Hi all,
I want to install the package r-rstanpandoc-bin. r-rstan is a bit of a nightmare regarding dependencies, since it depends on v8, pandoc, and some R packages at the same time (which are not fun to update via package manager).
At first, I tried to install it straight away with pamac, but it did not recognise pandoc-bin as providing pandoc. Since it’s something I could give up to, I went forward anyway to try it out, but v8 failed too. Now, v8 is provided by v8-r on Arch, according to the installation instructions provided by the developer. It obviously conflicts with the original v8 and it’s required by r-v8 (which is a different package), a dependency of r-rstan.v8-r offers a prepacked binary on its repository , which I proceeded to install. At this point, retrying to install r-rstan still prompts me to substitute both pandoc-bin with pandoc (annoying but fine) and v8-r with v8 (which is not).
And that’s where I got lost. The last thing I thought about trying is to compile v8-r using the source package, but I doubt it would solve much, because the same thing happens with pandoc-bin, despite providing pandoc.
What I thought it might be a possible solution is to install everything individually and to edit the PKGBUILD of r-rstan so to skip the dependency check or to explicitly use pandoc-bin and v8-r as dependencies, but it isn’t futureproof and I suspect it would be a last-resort solution. I also haven’t modified a PKGBUILD before, so I don’t really know
What are your thoughts about this? Do you think there’s any other possibility?
Thank you very much in advance!
nergal
28 September 2020 14:24
2
I have no experience in using Stan in R. That being said, is there a reason you are using the AUR package and not installing this from the source?
Home · stan-dev/rstan Wiki · GitHub
1 Like
guinux
28 September 2020 16:51
3
~ >>> pamac --version
Pamac 9.5.10-2
~ >>> pamac build r-rstan
Resolving dependencies...
Checking inter-conflicts...
To install (136):
pandoc-citeproc 0.17.0.2-39 (Required By: r-rstan) community 1.4 MB
haskell-xml-conduit 1.9.0.0-54 (Required By: r-rstan) community 357.2 kB
haskell-setenv 0.1.1.3-20 (Required By: r-rstan) community 6.7 kB
haskell-conduit-extra 1.3.5-47 (Required By: r-rstan) community 148.2 kB
haskell-text-icu 0.7.0.1-34 (Required By: r-rstan) community 448.6 kB
haskell-yaml 0.11.5.0-13 (Required By: r-rstan) community 190.1 kB
haskell-libyaml 0.1.2-56 (Required By: r-rstan) community 123.5 kB
haskell-conduit 1.3.2.1-7 (Required By: r-rstan) community 286.0 kB
haskell-mono-traversable 1.0.15.1-56 (Required By: r-rstan) community 449.2 kB
haskell-xml-types 0.3.8-3 (Required By: r-rstan) community 132.5 kB
haskell-resourcet 1.2.4.2-17 (Required By: r-rstan) community 75.3 kB
python2-colorama 0.4.3-1 (Required By: r-rstan) community 22.9 kB
python2 2.7.18-2 (Required By: r-rstan) extra
haskell-hs-bibutils 6.10.0.0-4 (Required By: r-rstan) community 517.5 kB
clang 10.0.1-1 (Required By: r-rstan) extra
compiler-rt 10.0.1-1 (Required By: r-rstan) extra
haskell-rfc5051 0.2-3 (Required By: r-rstan) community 283.6 kB
haskell-hsyaml-aeson 0.2.0.0-68 (Required By: r-rstan) community 27.5 kB
haskell-vector-algorithms 0.8.0.3-37 (Required By: r-rstan) community 187.4 kB
r 4.0.2-1 (Required By: r-rstan) extra 43.0 MB
haskell-typed-process 0.2.6.0-49 (Required By: r-rstan) community 63.5 kB
haskell-unliftio-core 0.2.0.1-4 (Required By: r-rstan) community 18.7 kB
pandoc 2.10.1-28 (Required By: r-rstan) community 7.9 MB
haskell-zip-archive 0.4.1-53 (Required By: r-rstan) community 103.4 kB
haskell-old-time 1.1.0.3-25 (Required By: r-rstan) community 79.6 kB
haskell-digest 0.0.1.2-20 (Required By: r-rstan) community 13.8 kB
haskell-unicode-transforms 0.3.7-10 (Required By: r-rstan) community 311.2 kB
haskell-tagsoup 0.14.8-49 (Required By: r-rstan) community 863.6 kB
haskell-texmath 0.12.0.3-2 (Required By: r-rstan) community 4.0 MB
haskell-xml 1.3.14-25 (Required By: r-rstan) community 127.0 kB
haskell-split 0.2.3.4-63 (Required By: r-rstan) community 35.3 kB
haskell-http-client-tls 0.3.5.3-299 (Required By: r-rstan) community 51.0 kB
haskell-http-client 0.7.2.1-25 (Required By: r-rstan) community 338.8 kB
haskell-streaming-commons 0.2.2.1-14 (Required By: r-rstan) community 175.8 kB
haskell-mime-types 0.1.0.9-9 (Required By: r-rstan) community 393.2 kB
haskell-http-types 0.12.3-81 (Required By: r-rstan) community 120.8 kB
haskell-cookie 0.4.5-7 (Required By: r-rstan) community 33.9 kB
haskell-hslua-module-text 0.2.1-77 (Required By: r-rstan) community 18.4 kB
haskell-hslua-module-system 0.2.2-14 (Required By: r-rstan) community 32.5 kB
haskell-temporary 1.3-97 (Required By: r-rstan) community 19.8 kB
haskell-hslua 1.1.2-24 (Required By: r-rstan) community 238.0 kB
lua53 5.3.5-1 (Required By: r-rstan) extra 258.8 kB
haskell-skylighting 0.8.5-49 (Required By: r-rstan) community 552.5 kB
haskell-skylighting-core 0.8.5-49 (Required By: r-rstan) community 667.8 kB
haskell-utf8-string 1.0.1.1-19 (Required By: r-rstan) community 63.8 kB
haskell-regex-pcre 0.95.0.0-6 (Required By: r-rstan) community 88.6 kB
haskell-regex-base 0.94.0.0-6 (Required By: r-rstan) community 67.4 kB
haskell-hxt 9.3.1.18-141 (Required By: r-rstan) community 1.5 MB
haskell-hxt-unicode 9.0.2.4-19 (Required By: r-rstan) community 161.6 kB
haskell-hxt-regex-xmlschema 9.2.0.3-23 (Required By: r-rstan) community 113.9 kB
haskell-hxt-charproperties 9.4.0.0-7 (Required By: r-rstan) community 931.8 kB
haskell-ansi-terminal 0.11-4 (Required By: r-rstan) community 107.6 kB
haskell-colour 2.3.5-62 (Required By: r-rstan) community 148.6 kB
haskell-jira-wiki-markup 1.3.2-14 (Required By: r-rstan) community 222.0 kB
haskell-ipynb 0.1.0.1-87 (Required By: r-rstan) community 121.9 kB
haskell-haddock-library 1.9.0-32 (Required By: r-rstan) community 212.1 kB
haskell-glob 0.10.1-15 (Required By: r-rstan) community 83.9 kB
haskell-doctemplates 0.8.2-43 (Required By: r-rstan) community 223.1 kB
haskell-text-conversions 0.3.0-45 (Required By: r-rstan) community 27.0 kB
haskell-errors 2.3.0-56 (Required By: r-rstan) community 56.3 kB
haskell-base16-bytestring 0.1.1.7-3 (Required By: r-rstan) community 15.0 kB
haskell-hsyaml 0.2.1.0-39 (Required By: r-rstan) community 435.4 kB
haskell-doclayout 0.3-32 (Required By: r-rstan) community 91.2 kB
haskell-safe 0.3.19-3 (Required By: r-rstan) community 64.2 kB
haskell-data-default 0.7.1.1-74 (Required By: r-rstan) community 7.1 kB
haskell-data-default-instances-old-locale 0.0.1-31 (Required By: r-rstan) community 6.9 kB
haskell-old-locale 1.0.0.7-25 (Required By: r-rstan) community 29.1 kB
haskell-data-default-instances-dlist 0.0.1-87 (Required By: r-rstan) community 7.0 kB
haskell-data-default-instances-containers 0.0.1-31 (Required By: r-rstan) community 8.0 kB
haskell-connection 0.3.1-52 (Required By: r-rstan) community 58.0 kB
haskell-tls 1.5.4-32 (Required By: r-rstan) community 1.1 MB
haskell-x509-validation 1.6.11-77 (Required By: r-rstan) community 64.7 kB
haskell-byteable 0.1.1-20 (Required By: r-rstan) community 11.5 kB
haskell-async 2.2.2-27 (Required By: r-rstan) community 48.1 kB
haskell-socks 0.6.1-45 (Required By: r-rstan) community 146.2 kB
haskell-cereal 0.5.8.1-7 (Required By: r-rstan) community 153.4 kB
haskell-data-default-class 0.1.2.0-19 (Required By: r-rstan) community 15.1 kB
haskell-commonmark-pandoc 0.2.0.1-1 (Required By: r-rstan) community 49.7 kB
haskell-pandoc-types 1.21-18 (Required By: r-rstan) community 566.8 kB
haskell-syb 0.7.1-7 (Required By: r-rstan) community 88.5 kB
haskell-quickcheck 2.14.1-27 (Required By: r-rstan) community 480.4 kB
haskell-erf 2.0.0.0-19 (Required By: r-rstan) community 15.0 kB
haskell-commonmark-extensions 0.2.0.1-11 (Required By: r-rstan) community 258.6 kB
haskell-emojis 0.1-34 (Required By: r-rstan) community 661.3 kB
haskell-commonmark 0.1.0.2-11 (Required By: r-rstan) community 1.2 MB
haskell-case-insensitive 1.2.1.0-26 (Required By: r-rstan) community 33.9 kB
haskell-blaze-html 0.9.1.2-44 (Required By: r-rstan) community 398.5 kB
haskell-blaze-markup 0.8.2.7-14 (Required By: r-rstan) community 81.7 kB
haskell-blaze-builder 0.4.1.0-14 (Required By: r-rstan) community 59.4 kB
haskell-base64-bytestring 1.2.0.0-10 (Required By: r-rstan) community 33.7 kB
haskell-aeson-pretty 0.8.8-73 (Required By: r-rstan) community 36.3 kB
haskell-cmdargs 0.10.20-14 (Required By: r-rstan) community 360.6 kB
haskell-sha 1.6.4.4-14 (Required By: r-rstan) community 79.5 kB
haskell-juicypixels 3.3.5-24 (Required By: r-rstan) community 1.2 MB
haskell-zlib 0.6.2.2-3 (Required By: r-rstan) community 124.9 kB
haskell-http 4000.3.15-5 (Required By: r-rstan) community 323.4 kB
haskell-network-uri 2.6.3.0-160 (Required By: r-rstan) community 99.3 kB
haskell-network 3.1.2.0-29 (Required By: r-rstan) community 285.6 kB
haskell-aeson 1.5.4.0-7 (Required By: r-rstan) community 1.0 MB
haskell-vector 0.12.1.2-42 (Required By: r-rstan) community 851.1 kB
haskell-uuid-types 1.0.3-45 (Required By: r-rstan) community 57.0 kB
haskell-random 1.2.0-18 (Required By: r-rstan) community 147.1 kB
haskell-splitmix 0.1.0.1-15 (Required By: r-rstan) community 35.9 kB
haskell-unordered-containers 0.2.12.0-14 (Required By: r-rstan) community 179.4 kB
haskell-time-compat 1.9.3-23 (Required By: r-rstan) community 49.7 kB
haskell-strict 0.4-15 (Required By: r-rstan) community 145.1 kB
haskell-these 1.1.1.1-15 (Required By: r-rstan) community 84.8 kB
haskell-assoc 1.0.2-14 (Required By: r-rstan) community 16.3 kB
haskell-bifunctors 5.5.7-42 (Required By: r-rstan) community 333.1 kB
haskell-th-abstraction 0.3.2.0-6 (Required By: r-rstan) community 134.0 kB
haskell-comonad 5.0.6-41 (Required By: r-rstan) community 91.2 kB
haskell-transformers-compat 0.6.5-7 (Required By: r-rstan) community 61.4 kB
haskell-distributive 0.6.2-22 (Required By: r-rstan) community 35.8 kB
haskell-tagged 0.8.6-12 (Required By: r-rstan) community 55.7 kB
haskell-base-orphans 0.8.2-49 (Required By: r-rstan) community 7.6 kB
haskell-dlist 1.0-10 (Required By: r-rstan) community 47.7 kB
haskell-data-fix 0.3.0-14 (Required By: r-rstan) community 34.3 kB
haskell-base-compat-batteries 0.11.1-45 (Required By: r-rstan) community 78.2 kB
haskell-base-compat 0.11.1-11 (Required By: r-rstan) community 78.1 kB
haskell-attoparsec 0.13.2.4-22 (Required By: r-rstan) community 336.1 kB
haskell-scientific 0.3.6.2-39 (Required By: r-rstan) community 97.3 kB
haskell-primitive 0.7.1.0-16 (Required By: r-rstan) community 226.5 kB
haskell-integer-logarithms 1.0.3-8 (Required By: r-rstan) community 25.5 kB
haskell-hashable 1.3.0.0-23 (Required By: r-rstan) community 73.4 kB
haskell-x509-system 1.6.6-145 (Required By: r-rstan) community 17.1 kB
haskell-x509-store 1.6.7-77 (Required By: r-rstan) community 31.3 kB
haskell-x509 1.7.5-78 (Required By: r-rstan) community 268.7 kB
haskell-cryptonite 0.27-17 (Required By: r-rstan) community 1.7 MB
haskell-asn1-parse 0.9.5-45 (Required By: r-rstan) community 18.5 kB
haskell-asn1-encoding 0.9.6-45 (Required By: r-rstan) community 95.4 kB
haskell-asn1-types 0.3.4-24 (Required By: r-rstan) community 87.9 kB
haskell-hourglass 0.2.12-69 (Required By: r-rstan) community 270.5 kB
haskell-pem 0.2.4-101 (Required By: r-rstan) community 24.2 kB
haskell-memory 0.15.0-36 (Required By: r-rstan) community 211.7 kB
haskell-basement 0.0.11-8 (Required By: r-rstan) community 858.1 kB
ghc-libs 8.10.2-1 (Required By: r-rstan) community 16.8 MB
To build (55):
r-rstan 2.21.2-1 AUR
r-stanheaders 2.21.0.6-1 (Required By: r-rstan) AUR
r-ggplot2 3.3.2-1 (Required By: r-rstan) AUR
r-isoband 0.2.2-1 (Required By: r-rstan) AUR
r-testthat 2.3.2-1 (Required By: r-rstan) AUR
r-evaluate 0.14-1 (Required By: r-rstan) AUR
r-pkgload 1.1.0-1 (Required By: r-rstan) AUR
r-rstudioapi 0.11-1 (Required By: r-rstan) AUR
r-praise 1.0.0-1 (Required By: r-rstan) AUR
r-scales 1.1.1-1 (Required By: r-rstan) AUR
r-farver 2.0.3-1 (Required By: r-rstan) AUR
r-labeling 0.3-1 (Required By: r-rstan) AUR
r-munsell 0.5.0-1 (Required By: r-rstan) AUR
r-colorspace 1.4.1-1 (Required By: r-rstan) AUR
r-rcolorbrewer 1.1.2-1 (Required By: r-rstan) AUR
r-viridislite 0.3.0-1 (Required By: r-rstan) AUR
r-tibble 3.0.3-1 (Required By: r-rstan) AUR
r-lifecycle 0.2.0-1 (Required By: r-rstan) AUR
r-magrittr 1.5-1 (Required By: r-rstan) AUR
r-pillar 1.4.6-1 (Required By: r-rstan) AUR
r-utf8 1.1.4-1 (Required By: r-rstan) AUR
r-pkgconfig 2.0.3-1 (Required By: r-rstan) AUR
r-vctrs 0.3.4-1 (Required By: r-rstan) AUR
r-ellipsis 0.3.1-1 (Required By: r-rstan) AUR
r-digest 0.6.25-1 (Required By: r-rstan) AUR
r-rlang 0.4.7-1 (Required By: r-rstan) AUR
r-inline 0.3.16-1 (Required By: r-rstan) AUR
r-gridextra 2.3-1 (Required By: r-rstan) AUR
r-gtable 0.3.0-1 (Required By: r-rstan) AUR
r-rcppparallel 5.0.2-1 (Required By: r-rstan) AUR
r-loo 2.3.1-1 (Required By: r-rstan) AUR
r-checkmate 2.0.0-1 (Required By: r-rstan) AUR
r-matrixstats 0.57.0-1 (Required By: r-rstan) AUR
r-pkgbuild 1.1.0-1 (Required By: r-rstan) AUR
r-callr 3.4.4-1 (Required By: r-rstan) AUR
r-processx 3.4.4-1 (Required By: r-rstan) AUR
r-ps 1.3.4-1 (Required By: r-rstan) AUR
r-cli 2.0.2-1 (Required By: r-rstan) AUR
r-glue 1.4.2-1 (Required By: r-rstan) AUR
r-fansi 0.4.1-1 (Required By: r-rstan) AUR
r-desc 1.2.0-1 (Required By: r-rstan) AUR
r-assertthat 0.2.1-1 (Required By: r-rstan) AUR
r-crayon 1.3.4-1 (Required By: r-rstan) AUR
r-prettyunits 1.1.1-1 (Required By: r-rstan) AUR
r-r6 2.4.1-1 (Required By: r-rstan) AUR
r-rprojroot 1.3.2-1 (Required By: r-rstan) AUR
r-backports 1.1.10-1 (Required By: r-rstan) AUR
r-withr 2.3.0-1 (Required By: r-rstan) AUR
r-v8 3.2.0-1 (Required By: r-rstan) AUR
r-jsonlite 1.7.1-1 (Required By: r-rstan) AUR
r-curl 4.3-1 (Required By: r-rstan) AUR
v8 8.3.110.13-3 (Required By: r-rstan) AUR
r-rcppeigen 0.3.3.7.0-1 (Required By: r-rstan) AUR
r-rcpp 1.0.5-1 (Required By: r-rstan) AUR
r-bh 1.72.0.3-1 (Required By: r-rstan) AUR
This half-solved it.
Installing v8-r alone as a binary AND installing from source apparently did the trick.
It’s still a mystery why I can’t build it with pamac if I have those two binaries @guinux reported
cscs
28 September 2020 20:57
5
Is there a reason we should encourage folks to use source manually instead of using (or creating) a PKGBUILD and thus its files are recognized and handled by the package manager along with the rest of the system?
nergal
28 September 2020 21:49
6
This is an R package (r-stan). Like any other R package on Linux, people install them from the source, i.e., from the curated Cran repository. I personally would not want my R installation to be a Frankenstein consisting of a mixture of Cran and AUR packages.
nergal
28 September 2020 22:18
7
Installing v8-r alone as a binary AND installing from source apparently did the trick.
Personal, this would be my preferred method if I would require these packages.
Pandoc is just a pain nowadays in R/Manjaro now that most of the bins are not maintained any more in AUR required to compile markdown/latex. I would guess that your issues stemmed from the pandoc-bin. I removed pandoc-bin and installed the full pandoc stack to get working markdown/latex in R. I have not had any issues with it other than the insane number of redundant packages…
2 Likes
I would normally agree with you, but in this case the developer explicitly suggested using the distro repository as an alternative. Happier to have everything in R nevertheless.
V8 too though, the main issue I was having here was being obliged to install v8 instead of v8-r, which is the one the v8 developer explicitly suggests for Arch . This doesn’t make any sense.
nergal
29 September 2020 02:59
9
At least you got a working stan package. Enjoy your Bayesian models!
1 Like
system
2 October 2020 02:59
10
This topic was automatically closed 3 days after the last reply. New replies are no longer allowed.
I will try to make some tests with/without pandoc-bin, because I want to avoid exactly the list of haskell dependencies