EDIT: The problem ended up to be that TERR 5.1.0 is actually based on R 3.6. and therefore Rtools35 was needed. The second problem was that I was trying to install the packages to a network location that was set as default for Rstudio due to the fact that it is installed within Parallels VM.
I've been struggling with this problem for the last few days. There are many posts on how to solve issues with rtools40, and I read everything I could find, but it still didn't solve this issue. It could be that the issue stems from the fact that I have to use Rstudio and TERR (TIBCO Enterprise Runtime for R =) and not R, and also everything is run within Parallels VM.
When installing a package (in this case it's Vegan, but also tried devtools, tidyverse and others) I get these are the errors:
> install.packages("vegan", verbose = TRUE)
also installing the dependencies 'lattice' 'Matrix' 'nlme' 'mgcv' 'cluster' 'MASS' 'permute'
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/lattice_0.20-41.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/lattice_0.20-41.zip'
Downloaded 1174416 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/Matrix_1.2-18.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/Matrix_1.2-18.zip'
Downloaded 4523013 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/nlme_3.1-149.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/nlme_3.1-149.zip'
Downloaded 2378266 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/mgcv_1.8-33.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/mgcv_1.8-33.zip'
Downloaded 3315098 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/cluster_2.1.0.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/cluster_2.1.0.zip'
Downloaded 593835 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/MASS_7.3-52.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/MASS_7.3-52.zip'
Downloaded 1191263 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/permute_0.9-5.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/permute_0.9-5.zip'
Downloaded 507227 bytes
Trying to download URL 'https://cloud.r-project.org/bin/windows/contrib/3.6/vegan_2.5-6.zip' to file 'C:\TEMP\TERR_06cc00291/downloaded_packages/vegan_2.5-6.zip'
Downloaded 3846550 bytes
* installing *binary* package lattice from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\lattice_0.20-41.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no lattice/MD5 file)
* installing *binary* package Matrix from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\Matrix_1.2-18.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no Matrix/MD5 file)
* installing *binary* package nlme from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\nlme_3.1-149.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no nlme/MD5 file)
* installing *binary* package mgcv from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\mgcv_1.8-33.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no mgcv/MD5 file)
* installing *binary* package cluster from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\cluster_2.1.0.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no cluster/MD5 file)
* installing *binary* package MASS from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\MASS_7.3-52.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no MASS/MD5 file)
* installing *binary* package permute from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\permute_0.9-5.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no permute/MD5 file)
* installing *binary* package vegan from "C:\\TEMP\\TERR_06cc00291\\downloaded_packages\\vegan_2.5-6.zip" to "\\\\Mac\\Home\\Documents\\TERR\\x86_64-w64-mingw32-library\\5.1"
'\\Mac\Home\Documents\TERR\x86_64-w64-mingw32-library\5.1'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* checking MD5 checksums
COULD NOT CHECK MD5 CHECKSUMS (probably no vegan/MD5 file)
This is my version info:
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 6.2
year 2020
month 05
day 20
svn rev 77560
language TERR
version.string TIBCO Enterprise Runtime for R version 5.1.0
(2020-05-20)
nickname Hale Hydra
TERR.version 5.1.0
TERR.edition Developer Edition
TERR.svn.rev 25477
build V131
compiler Intel
compiler.version Intel(R) C++ Intel(R) 64 Compiler XE for
applications running on Intel(R) 64, Version
15.0.3.208 Build 20150407
compiler.flags /W3 /Qdiag-error:63 /EHsc /D_SECURE_SCL=0 /MT /O3
/Qipo /Qinline-factor=100 /DNDEBUG
configuration Release
os.printable Microsoft Windows
use.mkl TRUE
use.openmp TRUE
And this is the output from several sys.which commands:
Sys.getenv('PATH')
[1] "C:\\rtools40\\usr\\bin;C:\\Program Files\\TIBCO\\terrde51\\bin\\x64;C:\\Program Files (x86)\\Parallels\\Parallels Tools\\Applications;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Windows\\System32\\OpenSSH\\;${RTOOLS40_HOME}\\usr\\bin;C:\\rtools40\\mingw32\\bin;C:\\Users\\adi\\AppData\\Local\\Microsoft\\WindowsApps;"
> system('where make')
C:\rtools40\usr\bin\make.exe
> Sys.which("ls.exe")
ls.exe
"C:\\rtools40\\usr\\bin\\ls.exe"
> Sys.which("gcc.exe")
gcc.exe
"C:\\rtools40\\mingw32\\bin\\gcc.exe"
I also tried changing the mingw32 to mingw64.
I would appreciate any suggestion as to how this can be solved!
You have the wrong version of Rtools.
From https://cloud.r-project.org/bin/windows/Rtools/:
This documentation is about rtools40, the current version used for R 4.0.0 and newer. For information about previous versions of Rtools that can be used with R 3.6.3 or older, please visit this page.
You have two ways to remedy this:
Upgrade R to be R-4.0 or newer. You might uninstall R-3.6 if you choose, but as long as your tools use the correct version of R-4 or newer, then it doesn't matter (you can have parallel version of R typically without much problem).
Downgrade to Rtools35. While you can keep Rtools40 around, you'll need to make sure that the PATH that R sees does not include Rtools40, which can be accomplished in the system configuration on env-vars, in your ~/.Rprofile/~/.Renviron, or in a project-specific version of those two files. (Or manually, every ... time ... you ... start ... R.)
It sounds like it's a computer on which you have control and admin rights, so unless you have reason to stay on R-3.6.2 (e.g., compatibility with others' systems, or your projects are not yet tested on R-4) then I'd recommend option 1.