problem during installing Rswarm and Rvsearch

[lucabate]

hi,
i'm countering issue installing Rswarm (and Rvsearch) :

path <- file.path(tempfile(pattern="Rswarm-"), "Rswarm")
dir.create(path, recursive=TRUE)
repo <- clone("https://github.com/lerch-a/Rswarm.git", path)
cloning into 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc/Rswarm'...
Receiving objects: 1% (1/51), 21 kb
Receiving objects: 11% (6/51), 21 kb
Receiving objects: 21% (11/51), 21 kb
Receiving objects: 31% (16/51), 21 kb
Receiving objects: 41% (21/51), 21 kb
Receiving objects: 52% (27/51), 21 kb
Receiving objects: 62% (32/51), 21 kb
Receiving objects: 72% (37/51), 21 kb
Receiving objects: 82% (42/51), 21 kb
Receiving objects: 92% (47/51), 21 kb
Receiving objects: 100% (51/51), 21 kb, done.
clone("https://github.com/torognes/swarm.git", file.path(path, "src", "swarm"))
cloning into 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc/Rswarm/src/swarm'...
Receiving objects: 1% (43/4233), 63 kb
Receiving objects: 11% (466/4233), 127 kb
Receiving objects: 21% (889/4233), 407 kb
Receiving objects: 31% (1313/4233), 463 kb
Receiving objects: 41% (1736/4233), 575 kb
Receiving objects: 51% (2159/4233), 688 kb
Receiving objects: 61% (2583/4233), 856 kb
Receiving objects: 71% (3006/4233), 1640 kb
Receiving objects: 81% (3429/4233), 2649 kb
Receiving objects: 91% (3853/4233), 3545 kb
Receiving objects: 100% (4233/4233), 3666 kb, done.
Local: master C:/Users/abate/AppData/Local/Temp/RtmpU561F2/Rswarm-25acf6e2dcc/Rswarm/src/swarm
Remote: master @ origin (https://github.com/torognes/swarm.git)
Head: [4bf8bfc] 2021-04-26: revert static_cast removal (compilation errors with GCC 4.8 and 4.9)
install(path)
checking for file 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc\Rswarm/DESCRIPTION' ... checking for file 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc\Rswarm/DESCRIPTION' ... √ checking for file 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc\Rswarm/DESCRIPTION'
- preparing 'Rswarm':
checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... √ checking DESCRIPTION meta-information

• cleaning src
  - checking for LF line-endings in source and make files and shell scripts
  - checking for empty or unneeded directories
  - building 'Rswarm_0.99.1.tar.gz'

Running "C:/PROGRA1/R/R-401.2/bin/x64/Rcmd.exe" INSTALL
"C:\Users\abate\AppData\Local\Temp\RtmpU561F2/Rswarm_0.99.1.tar.gz"
--install-tests

• installing to library 'C:/Users/abate/Documents/R/win-library/4.0' * installing source package 'Rswarm' ... ** using staged installation ** libs aucune DLL n'a pas été créé ERROR: compilation failed for package 'Rswarm' * removing 'C:/Users/abate/Documents/R/win-library/4.0/Rswarm' Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
  System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
  Type .Last.error.trace to see where the error occurred

.Last.error.trace
Stack trace:

1. devtools:::install(path)
2. pkgbuild::with_build_tools(required = FALSE, callr::rcmd("INSTALL", ...
3. withr::with_path(rtools_path(), code)
4. base:::force(code)
5. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
6. callr:::run_r(options)
7. base:::with(options, with_envvar(env, do.call(processx::run, ...
8. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
9. base:::eval(substitute(expr), data, enclos = parent.frame())
10. base:::eval(substitute(expr), data, enclos = parent.frame())
11. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
12. base:::force(code)
13. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
14. (function (command = NULL, args = character(), error_on_status = TRUE, ...
15. throw(new_process_error(res, call = sys.call(), echo = echo, ...
    x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed

Do you know how can I resolve it please.
I'm on W10.

Thanks

[lerch-a]

It looks like you are running HaplotypR on Windows. Rvsearch and Rswarm are difficult to compile on Windows.
Please install the binary package located at
https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip and
https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win.zip .
You should be able to install HaplotypR according to the instruction, after you installed the binary package of Rvsearch and Rswarm.

[lucabate]

ok, thanks De: "Anita Lerch" ***@***.***> À: "lerch-a/HaplotypR" ***@***.***> Cc: "M. Luc Abate" ***@***.***>, "Author" ***@***.***> Envoyé: Vendredi 28 Mai 2021 16:15:31 Objet: Re: [lerch-a/HaplotypR] problem during installing Rswarm and Rvsearch (#16) It looks like you are running HaplotypR on Windows. Rvsearch and Rswarm are difficult to compile on Windows. Please install the binary package located at [ https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip | https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip ] and [ https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win.zip | https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win.zip ] . You should be able to install HaplotypR according to the instruction, after you installed the binary package of Rvsearch and Rswarm. — You are receiving this because you authored the thread. Reply to this email directly, [ #16 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AJQOIESE7P4TLRGYIIFRM3LTP6QQHANCNFSM45WWEU4A | unsubscribe ] .

[lucabate]

Hi Anita, Sorry for disturbing you, I don't know how to install these packages (and yes i'm on windows, sorry for that ;-p ). I tried (on R) :

install.packages('https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip', repos = NULL, type = "win.binary")

Installation du package dans ‘C:/Users/abate/Documents/R/win-library/4.0’ (car ‘lib’ n'est pas spécifié) essai de l'URL 'https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip' Content type 'application/octet-stream' length 2013639 bytes (1.9 MB) downloaded 1.9 MB Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : impossible d'ouvrir la connexion De plus : Warning message: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : impossible d'ouvrir le fichier compressé 'Rvsearch_0.99.1-win/DESCRIPTION', cause probable : 'No such file or directory' also:

library('devtools') #library(git2r) devtools::install_github("lerch-a/Rvsearch")

Downloading GitHub repo lerch-a/Rvsearch@HEAD Erreur : Failed to install 'Rvsearch' from GitHub: Git does not seem to be installed on your system and this (as : [ https://rdrr.io/github/lerch-a/Rvsearch/ | https://rdrr.io/github/lerch-a/Rvsearch/ ] )

install.packages("remotes") remotes::install_github("lerch-a/Rvsearch")

Downloading GitHub repo lerch-a/Rvsearch@HEAD Erreur : Failed to install 'Rvsearch' from GitHub: Git does not seem to be installed on your system. Seem Git is needed but don't know how to resolve this. Thanks. De: "Anita Lerch" ***@***.***> À: "lerch-a/HaplotypR" ***@***.***> Cc: "M. Luc Abate" ***@***.***>, "Author" ***@***.***> Envoyé: Vendredi 28 Mai 2021 16:15:31 Objet: Re: [lerch-a/HaplotypR] problem during installing Rswarm and Rvsearch (#16) It looks like you are running HaplotypR on Windows. Rvsearch and Rswarm are difficult to compile on Windows. Please install the binary package located at [ https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip | https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win.zip ] and [ https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win.zip | https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win.zip ] . You should be able to install HaplotypR according to the instruction, after you installed the binary package of Rvsearch and Rswarm. — You are receiving this because you authored the thread. Reply to this email directly, [ #16 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AJQOIESE7P4TLRGYIIFRM3LTP6QQHANCNFSM45WWEU4A | unsubscribe ] .

[lerch-a]

You need to download them first to you computer, e.g. to "Downloads".
and then
install.packages('path to the binary R package in Downloads on your Computer')

[lucabate]

Hi Anita L., Still not working. I will try on another computer, may be not on windows !

install.packages('C:/Users/abate/Downloads/Rvsearch')

Installation du package dans ‘C:/Users/abate/Documents/R/win-library/4.0’ (car ‘lib’ n'est pas spécifié) Warning message: package ‘C:/Users/abate/Downloads/Rvsearch’ is not available (for R version 4.0.2) thanks. De: "Anita Lerch" ***@***.***> À: "lerch-a/HaplotypR" ***@***.***> Cc: "M. Luc Abate" ***@***.***>, "Author" ***@***.***> Envoyé: Mardi 1 Juin 2021 13:38:51 Objet: Re: [lerch-a/HaplotypR] problem during installing Rswarm and Rvsearch (#16) You need to download them first to you computer, e.g. to "Downloads". and then install.packages('path to the binary R package in Downloads on your Computer') — You are receiving this because you authored the thread. Reply to this email directly, [ #16 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AJQOIEWKDCGH6PZMHZSFMVTTQTBEXANCNFSM45WWEU4A | unsubscribe ] .

[lerch-a]

I see. You need R package version which is compiled with R version 4.0.2.
I do not have access right now to a windows computer, so can not provide you with a newer version.
But I try to write down an instruction how you can compile it yourself.
I have an important deadline coming up and can not work on it in the next few days. So you might need to wait a week.

[lucabate]

Ok, it will be great. Thanks. Good evening. Provenance : Courrier pour Windows 10 De : Anita Lerch Envoyé le :mardi 1 juin 2021 16:30 À : lerch-a/HaplotypR Cc : lucabate; Author Objet :Re: [lerch-a/HaplotypR] problem during installing Rswarm and Rvsearch(#16) I see. You need R package version which is compiled with R version 4.0.2. I do not have access right now to a windows computer, so can not provide you with a newer version. But I try to write down an instruction how you can compile it yourself. I have an important deadline coming up and can not work on it in the next few days. So you might need to wait a week. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[lerch-a]

here the link to new binary package of Rswarm and Rvsearch:
https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win_R-v4.1.zip
https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win_R-v4.1.zip

They were compiled with the newest R version 4.1. Maybe you need to update R.

[lucabate]

Many thanks Anita. Didn't managed to install, probably the problem is from my side. will keep in touch. De: "Anita Lerch" ***@***.***> À: "lerch-a/HaplotypR" ***@***.***> Cc: "M. Luc Abate" ***@***.***>, "Author" ***@***.***> Envoyé: Mardi 8 Juin 2021 13:59:48 Objet: Re: [lerch-a/HaplotypR] problem during installing Rswarm and Rvsearch (#16) here the lint to new binary package of Rswarm and Rvsearch: [ https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win_R-v4.1.zip | https://github.com/lerch-a/Rvsearch/releases/download/v0.99.1/Rvsearch_0.99.1-win_R-v4.1.zip ] [ https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win_R-v4.1.zip | https://github.com/lerch-a/Rswarm/releases/download/v0.99.1/Rswarm_0.99.1-win_R-v4.1.zip ] They were compiled with the newest R version 4.1. Maybe you need to update R. — You are receiving this because you authored the thread. Reply to this email directly, [ #16 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AJQOIEU66XDIYK5J4QB3SO3TRYA3JANCNFSM45WWEU4A | unsubscribe ] .