Gentoo Archives: gentoo-user

From: c0a800ff@×××××.com
To: gentoo-user@l.g.o
Subject: Re: [gentoo-user] Doubt about R support in gentoo
Date: Sat, 19 Nov 2016 15:26:28
Message-Id: 98b82c43-931d-49f9-d796-6e4fa8ea048e@gmail.com
In Reply to: Re: [gentoo-user] Doubt about R support in gentoo by Alec Ten Harmsel
1 On 11/19/16 12:50, Alec Ten Harmsel wrote:
2 >
3 >
4 > El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió:
5 >>
6 >> Hello everybody...
7 >>
8 >>
9 >> A single doubt here:
10 >>
11 >>
12 >> After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i
13 >> tried a package upgrade inside R and got that:
14 >>
15 >>
16 >> /> update.packages(checkBuilt=TRUE, ask=FALSE,
17 >> repos='http://cran.us.r-project.org')
18 >> trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz'
19 >> Content type 'application/x-gzip' length 1027358 bytes (1003 KB)
20 >> ==================================================
21 >> downloaded 1003 KB
22 >>
23 >> * installing *source* package ‘knitr’ ...
24 >> ** package ‘knitr’ successfully unpacked and MD5 sums checked
25 >> ** R
26 >> ** demo
27 >> ** inst
28 >> ** preparing package for lazy loading
29 >> Error in dyn.load(file, DLLpath = DLLpath, ...) :
30 >> *unable to load shared object
31 >> '/usr/lib64/R/library/stringi/libs/stringi.so':**
32 >> ** libicui18n.so.57: cannot open shared object file: No such file or
33 >> directory*
34 >> /
35 >>
36 >
37 > I am not super familiar with R - can you try rebuilding R itself before
38 > doing the CRAN package installs/upgrades? It looks like the path to ICU
39 > is hard-coded somehow.
40 >
41 >>
42 >> This kind of "bug" can I put inside bugs.gentoo.org or its a cran
43 >> package bug?
44 >>
45 >> It is not the first time and i'm in dout about how to proceed.
46 >>
47 >>
48 >
49 > If rebuildling R fixes this problem, you can file a bug so that
50 > developers somehow trigger an R rebuild whenever ICU is updated.
51 >
52 > Alec
53 >
54
55 Some R package update errors may be solved by creating a temporary
56 folder, for example ~/R/tmp (placing it under ~/R has the advantage of
57 sharing the same parent directory as the default per-user package
58 library), and then passing the following environment variable to R:
59 TMPDIR=$HOME/R/tmp. This allows certain configure scripts to be executed
60 if your /tmp is mounted noexec.
61
62 As for the stringi error, my system doesn't have it in the system-wide
63 library, either:
64
65 $ ls /usr/lib64/R/library/
66 KernSmooth compiler mgcv stats4
67 MASS datasets nlme survival
68 Matrix foreign nnet tcltk
69 base grDevices parallel tools
70 boot graphics rpart translations
71 class grid spatial utils
72 cluster lattice splines
73 codetools methods stats
74
75 But:
76 $ ls ~/R/x86_64-pc-linux-gnu-library/3.2/stringi
77 AUTHORS LICENSE R libs
78 CITATION Meta help
79 DESCRIPTION NAMESPACE html
80 INDEX NEWS include
81
82 Another possibility may be that your R has a useflag for icu (mine doesn't):
83
84 $ equery uses R
85 [ Legend : U - final flag setting for installation]
86 [ : I - package is installed with flag ]
87 [ Colors : set, unset ]
88 * Found these USE flags for dev-lang/R-3.2.2:
89 U I
90 ...
91 + + doc : Add extra documentation (API, Javadoc, etc). It is
92 recommended to enable per package instead of globally
93 - - icu : Enable ICU (Internationalization Components for
94 Unicode) support, using dev-libs/icu
95 - - java : Add support for Java
96 ...
97
98
99 Vitor

Replies

Subject Author
Re: [gentoo-user] Doubt about R support in gentoo Zhu Sha Zang <zhushazang@×××××××××.br>