Last updated on 2025-04-19 06:49:56 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| InSilicoVA | 2 | 4 | 7 | |
| InterVA4 | 13 | |||
| openVA | 3 | 10 | ||
| SUMMER | 3 | 10 |
Current CRAN status: WARN: 2, NOTE: 4, OK: 7
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, r-release-linux-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: whether startup messages can be suppressed
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: dependencies in R code
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: S3 generic/method consistency
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: replacement functions
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: foreign function calls
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: R code for possible problems
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: for missing documentation entries
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: for code/documentation mismatches
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.4.0
Check: Rd \usage sections
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
Version: 1.1.2
Check: whether startup messages can be suppressed
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: dependencies in R code
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: S3 generic/method consistency
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: replacement functions
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: foreign function calls
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: R code for possible problems
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: for missing documentation entries
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: for code/documentation mismatches
Result: WARN
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: Rd \usage sections
Result: NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: tests
Result: ERROR
Running 'testthat.r' [25s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
> library(testthat)
> library(openVA)
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
────────────────────── 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.
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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
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.1.2
Check: tests
Result: ERROR
Running 'testthat.r' [33s]
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-oldrel-windows-x86_64
Current CRAN status: NOTE: 3, OK: 10
Version: 2.0.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-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-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64