CRAN Package Check Results for Package ashr

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

Check Details

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