leandroroser
commented
3 months ago Hi Katie, let me check this in the next few days and will be back to you soon.
Open daviskec opened 3 months ago
leandroroser
commented
3 months ago Hi Katie, let me check this in the next few days and will be back to you soon.
daviskec
commented
1 month ago Hello, I don't know if you've had a chance to look at this problem since August, but I still can't install EcoGenetics and I'm having a hard time finding functions that do the same things!
Here's the error message: install_github("leandroroser/EcoGenetics-devel") Using GitHub PAT from the git credential store. Downloading GitHub repo leandroroser/EcoGenetics-devel@HEAD 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: glue (1.7.0 -> 1.8.0) [CRAN]
5: xfun (0.47 -> 0.48 ) [CRAN]
6: curl (5.2.2 -> 5.2.3) [CRAN]
7: igraph (2.0.3 -> 2.1.1) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 1 glue (1.7.0 -> 1.8.0) [CRAN] xfun (0.47 -> 0.48 ) [CRAN] curl (5.2.2 -> 5.2.3) [CRAN] igraph (2.0.3 -> 2.1.1) [CRAN] Installing 4 packages: glue, xfun, curl, igraph Installing packages into ‘C:/Users/katie/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/glue_1.8.0.zip' Content type 'application/zip' length 183740 bytes (179 KB) downloaded 179 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/xfun_0.48.zip' Content type 'application/zip' length 560768 bytes (547 KB) downloaded 547 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/curl_5.2.3.zip' Content type 'application/zip' length 3219415 bytes (3.1 MB) downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/igraph_2.1.1.zip' Content type 'application/zip' length 7126500 bytes (6.8 MB) downloaded 6.8 MB
package ‘glue’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘glue’ Warning: restored ‘glue’ package ‘xfun’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘xfun’ Warning: restored ‘xfun’ package ‘curl’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘curl’ Warning: restored ‘curl’ package ‘igraph’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘igraph’ Warning: restored ‘igraph’
The downloaded binary packages are in C:\Users\katie\AppData\Local\Temp\RtmpeecpRa\downloaded_packages ── R CMD build ───────────────────────────────────────────────────────────────────────────────── ✔ checking for file 'C:\Users\katie\AppData\Local\Temp\RtmpeecpRa\remotesb47c1acf24b1\leandroroser-EcoGenetics-devel-84cbc34/DESCRIPTION' ... ─ preparing 'EcoGenetics': ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts (419ms) ─ checking for empty or unneeded directories ─ building 'EcoGenetics_1.2.1-6.tar.gz'
Installing package into ‘C:/Users/katie/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified)
leandroroser
commented
4 weeks ago Hi Katie, I wasn´t able to fix this yet due to other commitments. I hope to have some time next month to fix it.
Leandro
On Fri, Aug 16, 2024 at 3:09 PM Katie Davis @.***> wrote:
Hello,
I was working with the EcoGenetics function genind2ecogen and having issues assigning data to the XY slot so I removed EcoGenetics and attempted to reinstall it to see if that resolved the problem. However I am now unable to install EcoGenetics.
I used the following installation code: remotes::install_github("leandroroser/EcoGenetics-devel")
My current R version is: 4.3.3 Angel Food Cake.
The error message:
`Using GitHub PAT from the git credential store. Downloading GitHub repo @.*** 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 (1.1.3 -> 1.1.4 ) [CRAN] 5: cli (3.6.2 -> 3.6.3 ) [CRAN] 6: Rcpp (1.0.12 -> 1.0.13) [CRAN] 7: fastmap (1.1.1 -> 1.2.0 ) [CRAN] 8: digest (0.6.35 -> 0.6.36) [CRAN] 9: fs (1.6.3 -> 1.6.4 ) [CRAN] 10: cachem (1.0.8 -> 1.1.0 ) [CRAN] 11: promises (1.2.1 -> 1.3.0 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 1 rlang (1.1.3 -> 1.1.4 ) [CRAN] cli (3.6.2 -> 3.6.3 ) [CRAN] Rcpp (1.0.12 -> 1.0.13) [CRAN] fastmap (1.1.1 -> 1.2.0 ) [CRAN] digest (0.6.35 -> 0.6.36) [CRAN] fs (1.6.3 -> 1.6.4 ) [CRAN] cachem (1.0.8 -> 1.1.0 ) [CRAN] promises (1.2.1 -> 1.3.0 ) [CRAN] Installing 8 packages: rlang, cli, Rcpp, fastmap, digest, fs, cachem, promises Installing packages into ‘C:/Users/katie/AppData/Local/R/win-library/4.3’ (as ‘lib’ is unspecified) trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.3/rlang_1.1.4.zip' Content type 'application/zip' length 1580772 bytes (1.5 MB) downloaded 1.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/cli_3.6.3.zip ' Content type 'application/zip' length 1339319 bytes (1.3 MB) downloaded 1.3 MB
trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.3/Rcpp_1.0.13.zip' Content type 'application/zip' length 2886396 bytes (2.8 MB) downloaded 2.8 MB
trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.3/fastmap_1.2.0.zip' Content type 'application/zip' length 133243 bytes (130 KB) downloaded 130 KB
trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.3/digest_0.6.36.zip' Content type 'application/zip' length 220087 bytes (214 KB) downloaded 214 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/fs_1.6.4.zip' Content type 'application/zip' length 409178 bytes (399 KB) downloaded 399 KB
trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.3/cachem_1.1.0.zip' Content type 'application/zip' length 72554 bytes (70 KB) downloaded 70 KB
trying URL ' https://cran.rstudio.com/bin/windows/contrib/4.3/promises_1.3.0.zip' Content type 'application/zip' length 2023307 bytes (1.9 MB) downloaded 1.9 MB
package ‘rlang’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘rlang’ Warning: restored ‘rlang’ package ‘cli’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘cli’ Warning: restored ‘cli’ package ‘Rcpp’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘Rcpp’ Warning: restored ‘Rcpp’ package ‘fastmap’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘fastmap’ Warning: restored ‘fastmap’ package ‘digest’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘digest’ Warning: restored ‘digest’ package ‘fs’ successfully unpacked and MD5 sums checked package ‘cachem’ 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’
The downloaded binary packages are in C:\Users\katie\AppData\Local\Temp\RtmpOqFzIq\downloaded_packages ── R CMD build ──────────────────────────────────────────────────────────────────────────────────── ✔ checking for file 'C:\Users\katie\AppData\Local\Temp\RtmpOqFzIq\remotes3c5cbed31b\leandroroser-EcoGenetics-devel-84cbc34/DESCRIPTION' (536ms) ─ preparing 'EcoGenetics': (481ms) ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts (638ms) ─ checking for empty or unneeded directories ─ building 'EcoGenetics_1.2.1-6.tar.gz'
Installing package into ‘C:/Users/katie/AppData/Local/R/win-library/4.3’ (as ‘lib’ is unspecified)
- installing source package 'EcoGenetics' ... using staged installation libs using Fortran compiler: 'GNU Fortran (GCC) 12.3.0' gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c geoddist.f -o geoddist.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c geodistv.f -o geodistv.o gcc -shared -s -static-libgcc -o EcoGenetics.dll tmp.def geoddist.o geodistv.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LC:/PROGRA1/R/R-431.3/bin/x64 -lR installing to C:/Users/katie/AppData/Local/R/win-library/4.3/00LOCK-EcoGenetics/00new/EcoGenetics/libs/x64 R data * moving datasets to lazyload DB Creating a generic function for 'nrow' from package 'base' in package 'EcoGenetics' Creating a generic function for 'ncol' from package 'base' in package 'EcoGenetics' Error : in method for 'ecoslot.XY<-' with signature 'object="ecogen"': arguments ('value') after '...' in the generic must appear in the method, in the same place at the end of the argument list Warning: namespace 'EcoGenetics' is not available and has been replaced by .GlobalEnv when processing object 'my_ecopop' Creating a generic function for 'nrow' from package 'base' in package 'EcoGenetics' Creating a generic function for 'ncol' from package 'base' in package 'EcoGenetics' Error : in method for 'ecoslot.XY<-' with signature 'object="ecogen"': arguments ('value') after '...' in the generic must appear in the method, in the same place at the end of the argument list Warning: namespace 'EcoGenetics' is not available and has been replaced by .GlobalEnv when processing object 'my_ecopop' inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'nrow' from package 'base' in package 'EcoGenetics' Creating a generic function for 'ncol' from package 'base' in package 'EcoGenetics' Error : in method for 'ecoslot.XY<-' with signature 'object="ecogen"': arguments ('value') after '...' in the generic must appear in the method, in the same place at the end of the argument list Error: unable to load R code in package 'EcoGenetics' Execution halted ERROR: lazy loading failed for package 'EcoGenetics'
- removing 'C:/Users/katie/AppData/Local/R/win-library/4.3/EcoGenetics' Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\katie\AppData\Local\R\win-library\4.3\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\katie\AppData\Local\R\win-library\4.3\rlang\libs\x64\rlang.dll: Permission denied 2: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\katie\AppData\Local\R\win-library\4.3\00LOCK\cli\libs\x64\cli.dll to C:\Users\katie\AppData\Local\R\win-library\4.3\cli\libs\x64\cli.dll: Permission denied 3: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\katie\AppData\Local\R\win-library\4.3\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Users\katie\AppData\Local\R\win-library\4.3\Rcpp\libs\x64\Rcpp.dll: Permission denied 4: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\katie\AppData\Local\R\win-library\4.3\00LOCK\fastmap\libs\x64\fastmap.dll to C:\Users\katie\AppData\Local\R\win-library\4.3\fastmap\libs\x64\fastmap.dll: Permission denied 5: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\katie\AppData\Local\R\win-library\4.3\00LOCK\digest\libs\x64\digest.dll to C:\Users\katie\AppData\Local\R\win-library\4.3\digest\libs\x64\digest.dll: Permission denied 6: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\katie\AppData\Local\R\win-library\4.3\00LOCK\promises\libs\x64\promises.dll to C:\Users\katie\AppData\Local\R\win-library\4.3\promises\libs\x64\promises.dll: Permission denied 7: In i.p(...) : installation of package ‘C:/Users/katie/AppData/Local/Temp/RtmpOqFzIq/file3c5c60f43dda/EcoGenetics_1.2.1-6.tar.gz’ had non-zero exit status`
Thanks in advance for the help!
— Reply to this email directly, view it on GitHub https://github.com/leandroroser/EcoGenetics-devel/issues/12, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSFKREITHBM3HSI2GBGL7LZRY53ZAVCNFSM6AAAAABMUPSKWKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ3TANZTGA3TENQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hello,
I was working with the EcoGenetics function
genind2ecogenand having issues assigning data to the XY slot so I removed EcoGenetics and attempted to reinstall it to see if that resolved the problem. However I am now unable to install EcoGenetics.I used the following installation code:
remotes::install_github("leandroroser/EcoGenetics-devel")My current R version is: 4.3.3 Angel Food Cake.
The error message:
Thanks in advance for the help!