CRAN Package Check Results for Maintainer ‘Zehang Richard Li <lizehang at gmail.com>’

Last updated on 2025-04-12 20:52:19 CEST.

Package	ERROR	NOTE	OK
InSilicoVA		4	10
InterVA4			14
openVA	1		14
SUMMER		7	7

Package InSilicoVA

Current CRAN status: NOTE: 4, OK: 10

Version: 1.4.0
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: csmf.diag.Rd: heidel.diag, gelman.diag Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64

Package InterVA4

Current CRAN status: OK: 14

Package openVA

Current CRAN status: ERROR: 1, OK: 14

Version: 1.1.2
Check: tests
Result: ERROR Running 'testthat.r' [36s] Running the tests in 'tests/testthat.r' failed. Complete output: > library(testthat) > library(openVA) ────────────────────── Attaching packages for openVA 1.1.2 ───────────────────── ✔ InSilicoVA 1.4.0 ✔ InterVA4 1.7.6 ✔ InterVA5 1.1.3 ✔ Tariff 1.0.5 ── Optional packages (require manual installation if not attached) ───────────── × nbc4va If you need to use these methods, you may need to load or install the packages: nbc4va. > > test_check("openVA") InSilicoVA Sampler Initiated, 200 Iterations to Sample Error in .jcall(obj, "[D", "Fit", dimensions.j, probbase.j, probbase_order.j, : java.awt.HeadlessException: The application does not have desktop access, but this program performed an operation which requires it. ..........10% completed ..........20% completed ..........30% completed ..........40% completed ..........50% completed ..........60% completed ..........70% completed ..........80% completed ..........90% completed ..........100% completed .10% completed .20% completed .30% completed .40% completed .50% completed .60% completed .70% completed .80% completed .90% completed .100% completed 100% completed Start re-sampling for significant Tariff cells Calculating ranks InSilicoVA Sampler Initiated, 200 Iterations to Sample Error in .jcall(obj, "[D", "Fit", dimensions.j, probbase.j, probbase_order.j, : java.awt.HeadlessException: The application does not have desktop access, but this program performed an operation which requires it. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 246 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('tests.algorithm.r:24:3'): Insilico - ID and output correct ────────── Error in `insilico.fit(data = data, isNumeric = isNumeric, updateCondProb = updateCondProb, keepProbbase.level = keepProbbase.level, CondProb = CondProb, CondProbNum = CondProbNum, datacheck = FALSE, datacheck.missing = FALSE, warning.write = FALSE, external.sep = FALSE, Nsim = Nsim, thin = thin, burnin = burnin, auto.length = auto.length, conv.csmf = conv.csmf, jump.scale = jump.scale, levels.prior = levels.prior, levels.strength = levels.strength, trunc.min = trunc.min, trunc.max = trunc.max, subpop = subpop, java_option = java_option, seed = seed, phy.code = phy.code, phy.cat = phy.cat, phy.unknown = phy.unknown, phy.external = phy.external, phy.debias = phy.debias, exclude.impossible.cause = FALSE, indiv.CI = indiv.CI, impossible.combination = impossible.combination, customization.dev = TRUE, Probbase_by_symp.dev = FALSE, probbase.dev = probbase.touse, table.dev = table.alpha, table.num.dev = table.num, gstable.dev = colnames(probbase.touse), nlevel.dev = 15)`: Backtrace: ▆ 1. └─openVA::codeVA(...) at tests.algorithm.r:24:3 2. ├─base::do.call("insilico.train", pairlist(args)[[1]][-1]) 3. └─InSilicoVA::insilico.train(...) 4. └─InSilicoVA::insilico.fit(...) ── Error ('tests.stackplot.r:22:1'): (code run outside of `test_that()`) ─────── Error in `insilico.fit(data = data, isNumeric = isNumeric, updateCondProb = updateCondProb, keepProbbase.level = keepProbbase.level, CondProb = CondProb, CondProbNum = CondProbNum, datacheck = FALSE, datacheck.missing = FALSE, warning.write = FALSE, external.sep = FALSE, Nsim = Nsim, thin = thin, burnin = burnin, auto.length = auto.length, conv.csmf = conv.csmf, jump.scale = jump.scale, levels.prior = levels.prior, levels.strength = levels.strength, trunc.min = trunc.min, trunc.max = trunc.max, subpop = subpop, java_option = java_option, seed = seed, phy.code = phy.code, phy.cat = phy.cat, phy.unknown = phy.unknown, phy.external = phy.external, phy.debias = phy.debias, exclude.impossible.cause = FALSE, indiv.CI = indiv.CI, impossible.combination = impossible.combination, customization.dev = TRUE, Probbase_by_symp.dev = FALSE, probbase.dev = probbase.touse, table.dev = table.alpha, table.num.dev = table.num, gstable.dev = colnames(probbase.touse), nlevel.dev = 15)`: Backtrace: ▆ 1. └─openVA::codeVA(...) at tests.stackplot.r:22:1 2. ├─base::do.call("insilico.train", pairlist(args)[[1]][-1]) 3. └─InSilicoVA::insilico.train(...) 4. └─InSilicoVA::insilico.fit(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 246 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Package SUMMER

Current CRAN status: NOTE: 7, OK: 7

Version: 2.0.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘INLA’ Flavors: r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.0.0
Check: installed package size
Result: NOTE installed size is 6.7Mb sub-directories of 1Mb or more: data 2.0Mb doc 3.1Mb help 1.0Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64