I've been looking into scanning my Remote conda-forge and cran repositories with JFROG Xray but it seems like it's not natively supported. So naturally if I make a watch the remote-repositories of conda-forge and cran are not available to be scanned.
Has anyone ran into this problem of wanting to scan conda or cran packages in XRAY, fixed it, and would be willing to give a few pointers on how you achieved it?
Conda and Cran scanning is still not supported but is in the near future roadmap of Xray.
Related
I tried to install julia 1.4.2 and 1.6.2 on my machine. Each can be started with the link, but firstly installed version which is 1.6.2 has correct environments generated, while secondly added version 1.4.2 has empty environment in my .julia/environment/ path. And, now I have no way to add packages for version 1.4.2 cause no Pkg is detected from 1.4.2. Did anybody know how to solve this?
I'm writing this because it took me several days to come to this result.
Bottom line: The stringi library version 1.1.3 (released March 2017) might have issues involving icudt. You can install stringi 1.1.2 using the following commands:
packageurl <- "https://cran.r-project.org/src/contrib/Archive/stringi/stringi_1.1.2.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
I put this together from some RStudio documentation on how to install an older package.
Background:
I was trying to install the forecast library in R. Originally, I was using R 3.1.2. I also installed R 3.3.3 and tried to install stringi it. I'm running CentOS 6.7 and don't have a choice to upgrade.
Forecast failed to install due to issues installing stringi. The stringi library failed to install due to errors downloading ICU data library (icudt)
It looks like stringi 1.1.3 added download/build logic regarding icudt, and upcoming version 1.1.4 has corrections to this logic (as of date 2017-04-02).
I went to the ICU project site: and downloaded/installed the ICU library that appeared to be specified in the error messages below:
checking whether we may compile src/icu55/common/umapfile.c... yes
checking whether we may compile src/icu55/common/putil.cpp... yes
checking whether we can fetch icudt... WARNING: ignoring environment value of R_HOME
downloading ICU data library (icudt)
output path: icu55/data/icudt55l.zip
Error in stri_download_icudt("icu55/data") :
could not find function "dir.exists"
Calls: identical -> stri_download_icudt
Execution halted
*** icudt could not be downloaded. stopping.
ERROR: configuration failed for package ‘stringi’
Searches online for icu55, icudt55l.zip, or any procedure that followed to get past this error didn't turn up a procedure that worked. I downloaded, built, and installed ICU 55.1 and also ICU 58.2. I also updated gcc and g++. The CRAN repository install notes for stringi 1.1.3 don't currently give a straightforward set of instructions to successfully install stringi when I have a working internet connection.
I started by asking this as a question and then found my answer. I'll post it anyways. I had added several links but needed to remove them because I don't have enough cred to get away with them.
This has nothing to do with ICU. This is a bug in stringi, which I have already fixed in version 1.1.5 (now on CRAN). The dir.exists() function is specific to R ≥ 3.2.0 - I wasn't aware of that. Sorry for inconvenience.
The stringi library version 1.1.3 (released March 2017) might have issues involving icudt. You can install stringi 1.1.2 using the following commands:
packageurl <- "https://cran.r-project.org/src/contrib/Archive/stringi/stringi_1.1.2.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
I'm trying to learn julia language and I want to install specifically 0.4.2 version of it. When I look at the julia's website, I see that 0.4.3's dmg file is in website, however I was not able to find and download the dmg of 0.4.2 version of julia. How could I do this ?
Yes, you can get it here:
https://s3.amazonaws.com/julialang/bin/osx/x64/0.4/julia-0.4.2-osx10.7+.dmg
Any reason you wanted 0.4.2 rather than the more current 0.4.3?
Installing Rcpp on Linux Ubuntu 12.04, with R2.15.2
NB both R and rcpp were installed yesterday; so I would expect the most recent versions, but Rcpp is installed as an out of date version!
> old.packages()
Package LibPath Installed Built ReposVer
Rcpp "Rcpp" "/usr/lib/R/site-library" "0.9.9" "2.14.1" "0.10.2"
rgl "rgl" "/usr/lib/R/site-library" "0.92.798" "2.12.1" "0.92.894"
Repository
Rcpp "http://www.stats.bris.ac.uk/R/src/contrib"
rgl "http://www.stats.bris.ac.uk/R/src/contrib"
> update.packages("Rcpp")
As the last line shows, it has not updated the package Rcpp at all; What is causing this and what can I do to resolve this?
NB Tried re-installing from two different repositories, both of which claimed to have the most recent version 0.10.2 of rcpp.
Regards
Jefe
You simply misunderstand.
The Rcpp you have is from Ubuntu and installed via apt-get et al. That version is frozen when the distro freezes. This is similar to how gcc, emacs, ... are not the most current version available now but the version taken when the distro was made.
And as an aside, even that Ubuntu version is now dated by one release as 12.10 is out...
So your question title is wrong. The version you have is installed correctly as the version that is part of Ubuntu 12.04. Makes sense now?
Now, if you install Rcpp from CRAN via install.packages() you will get the current version, idem for rgl.
(And there is also a PPA on launchpad which likely to have both as prebuild .deb packages.)
Lastly, and explained before, the path /usr/lib/R/site-library is for the r-cran-* packages you install as .deb files where /usr/local/lib/R/site-library is for your local
installs from R itself. Because of that split, the output of old.packages() that is driven from the former path, eg /usr/lib/R/site-library is bound to behind because it is managed by the distribution, here Ubuntu. You chose the distro for the stability of its components -- and you are free to augment it with CRAN packages in /usr/local/lib/R/site-library. And that is definitely a feature.
Witness this from my Ubuntu box:
R> old.packages(lib.loc="/usr/local/lib/R/site-library/")
NULL
R>
I've installed R in Ubuntu Lucid with the command
sudo aptitude install r-base
When I try to "install.packages" it seems to download source and then spend ages compiling it. How can I get it to just download and install the binaries, like I'm used to on Windows?
Is there any need to compile the packages myself? I'm running inside a VM so it would be great to keep things as slim as possible.
Thanks
CRAN only distributes source for Unix, in other words no binaries are offered (unlike for Windows). So you simply have to compile the packages locally.
That said, we have been working for a few years now on a system to turn CRAN source packages into Debian binary packages -- see cran2deb / debian.cran.r-project.org. We currently build i386 binaries for Debian testing and are in the process of rewriting the backend to offer amd64 for Debian again and then eventually i386 and amd64 for Ubuntu. This already offers well over two-thousand binary packages but not yet for all the flavours we would like to support eventually.
If and when that goal will be accomplished is hard to say; this is a volunteer effort and the main developer (Charles) recently lost his laptop.
CRAN packages are available in the Ubuntu package repository, but are updated with CRAN only when Ubuntu is updated. If you want to use the latest CRAN version of a package and the repository is not at the same version, you will need to go through the compilation/installation procedure.
Details in the Ubuntu R packages can be found on CRAN, which should give you all the information you require.
As this (the provision of binaries) is all volunteer effort on the part of the CRAN maintainers, R Core and other devoted members of the community (e.g. Dirk, Vincent and Michael for the Debian and Ubuntu packages), the main effort has gone into providing binaries for systems where self-compilation is more difficult as the necessary tools are not easily available, unlike on Linux.