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emacs 28.1 From: Ricardo Wurmus Date: Tue, 12 Jul 2022 19:19:48 +0200 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87pmiaxmov.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=2; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1657647147; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; 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dmarc=none; spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 2.05 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=MCuE6DED; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 01247D58C X-Spam-Score: 2.05 X-Migadu-Scanner: scn1.migadu.com X-TUID: Re6lFC89y6WB Hi, thank you for your bug report! > You find a related error if you try install.packages("isoband"), which co= uld work as a test case: > > /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib/libstd= c++.so.6: version > `GLIBCXX_3.4.26' not found (required by > /home/kept/Dotfiles/R/x86_64-unknown-linux-gnu-library/4.1/00LOCK-isoband= /00new/isoband/libs/isoband.so) =E2=80=9Cinstall.packages=E2=80=9D will only work if you carefully control = your environment. It will not do the right thing when you use it on a foreign distro, for example, because it would likely pick the system=E2=80= =99s compiler toolchain to build things that are eventually incompatible with the libraries used by R from Guix. Here=E2=80=99s an old blog post that explains the problem and how to work a= round it if you must use =E2=80=9Cinstall.packages=E2=80=9D: https://elephly.net/posts/2017-03-24-r-with-guix.html I haven=E2=80=99t been able to reproduce your problem, though. Here=E2=80= =99s what I did: --8<---------------cut here---------------start------------->8--- $ guix shell -C r-minimal r-rstan -D r-minimal -- R R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (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. > library(rstan) Loading required package: StanHeaders Loading required package: ggplot2 code for methods in class "Rcpp_model_base" was not checked for suspicious = field assignments (recommended package 'codetools' not available?) code for methods in class "Rcpp_model_base" was not checked for suspicious = field assignments (recommended package 'codetools' not available?) code for methods in class "Rcpp_stan_fit" was not checked for suspicious fi= eld assignments (recommended package 'codetools' not available?) code for methods in class "Rcpp_stan_fit" was not checked for suspicious fi= eld assignments (recommended package 'codetools' not available?) rstan (Version 2.21.5, GitRev: 2e1f913d3ca3) For execution on a local, multicore CPU with excess RAM we recommend calling options(mc.cores =3D parallel::detectCores()). To avoid recompilation of unchanged Stan programs, we recommend calling rstan_options(auto_write =3D TRUE) > scode <- " parameters { real y[2];=20 }=20 model { y[1] ~ normal(0, 1); y[2] ~ double_exponential(0, 2); }=20 " fit1 <- stan(model_code =3D scode, iter =3D 10, verbose =3D FALSE)=20 + + + + + + + + >=20 fit1 code for methods in class "Rcpp_stan_fit4model139796fca_b524cd829fcb9f50f67= 61f2451b62eec" was not checked for suspicious field assignments (recommende= d package 'codetools' not available?) code for methods in class "Rcpp_stan_fit4model139796fca_b524cd829fcb9f50f67= 61f2451b62eec" was not checked for suspicious field assignments (recommende= d package 'codetools' not available?) SAMPLING FOR MODEL 'b524cd829fcb9f50f6761f2451b62eec' NOW (CHAIN 1). Chain 1:=20 Chain 1: Gradient evaluation took 6e-06 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take= 0.06 seconds. Chain 1: Adjust your expectations accordingly! Chain 1:=20 Chain 1:=20 Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1:=20 Chain 1: Iteration: 1 / 10 [ 10%] (Warmup) Chain 1: Iteration: 2 / 10 [ 20%] (Warmup) Chain 1: Iteration: 3 / 10 [ 30%] (Warmup) Chain 1: Iteration: 4 / 10 [ 40%] (Warmup) Chain 1: Iteration: 5 / 10 [ 50%] (Warmup) Chain 1: Iteration: 6 / 10 [ 60%] (Sampling) Chain 1: Iteration: 7 / 10 [ 70%] (Sampling) Chain 1: Iteration: 8 / 10 [ 80%] (Sampling) Chain 1: Iteration: 9 / 10 [ 90%] (Sampling) Chain 1: Iteration: 10 / 10 [100%] (Sampling) Chain 1:=20 Chain 1: Elapsed Time: 0.000157 seconds (Warm-up) Chain 1: 0.000123 seconds (Sampling) Chain 1: 0.00028 seconds (Total) Chain 1:=20 SAMPLING FOR MODEL 'b524cd829fcb9f50f6761f2451b62eec' NOW (CHAIN 2). Chain 2:=20 Chain 2: Gradient evaluation took 3e-06 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take= 0.03 seconds. Chain 2: Adjust your expectations accordingly! Chain 2:=20 Chain 2:=20 Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2:=20 Chain 2: Iteration: 1 / 10 [ 10%] (Warmup) Chain 2: Iteration: 2 / 10 [ 20%] (Warmup) Chain 2: Iteration: 3 / 10 [ 30%] (Warmup) Chain 2: Iteration: 4 / 10 [ 40%] (Warmup) Chain 2: Iteration: 5 / 10 [ 50%] (Warmup) Chain 2: Iteration: 6 / 10 [ 60%] (Sampling) Chain 2: Iteration: 7 / 10 [ 70%] (Sampling) Chain 2: Iteration: 8 / 10 [ 80%] (Sampling) Chain 2: Iteration: 9 / 10 [ 90%] (Sampling) Chain 2: Iteration: 10 / 10 [100%] (Sampling) Chain 2:=20 Chain 2: Elapsed Time: 0.000146 seconds (Warm-up) Chain 2: 0.000132 seconds (Sampling) Chain 2: 0.000278 seconds (Total) Chain 2:=20 SAMPLING FOR MODEL 'b524cd829fcb9f50f6761f2451b62eec' NOW (CHAIN 3). Chain 3:=20 Chain 3: Gradient evaluation took 6e-06 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take= 0.06 seconds. Chain 3: Adjust your expectations accordingly! Chain 3:=20 Chain 3:=20 Chain 3: WARNING: No variance estimation is Chain 3: performed for num_warmup < 20 Chain 3:=20 Chain 3: Iteration: 1 / 10 [ 10%] (Warmup) Chain 3: Iteration: 2 / 10 [ 20%] (Warmup) Chain 3: Iteration: 3 / 10 [ 30%] (Warmup) Chain 3: Iteration: 4 / 10 [ 40%] (Warmup) Chain 3: Iteration: 5 / 10 [ 50%] (Warmup) Chain 3: Iteration: 6 / 10 [ 60%] (Sampling) Chain 3: Iteration: 7 / 10 [ 70%] (Sampling) Chain 3: Iteration: 8 / 10 [ 80%] (Sampling) Chain 3: Iteration: 9 / 10 [ 90%] (Sampling) Chain 3: Iteration: 10 / 10 [100%] (Sampling) Chain 3:=20 Chain 3: Elapsed Time: 0.000271 seconds (Warm-up) Chain 3: 0.000253 seconds (Sampling) Chain 3: 0.000524 seconds (Total) Chain 3:=20 SAMPLING FOR MODEL 'b524cd829fcb9f50f6761f2451b62eec' NOW (CHAIN 4). Chain 4:=20 Chain 4: Gradient evaluation took 5e-06 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take= 0.05 seconds. Chain 4: Adjust your expectations accordingly! Chain 4:=20 Chain 4:=20 Chain 4: WARNING: No variance estimation is Chain 4: performed for num_warmup < 20 Chain 4:=20 Chain 4: Iteration: 1 / 10 [ 10%] (Warmup) Chain 4: Iteration: 2 / 10 [ 20%] (Warmup) Chain 4: Iteration: 3 / 10 [ 30%] (Warmup) Chain 4: Iteration: 4 / 10 [ 40%] (Warmup) Chain 4: Iteration: 5 / 10 [ 50%] (Warmup) Chain 4: Iteration: 6 / 10 [ 60%] (Sampling) Chain 4: Iteration: 7 / 10 [ 70%] (Sampling) Chain 4: Iteration: 8 / 10 [ 80%] (Sampling) Chain 4: Iteration: 9 / 10 [ 90%] (Sampling) Chain 4: Iteration: 10 / 10 [100%] (Sampling) Chain 4:=20 Chain 4: Elapsed Time: 0.00014 seconds (Warm-up) Chain 4: 0.000132 seconds (Sampling) Chain 4: 0.000272 seconds (Total) Chain 4:=20 Warning message: The largest R-hat is 1.07, indicating chains have not mixed. Running the chains for more iterations may help. See https://mc-stan.org/misc/warnings.html#r-hat=20 > > Inference for Stan model: b524cd829fcb9f50f6761f2451b62eec. 4 chains, each with iter=3D10; warmup=3D5; thin=3D1;=20 post-warmup draws per chain=3D5, total post-warmup draws=3D20. mean se_mean sd 2.5% 25% 50% 75% 97.5% n_eff Rhat y[1] -0.02 0.20 1.02 -1.80 -0.68 -0.05 0.59 1.86 26 0.89 y[2] 2.06 0.49 1.81 -1.29 0.78 1.96 3.48 5.00 14 1.08 lp__ -1.65 0.17 0.85 -3.08 -2.20 -1.64 -1.01 -0.41 26 0.81 Samples were drawn using NUTS(diag_e) at Tue Jul 12 17:28:00 2022. For each parameter, n_eff is a crude measure of effective sample size, and Rhat is the potential scale reduction factor on split chains (at=20 convergence, Rhat=3D1). >=20 --8<---------------cut here---------------end--------------->8--- Could you please show us an example like the above that fails when run in =E2=80=9Cguix shell -C=E2=80=9D? Please also provide the output of =E2= =80=9Cguix describe -f channels=E2=80=9D. Thank you! --=20 Ricardo