solve centos_install() failing to change root dir for non-root via dnf system call
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added 6 commits
November 19, 2022 15:49
philipp-baumann
changed the title
centos_install() fails to change root dir for non-root via dnf system callcentos_install() failing to change root dir for non-root via dnf system call
r$> remotes::install_github("spectral-cockpit/rspm", ref = "fix/centos-non-root", force = TRUE)This seems to bootstrap missing r$> library("rspm")
enable()
Downloading and installing required utilities...
Not root, Subscription Management repositories not updated
This system is not registered with an entitlement server. You can use subscription-manager to register.
Last metadata expiration check: 10:57:24 ago on Sa 19 Nov 2022 11:59:47 CET.
patchelf-0.12-1.el8.x86_64.rpm 1.8 MB/s | 88 kB 00:00
391 blocks
Tracing function "install.packages" in package "utils"
Tracing function "update.packages" in package "utilsr$> library(rspm)
r$> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os Rocky Linux 8.7 (Green Obsidian)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Zurich
date 2022-11-19
pandoc NA
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
rspm * 0.2.2 2022-11-19 [1] Github (spectral-cockpit/rspm@04c6467)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
[1] /home/spectral-cockpit/R/x86_64-pc-linux-gnu-library/4.2
[2] /opt/R/4.2.1/lib/R/libraryHappy to see the workaround gives the desired result, but maybe you have a safer 🪂 in review of my draft. r$> library("magick")
Error in library("magick") : there is no package called ‘magick’
r$> rspm::enable()
Tracing function "install.packages" in package "utils"
Tracing function "update.packages" in package "utils"
r$> install.packages("magick")
Installing package into ‘/home/spectral-cockpit/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/all/__linux__/centos8/latest/src/contrib/magick_2.7.3.tar.gz'
Content type 'binary/octet-stream' length 9216733 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
* installing *binary* package ‘magick’ ...
* DONE (magick)
The downloaded source packages are in
‘/tmp/RtmpBC6K8f/downloaded_packages’
Inspecting installed packages...
Downloading and installing sysreqs...
Not root, Subscription Management repositories not updated
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Last metadata expiration check: 11:07:18 ago on Sa 19 Nov 2022 11:59:47 CET.
(1/7): ilmbase-2.2.0-13.el8.x86_64.rpm 2.1 MB/s | 113 kB 00:00
(2/7): libwmf-lite-0.2.9-8.el8_0.x86_64.rpm 1.3 MB/s | 75 kB 00:00
(3/7): libraqm-0.7.0-4.el8.x86_64.rpm 1.3 MB/s | 19 kB 00:00
(4/7): ImageMagick-c++-6.9.12.64-1.el8.x86_64.rpm 14 MB/s | 198 kB 00:00
(5/7): ImageMagick-libs-6.9.12.64-1.el8.x86_64.rpm 22 MB/s | 2.4 MB 00:00
(6/7): OpenEXR-libs-2.2.0-12.el8.x86_64.rpm 28 MB/s | 671 kB 00:00
(7/7): LibRaw-0.19.5-3.el8.x86_64.rpm 4.7 MB/s | 315 kB 00:00
1088 blocks
1350 blocks
16117 blocks
51 blocks
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307 blocks
6427 blocks
Configuring sysreqs...Love how clever rspm is, which makes it work without even restarting. r$> library("magick")
Linking to ImageMagick 6.9.12.50
Enabled features: cairo, fontconfig, freetype, ghostscript, lcms, pango, raw, rsvg, webp, x11
Disabled features: fftw, heic
Using 8 threads
r$> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os Rocky Linux 8.7 (Green Obsidian)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Zurich
date 2022-11-19
pandoc NA
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
magick * 2.7.3 2021-08-18 [1] RSPM (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
Rcpp 1.0.9 2022-07-08 [1] RSPM (R 4.2.0)
rspm * 0.2.2 2022-11-19 [1] Github (spectral-cockpit/rspm@04c6467)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
[1] /home/spectral-cockpit/R/x86_64-pc-linux-gnu-library/4.2
[2] /opt/R/4.2.1/lib/R/library
───────────────────────────────────────────────────────────────────────────────────────────────────────To quickly test the checking of additional non-root requirements in sudo dnf remove cpioThen, in R # no warning as expected because "patchelf" and "ldd" system libraries are still available
r$> rspm::enable()
Tracing function "install.packages" in package "utils"
Tracing function "update.packages" in package "utilsRemove {magick} and trying to reinstal it triggers informative error. r$> remove.packages("magick")
Removing package from ‘/home/spectral-cockpit/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
r$> library("magick")
Error in library("magick") : there is no package called ‘magick’
r$> rspm::install("magick")
Error: 'install' is not an exported object from 'namespace:rspm'
r$> install.packages("magick")
Installing package into ‘/home/spectral-cockpit/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/all/__linux__/centos8/latest/src/contrib/magick_2.7.3.tar.gz'
Content type 'binary/octet-stream' length 9216733 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
* installing *binary* package ‘magick’ ...
* DONE (magick)
The downloaded source packages are in
‘/tmp/RtmpX7nVE3/downloaded_packages’
Inspecting installed packages...
Downloading and installing sysreqs...
Not root, Subscription Management repositories not updated
This system is not registered with an entitlement server. You can use subscription-manager to register.
Last metadata expiration check: 11:19:53 ago on Sa 19 Nov 2022 11:59:47 CET.
(1/7): libraqm-0.7.0-4.el8.x86_64.rpm 428 kB/s | 19 kB 00:00
(2/7): ImageMagick-c++-6.9.12.64-1.el8.x86_64.rpm 3.6 MB/s | 198 kB 00:00
(3/7): OpenEXR-libs-2.2.0-12.el8.x86_64.rpm 9.5 MB/s | 671 kB 00:00
(4/7): ilmbase-2.2.0-13.el8.x86_64.rpm 4.0 MB/s | 113 kB 00:00
(5/7): libwmf-lite-0.2.9-8.el8_0.x86_64.rpm 7.0 MB/s | 75 kB 00:00
(6/7): ImageMagick-libs-6.9.12.64-1.el8.x86_64.rpm 47 MB/s | 2.4 MB 00:00
(7/7): LibRaw-0.19.5-3.el8.x86_64.rpm 6.8 MB/s | 315 kB 00:00
Error: Non-root requires 'rpm2cpio' and 'cpio' tools to unpack and copy RPM packages into home directory without admin (sudo) rights.Quit current R session. Then install missing in shell with
`sudo dnf install cpio`.
Restart R and run `rspm::enable()` again to proceed.
r$>Seems to work fine for me, except that the linked system deps for {magick}/ImageMagic still exist in the local shared library. |
|
Looking forward to get your feedback. :-) If the approach is sensible enough, there is probably a little bit more to be done downstream. Happy to try help with that and get your review for that. Cheers, Philipp |
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Thanks, I'll investigate this further to try to reproduce it in a Rocky Linux environment. I'd like to solve it via the rpm command exclusively to avoid depending on more tools, because rpm is always available, but rpm2cpio and cpio may not. |
|
Please try adding |
|
Closing in favor of #11. |
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Dear @Enchufa2 ,
First of all thanks a lot for offering a solution for binary installs with convoluted system deps in CentOS/RHEL(-alike) distros, closing a considerable gap around RSPM/bspm/renv. Really like the design and the clarity of how interfaces are coded! So it it was straight-forward to dig in deeper.
In the current version in main, when invoking
rspm::enable(), I got the error tracing back to the rpm install command viasystem().This is the current setup:
There seems to be no permission issue as outlined as possible reason for the same underlying message in #9 .
It looks like the flag
--root(-r) fordnfcmd is not working unless being root. At least for my rocky 8.7 miniserver. To be honest, I don't have enough knowledge of the inner mechanistics of .RPM and the dnf tool. Could be a bug ( https://bugzilla.redhat.com/show_bug.cgi?id=1963151 ) or actually just by design because some other root directories are touched (maybe it looks for rpmdb etc.). The--prefixtrick did also not work, probably for similar reasons.I found a workaround via extracting and copying the .RPM archive to the user directory of rspm, via
rpm2cpioand stdin intocpio. Found this strategy on stackoverflow (e.g., https://superuser.com/questions/209808/how-can-i-install-an-rpm-without-being-root ) and here : https://scicomp.ethz.ch/wiki/Unpacking_RPM_packages .