
running command 'C:/Users/errus/Desktop/structure/structure.exe' had status 1
Hoping you can help. I did try "delete.files = FALSE" that I saw in another question on here but I got an error.
Thank you,
Emily
Jose Luis Mijangos
Jul 31, 2025, 8:07:37 PMJul 31
to dartR
Hi Emily,
Could you please install the development version of dartR.popgen as shown below, and then run the rest of the code? Please let us know if that doesn’t work, and we’ll work out an alternative solution.
# Install development version of dartR.popgen
devtools::install_github("green-striped-gecko/dartR.popgen@dev")
library(dartRverse)
x <- platypus.gl
r1 <- gl.run.structure(x,
exec = "./structure",
k.range = 2:4,
num.k.rep = 1,
delete.files = FALSE
)
Before installing, make sure you:
1. Have R version ≥ 4.4.2. If not, follow these instructions: [https://www.danieldsjoberg.com/updater/index.html](https://www.danieldsjoberg.com/updater/index.html)
2. Clear your RStudio environment (Menu ▸ Session ▸ Clear Workspace).
3. Restart your R session (Menu ▸ Session ▸ Restart R).
4. Confirm that, when installation finishes, the final message is `* DONE (dartR.popgen)`.
Sometimes Google Groups alters quotation marks in R code, so please double-check that the quotes are correct.
Cheers,
Luis
Could you please install the development version of dartR.popgen as shown below, and then run the rest of the code? Please let us know if that doesn’t work, and we’ll work out an alternative solution.
# Install development version of dartR.popgen
devtools::install_github("green-striped-gecko/dartR.popgen@dev")
library(dartRverse)
x <- platypus.gl
r1 <- gl.run.structure(x,
exec = "./structure",
k.range = 2:4,
num.k.rep = 1,
delete.files = FALSE
)
Before installing, make sure you:
1. Have R version ≥ 4.4.2. If not, follow these instructions: [https://www.danieldsjoberg.com/updater/index.html](https://www.danieldsjoberg.com/updater/index.html)
2. Clear your RStudio environment (Menu ▸ Session ▸ Clear Workspace).
3. Restart your R session (Menu ▸ Session ▸ Restart R).
4. Confirm that, when installation finishes, the final message is `* DONE (dartR.popgen)`.
Sometimes Google Groups alters quotation marks in R code, so please double-check that the quotes are correct.
Cheers,
Luis
Emily Rush
Aug 3, 2025, 7:01:06 PMAug 3
to dartR
Hi Luis,
Thanks you for your response. I had tried installing that dev package previously but unfortunately just got errors. I have followed your advice at the bottom with closing and restarting but still get the same issue.
I am using R version 4.5.0 and I uninstalled the dartR.popgen I had in place previously prior to trying to install the development version.
When I run this:
# Install development version of dartR.popgen
devtools::install_github("green-striped-gecko/dartR.popgen@dev")It tells me that updates are available (for 22 packages), I have tried runing with no updates and all updates but the result is the same.
The final error after selecting to update packages is this:
The downloaded binary packages are in
C:\Users\errus\AppData\Local\Temp\RtmpULjSPf\downloaded_packages
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\errus\AppData\Local\Temp\RtmpULjSPf\remotes90981ea2985\green-striped-gecko-dartR.popgen-8c96f12/DESCRIPTION' ...
─ preparing 'dartR.popgen': (1.7s)
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts (407ms)
─ checking for empty or unneeded directories
─ building 'dartR.popgen_1.0.6.tar.gz' (921ms)
Installing package into ‘C:/Users/errus/AppData/Local/R/win-library/4.5’
(as ‘lib’ is unspecified)
ERROR: dependency 'LEA' is not available for package 'dartR.popgen'
Perhaps try a variation of:
install.packages('LEA')
* removing 'C:/Users/errus/AppData/Local/R/win-library/4.5/dartR.popgen'Warning messages:
1: package ‘LEA’ is not available for this version of R
A version of this package 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
2: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\Rcpp\libs\x64\Rcpp.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\promises\libs\x64\promises.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\promises\libs\x64\promises.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\purrr\libs\x64\purrr.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\purrr\libs\x64\purrr.dll: Permission denied
5: In i.p(...) :
installation of package ‘C:/Users/errus/AppData/Local/Temp/RtmpULjSPf/file90984a327127/dartR.popgen_1.0.6.tar.gz’ had non-zero exit status
> library(dartRverse)
Is there an alternative option? Would uninstalling Structure and then reinstalling help fix the saving issue or is it a common problem?
Thank you,
Emily
Jose Luis Mijangos
Aug 3, 2025, 9:37:28 PMAug 3
to dartR
Hi Emily,
Can you please try installing the two below packages from BiocManager as shown below and then please try installing again dartRverse as mentioned before.
install.packages("BiocManager")
BiocManager::install("SNPRelate")
BiocManager::install("LEA")
BiocManager::install("SNPRelate")
BiocManager::install("LEA")
Cheers,
Luis
Emily Rush
Aug 4, 2025, 1:18:07 AMAug 4
to dartR
Hi Luis, thank you. I have copied from the console below so that you can see the process and issues.
BiocManager installed, SNPRelate was an issue so i tried to force it to overwrite previous versions with no luck. LEA also looked to unpack and then at the end said permission was denied.
###Tried again to install SNPRelate
BiocManager::install("SNPRelate, force = TRUE")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.0 (2025-04-11 ucrt)
Installing package(s) 'SNPRelate, force = TRUE'
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.5.0/library
packages:
lattice, mgcv
Old packages: 'bigassertr', 'bigutilsr', 'broom', 'cowplot', 'curl', 'dendextend', 'DEoptimR', 'directlabels',
'emmeans', 'FactoMineR', 'gdsfmt', 'GGally', 'ggstats', 'glmnet', 'haven', 'httr2', 'maps', 'mice',
'openssl', 'pbkrtest', 'pcadapt', 'pheatmap', 'plotly', 'promises', 'purrr', 'Rcpp', 'rnaturalearth',
'rprojroot', 'Rsolnp', 'waldo'Update all/some/none? [a/s/n]:
a
also installing the dependency ‘future.apply’trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/future.apply_1.20.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/bigassertr_0.1.7.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/bigutilsr_0.3.11.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/broom_1.0.9.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/cowplot_1.2.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/curl_6.4.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/dendextend_1.19.1.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/DEoptimR_1.1-4.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/directlabels_2025.6.24.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/emmeans_1.11.2.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/FactoMineR_2.12.zip'
trying URL 'https://bioconductor.org/packages/3.21/bioc/bin/windows/contrib/4.5/gdsfmt_1.44.1.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/GGally_2.3.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/ggstats_0.10.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/glmnet_4.1-10.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/haven_2.5.5.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/httr2_1.2.1.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/maps_3.4.3.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/mice_3.18.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/openssl_2.3.3.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/pbkrtest_0.5.5.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/pcadapt_4.4.1.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/pheatmap_1.0.13.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/plotly_4.11.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/promises_1.3.3.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/purrr_1.1.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/Rcpp_1.1.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/rnaturalearth_1.1.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/rprojroot_2.1.0.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/Rsolnp_2.0.1.zip'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/waldo_0.6.2.zip'
package ‘future.apply’ successfully unpacked and MD5 sums checked
package ‘bigassertr’ successfully unpacked and MD5 sums checked
package ‘bigutilsr’ successfully unpacked and MD5 sums checked
package ‘broom’ successfully unpacked and MD5 sums checked
package ‘cowplot’ successfully unpacked and MD5 sums checked
package ‘curl’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘curl’
Warning: restored ‘curl’
package ‘dendextend’ successfully unpacked and MD5 sums checked
package ‘DEoptimR’ successfully unpacked and MD5 sums checked
package ‘directlabels’ successfully unpacked and MD5 sums checked
package ‘emmeans’ successfully unpacked and MD5 sums checked
package ‘FactoMineR’ successfully unpacked and MD5 sums checked
package ‘gdsfmt’ successfully unpacked and MD5 sums checked
package ‘GGally’ successfully unpacked and MD5 sums checked
package ‘ggstats’ successfully unpacked and MD5 sums checked
package ‘glmnet’ successfully unpacked and MD5 sums checked
package ‘haven’ successfully unpacked and MD5 sums checked
package ‘httr2’ successfully unpacked and MD5 sums checked
package ‘maps’ successfully unpacked and MD5 sums checked
package ‘mice’ successfully unpacked and MD5 sums checked
package ‘openssl’ successfully unpacked and MD5 sums checked
package ‘pbkrtest’ successfully unpacked and MD5 sums checked
package ‘pcadapt’ successfully unpacked and MD5 sums checked
package ‘pheatmap’ successfully unpacked and MD5 sums checked
package ‘plotly’ successfully unpacked and MD5 sums checked
package ‘promises’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘promises’
Warning: restored ‘promises’
package ‘purrr’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘purrr’
Warning: restored ‘purrr’
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
Warning: restored ‘Rcpp’
package ‘rnaturalearth’ successfully unpacked and MD5 sums checked
package ‘rprojroot’ successfully unpacked and MD5 sums checked
package ‘Rsolnp’ successfully unpacked and MD5 sums checked
package ‘waldo’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\errus\AppData\Local\Temp\RtmpULjSPf\downloaded_packages
Warning messages:
1: package ‘SNPRelate, force = TRUE’ is not available for Bioconductor version '3.21'
A version of this package 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
2: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\curl\libs\x64\curl.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\curl\libs\x64\curl.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\promises\libs\x64\promises.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\promises\libs\x64\promises.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\purrr\libs\x64\purrr.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\purrr\libs\x64\purrr.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\errus\AppData\Local\R\win-library\4.5\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Users\errus\AppData\Local\R\win-library\4.5\Rcpp\libs\x64\Rcpp.dll: Permission denied
library(dartRverse)
Reply all
Reply to author
Forward
0 new messages