Gentoo Archives: gentoo-science

From: Neil Shephard <nshephard@×××××.com>
To: Benda Xu <heroxbd@g.o>, gentoo-science@l.g.o
Subject: Re: [gentoo-science] Errors installing Rcpp using R_Overlay
Date: Thu, 22 Mar 2018 14:02:04
Message-Id: CADcCPCFC8XNinKOu1W3n0tZ3pyS4R8Nb_FacmvrpAToJXqvAAA@mail.gmail.com
1 Hi Benda,
2
3 [Sending this to gentoo-science mailing list as accidentally replied
4 direct, have also discovered a few other packages that have incorrect
5 versions]
6
7 Hi Benda,
8
9 Thanks for taking the time to resolve this, that has worked nicely and Rcpp
10 now emerges.
11
12 I continued trying to replace all the packages I have installed directly
13 through R with emerges from R_Overlay and opted to emerge the meta-package
14 tidyverse which pulls in a ton of packages as well as more explicit
15 packages that aren't pulled in. In doing so I've encountered three
16 problems....
17
18
19 1. Some ebuilds try to pull in old versions.
20 2. Some ebuilds from R_Overlay require "USE=minimal dev-lang/R" whilst
21 others require "USE=-minimal dev-lang/R" which makes it difficult to emerge
22 things.
23 3. I found one package that is on CRAN but for which there is no ebuild.
24
25
26
27 1. Old Versions
28 ============
29
30 I found the following old version were pulled in....
31
32 | Package | R_Overlay Version | CRAN version |
33 |-----------|-------------------|---------------|
34 | xml2 | 0.1.2 | 1.2.0 |
35 | lubridate | 1.7.0 | 1.7.3 |
36
37
38
39 2. dev-lang/R [-]minimal conflicts
40 ==========================
41
42 Tried emerging a bundle of packages and get conflicts relating to the
43 USE=minimal, also resulted in some slot conflicts that I couldn't see. Its
44 mostly the 'virtual/[pkg]' that require -minimal....
45
46 emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage
47 ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm lme4 glmnet rpart
48 caret survival Hmisc rms epitools pwr TrialSize longpower simglm
49 clusterPower samplesize PowerTOST blockrand bookdown
50 ...
51
52 !!! Multiple package instances within a single package slot have been pulled
53 !!! into the dependency graph, resulting in a slot conflict:
54
55 dev-lang/R:0
56
57 (dev-lang/R-3.4.4:0/0::slack, installed) pulled in by
58 dev-lang/R[-minimal] required by (virtual/cluster-0:0/0::R_Overlay,
59 ebuild scheduled for merge)
60 ^^^^^^^^
61
62 dev-lang/R[-minimal] required by (virtual/KernSmooth-0:0/0::R_Overlay,
63 installed)
64 ^^^^^^^^
65
66 dev-lang/R[-minimal] required by (virtual/MASS-0:0/0::R_Overlay,
67 installed)
68 ^^^^^^^^
69
70 dev-lang/R[-minimal] required by (virtual/Matrix-0:0/0::R_Overlay,
71 installed)
72 ^^^^^^^^
73
74 dev-lang/R[-minimal] required by (virtual/codetools-0:0/0::R_Overlay,
75 ebuild scheduled for merge)
76 ^^^^^^^^
77
78 dev-lang/R[-minimal] required by (virtual/class-0:0/0::R_Overlay,
79 ebuild scheduled for merge)
80 ^^^^^^^^
81
82 dev-lang/R[-minimal] required by (virtual/foreign-0:0/0::R_Overlay,
83 installed)
84 ^^^^^^^^
85
86 dev-lang/R[-minimal] required by (virtual/lattice-0:0/0::R_Overlay,
87 installed)
88 ^^^^^^^^
89
90 dev-lang/R[-minimal] required by (virtual/nlme-0:0/0::R_Overlay,
91 installed)
92 ^^^^^^^^
93
94 dev-lang/R[-minimal] required by (virtual/survival-0:0/0::R_Overlay,
95 ebuild scheduled for merge)
96 ^^^^^^^^
97
98 dev-lang/R[-minimal] required by (virtual/rpart-0:0/0::R_Overlay,
99 ebuild scheduled for merge)
100 ^^^^^^^^
101
102 dev-lang/R[-minimal] required by (virtual/nnet-0:0/0::R_Overlay, ebuild
103 scheduled for merge)
104 ^^^^^^^^
105
106
107 (dev-lang/R-3.4.4:0/0::slack, ebuild scheduled for merge) pulled in by
108 dev-lang/R[minimal] required by (sci-CRAN/Matrix-1.2.12:0/0::R_Overlay,
109 ebuild scheduled for merge)
110 ^^^^^^^
111
112 dev-lang/R[minimal] required by
113 (sci-CRAN/nlme-3.1.131.1:0/0::R_Overlay, ebuild scheduled for merge)
114 ^^^^^^^
115
116 dev-lang/R[minimal] required by (sci-CRAN/rpart-4.1.13:0/0::R_Overlay,
117 ebuild scheduled for merge)
118 ^^^^^^^
119
120 dev-lang/R[minimal] required by
121 (sci-CRAN/survival-2.41.3:0/0::R_Overlay, ebuild scheduled for merge)
122 ^^^^^^^
123
124 dev-lang/R[minimal] required by
125 (sci-CRAN/lattice-0.20.35:0/0::R_Overlay, ebuild scheduled for merge)
126 ^^^^^^^
127
128
129
130
131 The following USE changes are necessary to proceed:
132 (see "package.use" in the portage(5) man page for more details)
133 # required by sci-CRAN/survival-2.41.3::R_Overlay
134 # required by sci-CRAN/multcomp-1.4.8::R_Overlay
135 # required by sci-CRAN/rms-5.1.2::R_Overlay
136 # required by rms (argument)
137 >=dev-lang/R-3.4.4 minimal
138
139
140 Strangely virtual/rpart is listed as requiring USE=-minimal but the rpart
141 package itself requires USE=minimal.
142
143
144 3. Missing ebuild for one package
145 ==========================
146
147 I was going to try emergeing the blogdown package (
148 https://cran.r-project.org/web/packages/blogdown/) but there is no ebuild
149 for it in R_Overlay...
150
151 # emerge -av blogdown
152
153 emerge: there are no ebuilds to satisfy "blogdown".
154
155 emerge: searching for similar names...
156 emerge: Maybe you meant any of these: sci-CRAN/bookdown, sci-BIOC/ballgown,
157 app-admin/logmon?
158
159
160
161
162 One minor caeveat is that I'm using a locally bumped version of R as the
163 bugreport I've filed for bumping in portage (https://bugs.gentoo.org/632364)
164 hasn't been addressed yet. I'm currently using =dev-lang/R-3.4.4
165
166 I'm unsure how the ebuilds in R_Overlay are generated, is it automatically
167 based on available builds?
168
169 Thanks for yours and others work on this, having R packages managed by
170 portage is a real boon, as it removes the need to update.packages(ask =
171 FALSE) so regularly.
172
173 If there is something I can do to help please let me know.
174
175 Neil
176
177
178 --
179 *Natural selection is a mechanism for generating an exceedingly high **degree
180 of improbability.* - R.A. Fisher
181
182 *Ignorance more frequently begets confidence than does knowledge* - by
183 Charles Darwin
184
185 PGP Public : https://pgp.mit.edu/pks/lookup?op=get&search=0x0E7ECE9C10D7B4A0
186
187 Website - http://kimura.no-ip.info/
188 Photos - http://www.flickr.com/photos/slackline/

Replies

Subject Author
Re: [gentoo-science] Errors installing Rcpp using R_Overlay Benda Xu <heroxbd@g.o>