I am trying to an install R package for LTRpred, not available on CRAN, but only on GitHub, as follows:
library(devtools)
devtools::install_github("HajkD/LTRpred", args = c('--library="/home/aksr/software_downloads/R"'))
After some time, and hundreds of lines of STDOUT, that appeared like several updates / installs (of dependencies) were happening, it ended with this error message:
Installing package into ‘/home/aksr/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
ERROR: dependency ‘ggbio’ is not available for package ‘LTRpred’
* removing ‘/home/aksr/R/x86_64-pc-linux-gnu-library/3.6/LTRpred’
Error: Failed to install 'LTRpred' from GitHub:
(converted from warning) installation of package ‘/tmp/RtmphWCa63/file76071968d246/LTRpred_1.1.0.tar.gz’ had non-zero exit status
Another syntax variant also failed, as follows:
devtools::install_github("HajkD/LTRpred", args = '-l "/home/aksr/software_downloads/R"')
Downloading GitHub repo HajkD/LTRpred@master
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: R.methodsS3 (1.8.0 -> 1.8.1 ) [CRAN]
5: R.oo (1.23.0 -> 1.24.0) [CRAN]
# Option 3 chosen
Enter one or more numbers, or an empty line to skip updates:3
✔ checking for file ‘/tmp/Rtmpiub65q/remotesc5e63a461ae/HajkD-LTRpred-71a4a38/DESCRIPTION’ (1s)
─ preparing ‘LTRpred’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘LTRpred_1.1.0.tar.gz’
Installing package into ‘/home/aksr/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
ERROR: dependency ‘ggbio’ is not available for package ‘LTRpred’
* removing ‘/home/aksr/R/x86_64-pc-linux-gnu-library/3.6/LTRpred’
Error: Failed to install 'LTRpred' from GitHub:
(converted from warning) installation of package ‘/tmp/Rtmpiub65q/filec5e19e6e138/LTRpred_1.1.0.tar.gz’ had non-zero exit status
Error in validate_signal_args(msg, type, call, .subclass) :
unused arguments (call, .subclass)
Have my installation attempts failed, because of lack of root privileges on a multi-user HPCC, or because some (7 packages) dependencies are not available for this version of R version 3.6.3 (2020-02-29) -- "Holding the Windsock" , or both?
BTW, the syntax variants I've tried (shown above, as well as NOT shown above) are all from this stackoverflow post.
For CRAN packages, executing install.packages('package', lib="/my/chosen/local/path") is so simple. Isn't there an equivalent for install_github or some variant thereof? I hope this is a correct forum to seek help for my problem, and to get a successful install ASAP. Thanks, in advance!
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.3.0 usethis_1.6.1
loaded via a namespace (and not attached):
[1] magrittr_1.5 pkgload_1.1.0 R6_2.4.1 rlang_0.4.7
[5] fansi_0.4.1 tools_3.6.3 pkgbuild_1.1.0 sessioninfo_1.1.1
[9] cli_2.0.2 withr_2.2.0 ellipsis_0.3.1 remotes_2.2.0
[13] assertthat_0.2.1 digest_0.6.25 rprojroot_1.3-2 crayon_1.3.4
[17] processx_3.4.3 callr_3.4.3 fs_1.5.0 ps_1.3.4
[21] curl_4.3 testthat_2.3.2 memoise_1.1.0 glue_1.4.1
[25] compiler_3.6.3 desc_1.2.0 backports_1.1.9 prettyunits_1.1.1
Oh, and I don't understand the part about installing to a local dir? That's not your problem, regardless, and you can set that using
.libPathsanyway, and if you don't have a local library dir,BiocManageris gonna ask you if you want to set one up and will do it for you. So I would do it one of the regular ways rather than trying to getinstall_githubto do your bidding.You're on a roll today James
My sincere apologies for mis-posting here. But thank you SO VERY MUCH for your help. These 2 lines worked for my install, I think, though with order of magnitude (~ 3.2K lines) more content in my STDOUT. It ended with
My concern is with the part that reads -
Installation path not writeableHowever, loading the package does not return an error
And I can see the help menu using
I still need to install a couple of non-R dependencies, and then I'l run a small and quick test.
Once again, thanks a TON! :) And sorry for any trouble....
If you are a non-privileged user on Linux and you are using a system-wide install of R, then the library dir for the packages that come with R will be a directory in which you have no write privileges. So you won't be able to update things like MASS or mgcv or nlme or survival, because you don't have the privileges to do so. Which is what that note is telling you.