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Old 24th October 2017
hanzer's Avatar
hanzer hanzer is offline
Real Name: Adam Jensen
just passing through
 
Join Date: Oct 2013
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Default R install problem on 6.2-Release

Hi,
I attempted to install R in a typical way:

$ doas pkg_add R

but it looks like there was maybe transport error?
Code:
...[snip]...
R-3.4.1p0:tk-8.5.19p0: ok                                                       
R-3.4.1p0:zip-3.0p0: ok                                        
R-3.4.1p0:gtar-1.29: ok                                               
Fatal error: Ustar [https://ftp.openbsd.org/pub/OpenBSD/6.2/packages/amd64/R-3.4.1p0.tgz][lib/R/
library/survival/data/Rdata.rdb]: Premature end of archive                           
Adjusting sha for /usr/local/lib/R/library/survival/data/pkg.Ay9UsKonjG from qYKF5zC3LVKeQzgymjp
SPRQ60znAHu+MVlUgrNh1lFI= to 47DEQpj8HBSa+/TImW+5JCeuQeRkm5NMpJWZG3hSuFU=            
Look in /usr/local/share/doc/pkg-readmes for extra documentation.
So, in hope of cleaning things up, I try:

$ doas pkg_delete R
$ doas pkg_add R
$ pkg_check -vvv
Code:
Packing-list sanity: ok
Direct dependencies: ok
Reverse dependencies: ok
Files from packages: ok
--- .libs-partial-R-3.4.1p0 -------------------
lib should exist
lib is not a directory
lib/R should exist
lib/R is not a directory
lib/R/lib should exist
lib/R/lib is not a directory
lib/R/lib/libR.so.33.0 should exist
lib/R/lib/libR.so.33.0 is not a file
can't read lib/R/lib/libR.so.33.0
lib/R/lib/libRblas.so.33.0 should exist
lib/R/lib/libRblas.so.33.0 is not a file
can't read lib/R/lib/libRblas.so.33.0
lib/R/lib/libRlapack.so.33.0 should exist
lib/R/lib/libRlapack.so.33.0 is not a file
can't read lib/R/lib/libRlapack.so.33.0
--- dbus-daemon-launch-helper-1.10.22p0 -------------------
can't read /usr/local/libexec/dbus-daemon-launch-helper
I thought about manually deleting the R package file so another attempt at pkg_install would retry the download but, and this is really goofy, I don't know where the packages are saved in the filesystem.

Any ideas about how to proceed?
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Old 24th October 2017
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jggimi jggimi is offline
More noise than signal
 
Join Date: May 2008
Location: USA
Posts: 6,013
Default

Look for a "partial-R" package. If you have one, pkg_delete(1) it, then retry. (I'm not sure if pkg_check(8) will clean up partial packages.)

Yes, premature end-of-archive means that tar(1) received a short file.
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Old 24th October 2017
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hanzer hanzer is offline
Real Name: Adam Jensen
just passing through
 
Join Date: Oct 2013
Location: EST USA
Posts: 267
Default

$ pkg_info -A | grep -i partial
.libs-partial-R-3.4.1p0 Stub libraries for partial-R-3.4.1p0

$ doas pkg_delete .libs-partial-R-3.4.1p0
Code:
.libs-partial-R-3.4.1p0: ok
Read shared items: ok
--- -.libs-partial-R-3.4.1p0 -------------------
Error deleting directory lib/R/lib: No such file or directory
Error deleting directory lib/R: No such file or directory
Error deleting directory lib: No such file or directory
Error deleting directory .: Invalid argument
$ doas pkg_add R
$ pkg_check -vvv
Code:
Packing-list sanity: ok
Direct dependencies: ok
Reverse dependencies: ok
Files from packages: ok
--- dbus-daemon-launch-helper-1.10.22p0 -------------------
can't read /usr/local/libexec/dbus-daemon-launch-helper
Disco! I don't know what the dbus issue is or where it came from but I'll save that for another day. Thanks!

BTW - Does anyone know where in the filesystem the package.tgz files are kept?
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Old 24th October 2017
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jggimi jggimi is offline
More noise than signal
 
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They're not retained unless PKG_CACHE is set. See pkg_add(1).

The package database is found in /var/db/pkg/.

Edited to add: I think you might have a partial-R-3.4.1p0 still installed.

Last edited by jggimi; 24th October 2017 at 06:45 PM. Reason: pkg_info reference
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Old 24th October 2017
hanzer's Avatar
hanzer hanzer is offline
Real Name: Adam Jensen
just passing through
 
Join Date: Oct 2013
Location: EST USA
Posts: 267
Default

Quote:
Originally Posted by jggimi View Post
They're not retained unless PKG_CACHE is set. See pkg_add(1).
Oh, geez; I might have downloaded the R package like 5 or 6 times while flailing about with this issue... Oops, sorry package hoster (is that a word?).

Quote:
Originally Posted by jggimi View Post
Edited to add: I think you might have a partial-R-3.4.1p0 still installed.
Don't know mess yo wit my head man.

Code:
hanzer@lucidrine:/home/hanzer:619 $ pkg_info -A | grep -i partial 
hanzer@lucidrine:/home/hanzer:620 $ pkg_check                     
Packing-list sanity: ok
Direct dependencies: ok
Reverse dependencies: ok
Files from packages: ok
--- dbus-daemon-launch-helper-1.10.22p0 -------------------
can't read /usr/local/libexec/dbus-daemon-launch-helper
hanzer@lucidrine:/home/hanzer:621 $ R --version
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-unknown-openbsd6.2 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.

hanzer@lucidrine:/home/hanzer:622 $ R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-unknown-openbsd6.2 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> q()
Save workspace image? [y/n/c]: n
hanzer@lucidrine:/home/hanzer:623 $
What do you see, jggimi?
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Old 24th October 2017
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jggimi jggimi is offline
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If you $ pkg_info | grep R and only see one package, then you're good.
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Old 24th October 2017
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hanzer hanzer is offline
Real Name: Adam Jensen
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S'all good, man
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