search for: install_packages

Hi, i want to use Puppet to install all packages from a webserver (no repository) . Therefore I wrote following Script: class install_package { case "$operatingsystem" { SLES: { notify {"${operatingsystem} ${operatingsystemrelease} detected":} notify {"Installing $packagename now:":}

...;errmsg" * removing ?/home/example/R/x86_64-pc-linux-gnu-library/3.4/samplepackage? It should instead be using that errmsg() function to print the more helpful error message: "invalid value of LazyData field in DESCRIPTION". I've traced it down to this line of code in tools:::.install_packages() https://github.com/wch/r-source/blob/trunk/src/library/tools/R/install.R#L977 . The errmsg() function actually is defined earlier on in the function, but there seems to be a scoping issue that makes it not available here. I've uploaded a sample project to reproduce the bug here: https://gith...

I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. [1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi" Browse[2]> dir(new) [1] "DESCRIPTION"...

Not much progress..... I step through debug and it gets to the do.install() function which immediately errors with the same "configuration not executable" error. So, made a tempfunc that was a copy of tools:::.install_packages and edited the file_test("-x","configure") line to return a TRUE now I get a Permission Denied error (even if I run as root) > tempfunc("/home/meconk/stringi_1.1.5.tar.gz") * installing to library '/usr/lib64/R/library' * installing *source* package 's...

...================================= downloaded 15 Kb trying URL 'http://cran.sixsigmaonline.org/src/contrib/R.oo_1.6.6.tar.gz' Content type 'application/x-gzip' length 361830 bytes (353 Kb) opened URL ================================================== downloaded 353 Kb > tools:::.install_packages() * installing *source* package ?R.methodsS3? ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... * DONE (R.methodsS3) > > tools:::.install_packages() * installing *source* package ?R.oo? ... ** R ** inst ** preparing pack...

...-x","configure") line, then print my working directory, and ctrl-Z out of R to look at the files there. That should confirm that configure is not executable. Then the hard part is figuring out why it isn't.... Duncan > > So, made a tempfunc that was a copy of tools:::.install_packages and edited the file_test("-x","configure") line to return a TRUE > > now I get a Permission Denied error (even if I run as root) > >> tempfunc("/home/meconk/stringi_1.1.5.tar.gz") > * installing to library '/usr/lib64/R/library' > * install...

On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. I don't know what is causing this bug. Perhaps a Linux user can reproduce it and fix it. Here's what I s...

Duncan Murdoch writes: > On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. > > I don't know what is causing this bug. Perhaps a Linux user can > reproduce it and fix it. &...

Hi, Having finally gotten around to installing R-2.9.0, I find that while the docs still say I can invoke the --no-latex option, R CMD INSTALL has decided that I can't. Nor is there any notice of this that I can find in the 2.9 series news. Is this just a trifling oversight that will be repaired? Jim

Hello, I've looked in tools:::.install_packages for some sort of hook that would let packages developers point to further instructions after a package is installed. For example, some packages need to setup environment variables, ... Is there something I have missed ? Romain -- Romain Francois Independent R Consultant +33(0) 6 28 91 30 30...

I was trying to ByteCompile a package that I made. The package compiles successfully with byte compile set to FALSE. When I set ByteCompile to TRUE, I receive the following error message while doing R CMD INSTALL /usr/lib/R/bin/INSTALL: line 34: 9964 Done echo 'tools:::.install_packages()' 9965 Segmentation fault | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} I have not been able to understand the problem. Can someone help me understand the problem so that it can be fixed? Thanks, Mayank ________________________________ This e...

...TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))}) 29: try(.install_package_indices(".", instdir)) 30: do_install_source(pkg_name, instdir, pkg, desc) 31: do_install(pkg) 32: tools:::.install_packages() aborting ... Segmentation Fault - core dumped The downloaded packages are in '/tmp/RtmpVwIBsr/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages("Matrix") : installation of package 'Matrix' had non-z...

...runs a separate process to do the installs. If you want to track this down you can debug the code as follows. 1. Manually download the tarball, using any method (perhaps download.packages("stringi", destdir = ".", type = "source"). 2. In R, run debug(tools:::.install_packages) tools:::.install_packages("stringi_1.1.5.tar.gz") You can single step until you see the message, and try to diagnose why it is happening. Watch out, this function will exit R at the end. Duncan Murdoch > [meconk at dcex1102shinypr ~]$ ls -l stringi/configure > -rwxr-xr-x 1 mec...

...------------------ diff --git a/src/scripts/INSTALL b/src/scripts/INSTALL index 42470c2...4c7bae9 100755 --- a/src/scripts/INSTALL +++ b/src/scripts/INSTALL @@ -9,4 +9,4 @@ while test -n "${1}"; do done ## NB: Apple's ICU needs LC_COLLATE set when R is started. -echo 'tools:::.install_packages()' | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --slave --args ${args} +echo 'tools:::.install_packages()' | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --vanilla --slave --args ${args} diff --git a/src/scripts/REMOVE b/src/scripts/REMOVE...

...Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))}) 16: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))) 17: do_install_source(pkg_name, instdir, pkg, desc) 18: do_install(pkg) 19: tools:::.install_packages() aborting ... /usr/local/lib64/R/bin/INSTALL: line 34: 26393 Done echo 'tools:::.install_packages()' 26394 Segmentation fault (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} The downloaded packages are in ?/tmp/Rtmpbi9cKk/downloa...

....com] Sent: Thursday, June 22, 2017 6:18 PM To: Duncan Murdoch Cc: Conklin, Mike (GfK); Martin Maechler; r-help at r-project.org Subject: Re: [R] Missing dependencies in pkg installs Duncan Murdoch writes: > On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. > > I don't know what is causing this bug. Perhaps a Linux user can > reproduce it and fix it. &gt...

...rary/ DELETE,ISDIR 00LOCK-abc IIUC the new 'MOVED_TO,ISDIR abc' event is triggered by the package installation folder being moved from the temporary location to the final location. However I wonder about the CREATE,ISDIR abc event. It looks like even for a staged installation tools:::.install_packages() still creates the empty abc dir. This should no longer be necessary because this empty folder is replaced later by the 'MOVED_TO,ISDIR abc' event. Am I missing something? Another thing: the times indicate that the 'MOVED_TO,ISDIR abc' event (move from temp to final location)...

Following Duncan's instructions I find that the system and R find that configure IS executable but if trying to install via install.packages I get the same error. I also tried using R CMD INSTALL from the terminal and install.packages with a local file pointing to the very same tar.gz file that shows the executable bit set. All result in the same "configure is not executable" result.

...home/example/R/x86_64-pc-linux-gnu-library/3.4/samplepackage? > It should instead be using that errmsg() function to print the more > helpful error message: "invalid value of LazyData field in DESCRIPTION". > I've traced it down to this line of code in tools:::.install_packages() > https://github.com/wch/r-source/blob/trunk/src/library/tools/R/install.R#L977 > . The errmsg() function actually is defined earlier on in the function, > but there seems to be a scoping issue that makes it not available here. > I've uploaded a sample project to...

> Turns out that RStudio replaces the install.packages object in the utils > package. > Duncan Murdoch So RStudio unlocks the bindings and alters the exported environment? That seems like another reason to stick to the terminal interface. >> Thank you. tools:::.install_packages works. > I'm glad it works, but it shouldn't be necessary to use (and is not > part of the API: not documented to keep working this way). > Best regards, > Ivan [Krylov] Thank you for letting me know. I hope I can avoid using private functions in future. As noted below, my fun...