Last updated on 2019-02-05 10:51:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2-7 | 23.03 | 82.82 | 105.85 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.2-7 | 19.89 | 64.63 | 84.52 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.2-7 | 131.35 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.2-7 | 124.68 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 2.2-7 | 56.00 | 318.00 | 374.00 | NOTE | |
| r-patched-linux-x86_64 | 2.2-7 | 23.82 | 78.20 | 102.02 | ERROR | |
| r-patched-solaris-x86 | 2.2-7 | 240.90 | NOTE | |||
| r-release-linux-x86_64 | 2.2-7 | 24.25 | 77.45 | 101.70 | ERROR | |
| r-release-windows-ix86+x86_64 | 2.2-7 | 41.00 | 254.00 | 295.00 | NOTE | |
| r-release-osx-x86_64 | 2.2-7 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 2.2-7 | 53.00 | 328.00 | 381.00 | NOTE | |
| r-oldrel-osx-x86_64 | 2.2-7 | NOTE |
Version: 2.2-7
Check: examples
Result: ERROR
Running examples in ‘ashr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ash
> ### Title: Adaptive Shrinkage
> ### Aliases: ash ash.workhorse
>
> ### ** Examples
>
>
> beta = c(rep(0,100),rnorm(100))
> sebetahat = abs(rnorm(200,0,1))
> betahat = rnorm(200,beta,sebetahat)
> beta.ash = ash(betahat, sebetahat)
Error in is.list(x) :
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
Calls: ash ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.2-7
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ashr)
>
> test_check("ashr")
── 1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), g = trueg) at testthat/test_binom.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), mode = "estimate") at testthat/test_binom.R:23
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 3. Error: lik_binom (identity link) with big n gives similar answers to norma
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n)) at testthat/test_binom.R:39
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#5
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), g = trueg, prior = "uniform") at testthat/test_binom.R:59
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#7
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), mode = "estimate") at testthat/test_binom.R:75
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 6. Error: df switches (@test_df.R#8) ───────────────────────────────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash.workhorse(betahat = betahat[1:5], sebetahat = sebetahat[1:5], df = Inf) at testthat/test_df.R:8
2: estimate_mixprop(data, g, prior, optmethod = optmethod, control = control, weights = weights)
3: do.call(optmethod, args = list(matrix_lik = matrix_lik, prior = prior, pi_init = pi_init,
control = control))
4: mixIP(matrix_lik = structure(c(1, 0.000993141072021091, 0.751594138244189, 0.480506102213957,
0.000127752493421005, 0.999999300351534, 0.00099571957030837, 0.751760654933696,
0.480630988938211, 0.000130456679523104, 0.999998598989935, 0.000998301045853174,
0.751927093803026, 0.480755857804589, 0.000133188181772012, 0.999997191128138, 0.00100347293448217,
0.752259738176577, 0.481005541964548, 0.000138733698076604, 0.999994354856764, 0.00101385250226441,
0.752924094130841, 0.481504695999367, 0.000150158737216649, 0.999988600174233, 0.00103475512283547,
0.75424908020497, 0.48250214697765, 0.000174376751015297, 0.999976762661325, 0.00107713688689031,
0.756884191648695, 0.484493620971243, 0.000228543519674271, 0.999951778328632, 0.00116422716300056,
0.762095311780531, 0.488462860486869, 0.000361930407957411, 0.999896598627926, 0.0013478798337255,
0.772283845447586, 0.496346535221033, 0.000746854177007261, 0.999765603283405, 0.00175439215142833,
0.791747463447666, 0.511894944155507, 0.0021456188623168, 0.99942271318594, 0.00273473614619273,
0.827187755754853, 0.542118827105042, 0.00885923754792946, 0.998426157226074, 0.00544722153622918,
0.885388330995896, 0.599106527486294, 0.0495488596988368, 0.995287390161415, 0.0145020567402157,
0.96014810780001, 0.699617542159869, 0.28745254866477, 0.985130856241669, 0.0511315742895792,
1, 0.851152252268936, 0.936445159851178, 0.953887393443776, 0.208862597987872, 0.906270108894674,
1, 1, 0.872006311422054, 0.680460592523044, 0.687845499733546, 0.985720228868147,
0.711621030875185, 0.715088568208871, 1, 0.488122544115151, 0.765289750680224, 0.503192069838324,
0.525333800107958, 0.75440198569814, 0.345156430854286, 0.543351149872505, 0.355810524821973
), .Dim = c(5L, 18L)), prior = c(10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1), pi_init = c(0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556),
control = list())
5: check_mosek_license()
6: tryCatch({
out <- Rmosek::mosek(x, opts = list(verbose = 0))
if (out$response$code != 0)
stop(paste("MOSEK is installed, but failed to run. A common issue is that\n",
"the license is expired unavailable. To troubleshoot, see:\n", "https://github.com/stephens999/ashr/blob/master/inst/rmosek-mac.md\n",
"https://github.com/stephens999/ashr/blob/master/inst/rmosek-linux.md"))
})
7: tryCatchList(expr, classes, parentenv, handlers)
8: Rmosek::mosek(x, opts = list(verbose = 0))
9: stop(msg)
── 7. Error: PosteriorMean is equal to weighted component-specific posterior mea
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_flashdata.R:2
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 8. Error: PosteriorSD squared is equal to weighted component mean2 minus post
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11) ─────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:11
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 10. Error: comp_postmean for missing data is 0 (@test_flashdata.R#16) ──────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:16
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 11. Error: comp_postprob for missing data is fitted pi (@test_flashdata.R#21)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:21
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 12. Error: prior is returned with correct components for flash data (@test_fl
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, method = "fdr", outputlevel = 5, pi_thresh = 1e-06) at testthat/test_flashdata.R:26
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 13. Error: logF error with df=(10,10) gives similar answers to normal error (
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(x, s) at testthat/test_logF.R:13
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 14. Error: sum of calc_vlogLR is same as calc_logLR (@test_loglik.R#52) ────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ashr::ash(z, 1, df = 4) at testthat/test_loglik.R:52
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 15. Error: missing data don't change results (@test_missing.R#4) ───────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, s) at testthat/test_missing.R:4
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 16. Error: ash mode 1 gives same results as mode 0 but shifted by 1 (@test_mo
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_mode.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 17. Error: new results match old ones (@test_old_vs_new.R#6) ──────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_old_vs_new.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 18. Error: control is passed to optmethod correctly when method is mixIP (@te
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, control = list(rtol = 0.1), outputlevel = 3) at testthat/test_optmethod.R:17
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 19. Error: lik_pois (identity link) fitted g is close to true g (@test_pois.R
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), g = trueg) at testthat/test_pois.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 20. Error: lik_pois (identity link) fitted mode is close to true mode (@test_
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), mode = "estimate") at testthat/test_pois.R:20
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 21. Error: lik_pois (identity link) with high intensities gives similar answe
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x)) at testthat/test_pois.R:35
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 22. Error: lik_pois (log link) fitted g is close to true g (@test_pois.R#54)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), g = trueg) at testthat/test_pois.R:54
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 23. Error: lik_pois (log link) fitted mode is close to true mode (@test_pois.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), mode = "estimate") at testthat/test_pois.R:68
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 24. Error: get_post_sample works as expected (@test_postsample.R#7) ────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, se, "normal") at testthat/test_postsample.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 25. Error: test pruning with and without flash (@test_prune.R#14) ─────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_prune.R:14
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 26. Error: ash with automatic truncfun gives similar answers to default (@tes
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_truncgen.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 27. Error: optimization with weights matches expectations (@test_w_mixEM.R#8)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, optmethod = "mixIP", weights = c(rep(1, 50), rep(0, 50)), g = get_fitted_g(z.ash)) at testthat/test_w_mixEM.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 1 FAILED: 27
1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#8)
2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#23)
3. Error: lik_binom (identity link) with big n gives similar answers to normal likelihood (@test_binom.R#39)
4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#59)
5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#75)
6. Error: df switches (@test_df.R#8)
7. Error: PosteriorMean is equal to weighted component-specific posterior means (@test_flashdata.R#2)
8. Error: PosteriorSD squared is equal to weighted component mean2 minus posterior mean all squared (@test_flashdata.R#6)
9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11)
1. ...
Error: testthat unit tests failed
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.2-7
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘adaptive_shrinkage.Rmd’ using rmarkdown
Quitting from lines 87-89 (adaptive_shrinkage.Rmd)
Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
--- failed re-building ‘adaptive_shrinkage.Rmd’
SUMMARY: processing the following file failed:
‘adaptive_shrinkage.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.2-7
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ashr)
>
> test_check("ashr")
── 1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), g = trueg) at testthat/test_binom.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), mode = "estimate") at testthat/test_binom.R:23
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 3. Error: lik_binom (identity link) with big n gives similar answers to norma
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n)) at testthat/test_binom.R:39
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#5
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), g = trueg, prior = "uniform") at testthat/test_binom.R:59
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#7
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), mode = "estimate") at testthat/test_binom.R:75
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 6. Error: df switches (@test_df.R#8) ───────────────────────────────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash.workhorse(betahat = betahat[1:5], sebetahat = sebetahat[1:5], df = Inf) at testthat/test_df.R:8
2: estimate_mixprop(data, g, prior, optmethod = optmethod, control = control, weights = weights)
3: do.call(optmethod, args = list(matrix_lik = matrix_lik, prior = prior, pi_init = pi_init,
control = control))
4: mixIP(matrix_lik = structure(c(1, 0.000993141072021091, 0.751594138244189, 0.480506102213957,
0.000127752493421005, 0.999999300351534, 0.00099571957030837, 0.751760654933696,
0.480630988938211, 0.000130456679523104, 0.999998598989935, 0.000998301045853174,
0.751927093803026, 0.480755857804589, 0.000133188181772012, 0.999997191128138, 0.00100347293448217,
0.752259738176577, 0.481005541964548, 0.000138733698076604, 0.999994354856764, 0.00101385250226441,
0.752924094130841, 0.481504695999367, 0.000150158737216649, 0.999988600174233, 0.00103475512283547,
0.75424908020497, 0.48250214697765, 0.000174376751015297, 0.999976762661325, 0.00107713688689031,
0.756884191648695, 0.484493620971243, 0.000228543519674271, 0.999951778328632, 0.00116422716300056,
0.762095311780531, 0.488462860486869, 0.000361930407957411, 0.999896598627926, 0.0013478798337255,
0.772283845447586, 0.496346535221033, 0.000746854177007261, 0.999765603283405, 0.00175439215142833,
0.791747463447666, 0.511894944155507, 0.0021456188623168, 0.99942271318594, 0.00273473614619273,
0.827187755754853, 0.542118827105042, 0.00885923754792946, 0.998426157226074, 0.00544722153622918,
0.885388330995896, 0.599106527486294, 0.0495488596988368, 0.995287390161415, 0.0145020567402157,
0.96014810780001, 0.699617542159869, 0.28745254866477, 0.985130856241669, 0.0511315742895792,
1, 0.851152252268936, 0.936445159851178, 0.953887393443776, 0.208862597987872, 0.906270108894674,
1, 1, 0.872006311422054, 0.680460592523044, 0.687845499733546, 0.985720228868147,
0.711621030875185, 0.715088568208871, 1, 0.488122544115151, 0.765289750680224, 0.503192069838324,
0.525333800107958, 0.75440198569814, 0.345156430854286, 0.543351149872505, 0.355810524821973
), .Dim = c(5L, 18L)), prior = c(10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1), pi_init = c(0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556),
control = list())
5: check_mosek_license()
6: tryCatch({
out <- Rmosek::mosek(x, opts = list(verbose = 0))
if (out$response$code != 0)
stop(paste("MOSEK is installed, but failed to run. A common issue is that\n",
"the license is expired unavailable. To troubleshoot, see:\n", "https://github.com/stephens999/ashr/blob/master/inst/rmosek-mac.md\n",
"https://github.com/stephens999/ashr/blob/master/inst/rmosek-linux.md"))
})
7: tryCatchList(expr, classes, parentenv, handlers)
8: Rmosek::mosek(x, opts = list(verbose = 0))
9: stop(msg)
── 7. Error: PosteriorMean is equal to weighted component-specific posterior mea
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_flashdata.R:2
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 8. Error: PosteriorSD squared is equal to weighted component mean2 minus post
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11) ─────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:11
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 10. Error: comp_postmean for missing data is 0 (@test_flashdata.R#16) ──────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:16
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 11. Error: comp_postprob for missing data is fitted pi (@test_flashdata.R#21)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:21
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 12. Error: prior is returned with correct components for flash data (@test_fl
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, method = "fdr", outputlevel = 5, pi_thresh = 1e-06) at testthat/test_flashdata.R:26
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 13. Error: logF error with df=(10,10) gives similar answers to normal error (
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(x, s) at testthat/test_logF.R:13
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 14. Error: sum of calc_vlogLR is same as calc_logLR (@test_loglik.R#52) ────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ashr::ash(z, 1, df = 4) at testthat/test_loglik.R:52
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 15. Error: missing data don't change results (@test_missing.R#4) ───────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, s) at testthat/test_missing.R:4
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 16. Error: ash mode 1 gives same results as mode 0 but shifted by 1 (@test_mo
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_mode.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 17. Error: new results match old ones (@test_old_vs_new.R#6) ──────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_old_vs_new.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 18. Error: control is passed to optmethod correctly when method is mixIP (@te
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, control = list(rtol = 0.1), outputlevel = 3) at testthat/test_optmethod.R:17
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 19. Error: lik_pois (identity link) fitted g is close to true g (@test_pois.R
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), g = trueg) at testthat/test_pois.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 20. Error: lik_pois (identity link) fitted mode is close to true mode (@test_
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), mode = "estimate") at testthat/test_pois.R:20
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 21. Error: lik_pois (identity link) with high intensities gives similar answe
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x)) at testthat/test_pois.R:35
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 22. Error: lik_pois (log link) fitted g is close to true g (@test_pois.R#54)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), g = trueg) at testthat/test_pois.R:54
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 23. Error: lik_pois (log link) fitted mode is close to true mode (@test_pois.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), mode = "estimate") at testthat/test_pois.R:68
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 24. Error: get_post_sample works as expected (@test_postsample.R#7) ────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, se, "normal") at testthat/test_postsample.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 25. Error: test pruning with and without flash (@test_prune.R#14) ─────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_prune.R:14
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 26. Error: ash with automatic truncfun gives similar answers to default (@tes
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_truncgen.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 27. Error: optimization with weights matches expectations (@test_w_mixEM.R#8)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, optmethod = "mixIP", weights = c(rep(1, 50), rep(0, 50)), g = get_fitted_g(z.ash)) at testthat/test_w_mixEM.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 1 FAILED: 27
1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#8)
2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#23)
3. Error: lik_binom (identity link) with big n gives similar answers to normal likelihood (@test_binom.R#39)
4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#59)
5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#75)
6. Error: df switches (@test_df.R#8)
7. Error: PosteriorMean is equal to weighted component-specific posterior means (@test_flashdata.R#2)
8. Error: PosteriorSD squared is equal to weighted component mean2 minus posterior mean all squared (@test_flashdata.R#6)
9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.2-7
Check: examples
Result: ERROR
Running examples in ‘ashr-Ex.R’ failed
The error most likely occurred in:
> ### Name: ash
> ### Title: Adaptive Shrinkage
> ### Aliases: ash ash.workhorse
>
> ### ** Examples
>
>
> beta = c(rep(0,100),rnorm(100))
> sebetahat = abs(rnorm(200,0,1))
> betahat = rnorm(200,beta,sebetahat)
> beta.ash = ash(betahat, sebetahat)
Error in is.list(x) :
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
Calls: ash ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.2-7
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ashr)
>
> test_check("ashr")
── 1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), g = trueg) at testthat/test_binom.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), mode = "estimate") at testthat/test_binom.R:23
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 3. Error: lik_binom (identity link) with big n gives similar answers to norma
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n)) at testthat/test_binom.R:39
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#5
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), g = trueg, prior = "uniform") at testthat/test_binom.R:59
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#7
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), mode = "estimate") at testthat/test_binom.R:75
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 6. Error: df switches (@test_df.R#8) ───────────────────────────────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash.workhorse(betahat = betahat[1:5], sebetahat = sebetahat[1:5], df = Inf) at testthat/test_df.R:8
2: estimate_mixprop(data, g, prior, optmethod = optmethod, control = control, weights = weights)
3: do.call(optmethod, args = list(matrix_lik = matrix_lik, prior = prior, pi_init = pi_init,
control = control))
4: mixIP(matrix_lik = structure(c(1, 0.000993141072021091, 0.751594138244189, 0.480506102213957,
0.000127752493421005, 0.999999300351534, 0.00099571957030837, 0.751760654933696,
0.480630988938211, 0.000130456679523104, 0.999998598989935, 0.000998301045853174,
0.751927093803026, 0.480755857804589, 0.000133188181772012, 0.999997191128138, 0.00100347293448217,
0.752259738176577, 0.481005541964548, 0.000138733698076604, 0.999994354856764, 0.00101385250226441,
0.752924094130841, 0.481504695999367, 0.000150158737216649, 0.999988600174233, 0.00103475512283547,
0.75424908020497, 0.48250214697765, 0.000174376751015297, 0.999976762661325, 0.00107713688689031,
0.756884191648695, 0.484493620971243, 0.000228543519674271, 0.999951778328632, 0.00116422716300056,
0.762095311780531, 0.488462860486869, 0.000361930407957411, 0.999896598627926, 0.0013478798337255,
0.772283845447586, 0.496346535221033, 0.000746854177007261, 0.999765603283405, 0.00175439215142833,
0.791747463447666, 0.511894944155507, 0.0021456188623168, 0.99942271318594, 0.00273473614619273,
0.827187755754853, 0.542118827105042, 0.00885923754792946, 0.998426157226074, 0.00544722153622918,
0.885388330995896, 0.599106527486294, 0.0495488596988368, 0.995287390161415, 0.0145020567402157,
0.96014810780001, 0.699617542159869, 0.28745254866477, 0.985130856241669, 0.0511315742895792,
1, 0.851152252268936, 0.936445159851178, 0.953887393443776, 0.208862597987872, 0.906270108894674,
1, 1, 0.872006311422054, 0.680460592523044, 0.687845499733546, 0.985720228868147,
0.711621030875185, 0.715088568208871, 1, 0.488122544115151, 0.765289750680224, 0.503192069838324,
0.525333800107958, 0.75440198569814, 0.345156430854286, 0.543351149872505, 0.355810524821973
), .Dim = c(5L, 18L)), prior = c(10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1), pi_init = c(0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556),
control = list())
5: check_mosek_license()
6: tryCatch({
out <- Rmosek::mosek(x, opts = list(verbose = 0))
if (out$response$code != 0)
stop(paste("MOSEK is installed, but failed to run. A common issue is that\n",
"the license is expired unavailable. To troubleshoot, see:\n", "https://github.com/stephens999/ashr/blob/master/inst/rmosek-mac.md\n",
"https://github.com/stephens999/ashr/blob/master/inst/rmosek-linux.md"))
})
7: tryCatchList(expr, classes, parentenv, handlers)
8: Rmosek::mosek(x, opts = list(verbose = 0))
9: stop(msg)
── 7. Error: PosteriorMean is equal to weighted component-specific posterior mea
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_flashdata.R:2
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 8. Error: PosteriorSD squared is equal to weighted component mean2 minus post
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11) ─────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:11
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 10. Error: comp_postmean for missing data is 0 (@test_flashdata.R#16) ──────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:16
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 11. Error: comp_postprob for missing data is fitted pi (@test_flashdata.R#21)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:21
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 12. Error: prior is returned with correct components for flash data (@test_fl
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, method = "fdr", outputlevel = 5, pi_thresh = 1e-06) at testthat/test_flashdata.R:26
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 13. Error: logF error with df=(10,10) gives similar answers to normal error (
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(x, s) at testthat/test_logF.R:13
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 14. Error: sum of calc_vlogLR is same as calc_logLR (@test_loglik.R#52) ────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ashr::ash(z, 1, df = 4) at testthat/test_loglik.R:52
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 15. Error: missing data don't change results (@test_missing.R#4) ───────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, s) at testthat/test_missing.R:4
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 16. Error: ash mode 1 gives same results as mode 0 but shifted by 1 (@test_mo
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_mode.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 17. Error: new results match old ones (@test_old_vs_new.R#6) ──────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_old_vs_new.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 18. Error: control is passed to optmethod correctly when method is mixIP (@te
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, control = list(rtol = 0.1), outputlevel = 3) at testthat/test_optmethod.R:17
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 19. Error: lik_pois (identity link) fitted g is close to true g (@test_pois.R
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), g = trueg) at testthat/test_pois.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 20. Error: lik_pois (identity link) fitted mode is close to true mode (@test_
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), mode = "estimate") at testthat/test_pois.R:20
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 21. Error: lik_pois (identity link) with high intensities gives similar answe
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x)) at testthat/test_pois.R:35
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 22. Error: lik_pois (log link) fitted g is close to true g (@test_pois.R#54)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), g = trueg) at testthat/test_pois.R:54
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 23. Error: lik_pois (log link) fitted mode is close to true mode (@test_pois.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), mode = "estimate") at testthat/test_pois.R:68
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 24. Error: get_post_sample works as expected (@test_postsample.R#7) ────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, se, "normal") at testthat/test_postsample.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 25. Error: test pruning with and without flash (@test_prune.R#14) ─────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_prune.R:14
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 26. Error: ash with automatic truncfun gives similar answers to default (@tes
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_truncgen.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 27. Error: optimization with weights matches expectations (@test_w_mixEM.R#8)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, optmethod = "mixIP", weights = c(rep(1, 50), rep(0, 50)), g = get_fitted_g(z.ash)) at testthat/test_w_mixEM.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 1 FAILED: 27
1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#8)
2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#23)
3. Error: lik_binom (identity link) with big n gives similar answers to normal likelihood (@test_binom.R#39)
4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#59)
5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#75)
6. Error: df switches (@test_df.R#8)
7. Error: PosteriorMean is equal to weighted component-specific posterior means (@test_flashdata.R#2)
8. Error: PosteriorSD squared is equal to weighted component mean2 minus posterior mean all squared (@test_flashdata.R#6)
9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.2-7
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘adaptive_shrinkage.Rmd’ using rmarkdown
Quitting from lines 87-89 (adaptive_shrinkage.Rmd)
Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
--- failed re-building ‘adaptive_shrinkage.Rmd’
SUMMARY: processing the following file failed:
‘adaptive_shrinkage.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.2-7
Check: tests
Result: ERROR
Running ‘testthat.R’ [12s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ashr)
>
> test_check("ashr")
── 1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), g = trueg) at testthat/test_binom.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n), mode = "estimate") at testthat/test_binom.R:23
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 3. Error: lik_binom (identity link) with big n gives similar answers to norma
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n)) at testthat/test_binom.R:39
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#5
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), g = trueg, prior = "uniform") at testthat/test_binom.R:59
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#7
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_binom(x, n, link = "logit"), mode = "estimate") at testthat/test_binom.R:75
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 6. Error: df switches (@test_df.R#8) ───────────────────────────────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash.workhorse(betahat = betahat[1:5], sebetahat = sebetahat[1:5], df = Inf) at testthat/test_df.R:8
2: estimate_mixprop(data, g, prior, optmethod = optmethod, control = control, weights = weights)
3: do.call(optmethod, args = list(matrix_lik = matrix_lik, prior = prior, pi_init = pi_init,
control = control))
4: mixIP(matrix_lik = structure(c(1, 0.000993141072021091, 0.751594138244189, 0.480506102213957,
0.000127752493421005, 0.999999300351534, 0.00099571957030837, 0.751760654933696,
0.480630988938211, 0.000130456679523104, 0.999998598989935, 0.000998301045853174,
0.751927093803026, 0.480755857804589, 0.000133188181772012, 0.999997191128138, 0.00100347293448217,
0.752259738176577, 0.481005541964548, 0.000138733698076604, 0.999994354856764, 0.00101385250226441,
0.752924094130841, 0.481504695999367, 0.000150158737216649, 0.999988600174233, 0.00103475512283547,
0.75424908020497, 0.48250214697765, 0.000174376751015297, 0.999976762661325, 0.00107713688689031,
0.756884191648695, 0.484493620971243, 0.000228543519674271, 0.999951778328632, 0.00116422716300056,
0.762095311780531, 0.488462860486869, 0.000361930407957411, 0.999896598627926, 0.0013478798337255,
0.772283845447586, 0.496346535221033, 0.000746854177007261, 0.999765603283405, 0.00175439215142833,
0.791747463447666, 0.511894944155507, 0.0021456188623168, 0.99942271318594, 0.00273473614619273,
0.827187755754853, 0.542118827105042, 0.00885923754792946, 0.998426157226074, 0.00544722153622918,
0.885388330995896, 0.599106527486294, 0.0495488596988368, 0.995287390161415, 0.0145020567402157,
0.96014810780001, 0.699617542159869, 0.28745254866477, 0.985130856241669, 0.0511315742895792,
1, 0.851152252268936, 0.936445159851178, 0.953887393443776, 0.208862597987872, 0.906270108894674,
1, 1, 0.872006311422054, 0.680460592523044, 0.687845499733546, 0.985720228868147,
0.711621030875185, 0.715088568208871, 1, 0.488122544115151, 0.765289750680224, 0.503192069838324,
0.525333800107958, 0.75440198569814, 0.345156430854286, 0.543351149872505, 0.355810524821973
), .Dim = c(5L, 18L)), prior = c(10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1), pi_init = c(0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556,
0.0555555555555556, 0.0555555555555556, 0.0555555555555556, 0.0555555555555556),
control = list())
5: check_mosek_license()
6: tryCatch({
out <- Rmosek::mosek(x, opts = list(verbose = 0))
if (out$response$code != 0)
stop(paste("MOSEK is installed, but failed to run. A common issue is that\n",
"the license is expired unavailable. To troubleshoot, see:\n", "https://github.com/stephens999/ashr/blob/master/inst/rmosek-mac.md\n",
"https://github.com/stephens999/ashr/blob/master/inst/rmosek-linux.md"))
})
7: tryCatchList(expr, classes, parentenv, handlers)
8: Rmosek::mosek(x, opts = list(verbose = 0))
9: stop(msg)
── 7. Error: PosteriorMean is equal to weighted component-specific posterior mea
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_flashdata.R:2
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 8. Error: PosteriorSD squared is equal to weighted component mean2 minus post
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11) ─────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4, mixcompdist = "normal") at testthat/test_flashdata.R:11
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 10. Error: comp_postmean for missing data is 0 (@test_flashdata.R#16) ──────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:16
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 11. Error: comp_postprob for missing data is fitted pi (@test_flashdata.R#21)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(c(NA, z), 1, outputlevel = 4) at testthat/test_flashdata.R:21
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 12. Error: prior is returned with correct components for flash data (@test_fl
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, method = "fdr", outputlevel = 5, pi_thresh = 1e-06) at testthat/test_flashdata.R:26
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 13. Error: logF error with df=(10,10) gives similar answers to normal error (
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(x, s) at testthat/test_logF.R:13
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 14. Error: sum of calc_vlogLR is same as calc_logLR (@test_loglik.R#52) ────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ashr::ash(z, 1, df = 4) at testthat/test_loglik.R:52
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 15. Error: missing data don't change results (@test_missing.R#4) ───────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, s) at testthat/test_missing.R:4
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 16. Error: ash mode 1 gives same results as mode 0 but shifted by 1 (@test_mo
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_mode.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 17. Error: new results match old ones (@test_old_vs_new.R#6) ──────────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_old_vs_new.R:6
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 18. Error: control is passed to optmethod correctly when method is mixIP (@te
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, control = list(rtol = 0.1), outputlevel = 3) at testthat/test_optmethod.R:17
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 19. Error: lik_pois (identity link) fitted g is close to true g (@test_pois.R
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), g = trueg) at testthat/test_pois.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 20. Error: lik_pois (identity link) fitted mode is close to true mode (@test_
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x), mode = "estimate") at testthat/test_pois.R:20
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 21. Error: lik_pois (identity link) with high intensities gives similar answe
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x)) at testthat/test_pois.R:35
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 22. Error: lik_pois (log link) fitted g is close to true g (@test_pois.R#54)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), g = trueg) at testthat/test_pois.R:54
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 23. Error: lik_pois (log link) fitted mode is close to true mode (@test_pois.
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(rep(0, length(x)), 1, lik = lik_pois(x, link = "log"), mode = "estimate") at testthat/test_pois.R:68
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 24. Error: get_post_sample works as expected (@test_postsample.R#7) ────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, se, "normal") at testthat/test_postsample.R:7
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 25. Error: test pruning with and without flash (@test_prune.R#14) ─────────
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, outputlevel = 4) at testthat/test_prune.R:14
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 26. Error: ash with automatic truncfun gives similar answers to default (@tes
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1) at testthat/test_truncgen.R:22
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
── 27. Error: optimization with weights matches expectations (@test_w_mixEM.R#8)
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
1: ash(z, 1, optmethod = "mixIP", weights = c(rep(1, 50), rep(0, 50)), g = get_fitted_g(z.ash)) at testthat/test_w_mixEM.R:8
2: utils::modifyList(ash.workhorse(betahat, sebetahat, mixcompdist = mixcompdist, df = df,
...), list(call = match.call()))
3: stopifnot(is.list(x), is.list(val))
4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir),
error = function(e) {
e$call <- cl.i
stop(e)
}), warning = function(w) {
w$call <- cl.i
w
})
5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
e$call <- cl.i
stop(e)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 1 FAILED: 27
1. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#8)
2. Error: lik_binom (identity link) fitted g is close to true g (@test_binom.R#23)
3. Error: lik_binom (identity link) with big n gives similar answers to normal likelihood (@test_binom.R#39)
4. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#59)
5. Error: lik_binom (logit link) fitted g is close to true g (@test_binom.R#75)
6. Error: df switches (@test_df.R#8)
7. Error: PosteriorMean is equal to weighted component-specific posterior means (@test_flashdata.R#2)
8. Error: PosteriorSD squared is equal to weighted component mean2 minus posterior mean all squared (@test_flashdata.R#6)
9. Error: comp_postmean for null component is 0 (@test_flashdata.R#11)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.2-7
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Flavor: r-devel-windows-ix86+x86_64
Version: 2.2-7
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Quitting from lines 87-89 (adaptive_shrinkage.Rmd)
Error: processing vignette ‘adaptive_shrinkage.Rmd’ failed with diagnostics:
Unknown exported object. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.2-7
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: ‘REBayes’ ‘Rmosek’
Flavors: r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64