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Last updated on 2026-07-21 18:50:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.25.1 | 11.93 | 239.68 | 251.61 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0.25.1 | 8.69 | 174.39 | 183.08 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.0.25.1 | 20.00 | 351.88 | 371.88 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.25.1 | 168.87 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.25.1 | 14.00 | 240.00 | 254.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.25.1 | 12.25 | 222.61 | 234.86 | OK | |
| r-release-linux-x86_64 | 1.0.25.1 | 10.63 | 225.57 | 236.20 | OK | |
| r-release-macos-arm64 | 1.0.25.1 | 3.00 | 62.00 | 65.00 | NOTE | |
| r-release-macos-x86_64 | 1.0.25.1 | 9.00 | 235.00 | 244.00 | OK | |
| r-release-windows-x86_64 | 1.0.25.1 | 13.00 | 243.00 | 256.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.25.1 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.0.25.1 | 8.00 | 281.00 | 289.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.25.1 | 18.00 | 312.00 | 330.00 | OK |
Version: 1.0.25.1
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
bbmle/tests/binomtest1.R (.Names: 1)
bbmle/tests/formulatest.R (.Label: 2, .Names: 2)
bbmle/tests/mortanal.R (.Label: 2, .Names: 1)
bbmle/tests/startvals2.R (.Names: 2, .Label: 1)
'.Names' should be changed to 'names'.
'.Label' should be changed to 'levels'.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 1.0.25.1
Check: tests
Result: NOTE
Running ‘BIC.R’ [2s/3s]
Comparing ‘BIC.Rout’ to ‘BIC.Rout.save’ ... OK
Running ‘ICtab.R’ [2s/3s]
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’ [0s/0s]
Running ‘binomtest1.R’ [3s/5s]
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ...
12,14d11
< Warning message:
< In structure(list(Initial = as.integer(c(5, 5, 10, 10, 15, 15, 20, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘boundstest.R’ [0s/0s]
Running ‘controleval.R’ [2s/3s]
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘eval.R’ [3s/5s]
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’ [4s/5s]
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ...
29,31d28
< Warning message:
< In structure(list(TBL = as.integer(c(9, 9, 9, 12, 12, 12, 21, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
335,341d331
< Warning messages:
< 1: In structure(as.integer(c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(15, 15, 15, 15, 15, 15, 15, 15, 15, 15, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(exper = as.integer(c(1, 1, 1, 1, 1, 1, 1, 1, 1, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘glmcomp.R’ [4s/4s]
Comparing ‘glmcomp.Rout’ to ‘glmcomp.Rout.save’ ... OK
Running ‘gradient_vecpar_profile.R’ [17s/23s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’ [3s/4s]
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ... OK
Running ‘impsamp.R’ [3s/3s]
Running ‘methods.R’ [3s/3s]
Comparing ‘methods.Rout’ to ‘methods.Rout.save’ ... OK
Running ‘mortanal.R’ [3s/4s]
Comparing ‘mortanal.Rout’ to ‘mortanal.Rout.save’ ...
48,54d47
< Warning messages:
< 1: In structure(as.integer(c(20, 77, 79, 21, 33, 40, 11, 28, 43, 85, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(indiv = structure(as.integer(c(20, 77, 79, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘optimize.R’ [3s/3s]
Comparing ‘optimize.Rout’ to ‘optimize.Rout.save’ ... OK
Running ‘optimizers.R’ [2s/3s]
Comparing ‘optimizers.Rout’ to ‘optimizers.Rout.save’ ... OK
Running ‘optimx.R’ [11s/13s]
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ... OK
Running ‘order.R’ [3s/4s]
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’ [3s/3s]
Comparing ‘parscale.Rout’ to ‘parscale.Rout.save’ ... OK
Running ‘predict.R’ [3s/3s]
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘prof_newmin.R’ [3s/3s]
Running ‘prof_spec.R’ [3s/4s]
Running ‘profbound.R’ [3s/4s]
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ... OK
Running ‘richards.R’ [13s/16s]
Comparing ‘richards.Rout’ to ‘richards.Rout.save’ ... OK
Running ‘startvals.R’ [2s/4s]
Comparing ‘startvals.Rout’ to ‘startvals.Rout.save’ ... OK
Running ‘startvals2.R’ [3s/4s]
Comparing ‘startvals2.Rout’ to ‘startvals2.Rout.save’ ...
165,171d164
< Warning messages:
< 1: In structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(c(34L, 57L, 77L, 114L, 115L, 116L, 117L, 125L, 141L, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(list(TOTCONES = c(19, 42, 40, 68, 5, 0, 21, 114, 37, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘test-relist1.R’ [3s/3s]
Comparing ‘test-relist1.Rout’ to ‘test-relist1.Rout.save’ ... OK
Running ‘testbounds.R’ [2s/3s]
Comparing ‘testbounds.Rout’ to ‘testbounds.Rout.save’ ... OK
Running ‘testderiv.R’ [3s/3s]
Comparing ‘testderiv.Rout’ to ‘testderiv.Rout.save’ ... OK
Running ‘testenv.R’ [3s/4s]
Comparing ‘testenv.Rout’ to ‘testenv.Rout.save’ ... OK
Running ‘testparpred.R’ [3s/3s]
Comparing ‘testparpred.Rout’ to ‘testparpred.Rout.save’ ... OK
Running ‘tmptest.R’ [2s/4s]
Comparing ‘tmptest.Rout’ to ‘tmptest.Rout.save’ ... OK
Running ‘update.R’ [3s/3s]
Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.25.1
Check: tests
Result: NOTE
Running ‘BIC.R’ [2s/2s]
Comparing ‘BIC.Rout’ to ‘BIC.Rout.save’ ... OK
Running ‘ICtab.R’ [2s/2s]
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’ [0s/0s]
Running ‘binomtest1.R’ [2s/3s]
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ...
12,14d11
< Warning message:
< In structure(list(Initial = as.integer(c(5, 5, 10, 10, 15, 15, 20, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘boundstest.R’ [0s/0s]
Running ‘controleval.R’ [2s/2s]
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘eval.R’ [2s/3s]
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’ [3s/3s]
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ...
29,31d28
< Warning message:
< In structure(list(TBL = as.integer(c(9, 9, 9, 12, 12, 12, 21, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
335,341d331
< Warning messages:
< 1: In structure(as.integer(c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(15, 15, 15, 15, 15, 15, 15, 15, 15, 15, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(exper = as.integer(c(1, 1, 1, 1, 1, 1, 1, 1, 1, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘glmcomp.R’ [3s/4s]
Comparing ‘glmcomp.Rout’ to ‘glmcomp.Rout.save’ ... OK
Running ‘gradient_vecpar_profile.R’ [13s/18s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’ [2s/3s]
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ... OK
Running ‘impsamp.R’ [2s/3s]
Running ‘methods.R’ [2s/3s]
Comparing ‘methods.Rout’ to ‘methods.Rout.save’ ... OK
Running ‘mortanal.R’ [2s/3s]
Comparing ‘mortanal.Rout’ to ‘mortanal.Rout.save’ ...
48,54d47
< Warning messages:
< 1: In structure(as.integer(c(20, 77, 79, 21, 33, 40, 11, 28, 43, 85, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(indiv = structure(as.integer(c(20, 77, 79, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘optimize.R’ [2s/3s]
Comparing ‘optimize.Rout’ to ‘optimize.Rout.save’ ... OK
Running ‘optimizers.R’ [2s/2s]
Comparing ‘optimizers.Rout’ to ‘optimizers.Rout.save’ ... OK
Running ‘optimx.R’ [9s/11s]
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ... OK
Running ‘order.R’ [2s/2s]
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’ [2s/2s]
Comparing ‘parscale.Rout’ to ‘parscale.Rout.save’ ... OK
Running ‘predict.R’ [2s/3s]
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘prof_newmin.R’ [2s/2s]
Running ‘prof_spec.R’ [2s/3s]
Running ‘profbound.R’ [2s/3s]
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ... OK
Running ‘richards.R’ [10s/13s]
Comparing ‘richards.Rout’ to ‘richards.Rout.save’ ... OK
Running ‘startvals.R’ [2s/2s]
Comparing ‘startvals.Rout’ to ‘startvals.Rout.save’ ... OK
Running ‘startvals2.R’ [2s/3s]
Comparing ‘startvals2.Rout’ to ‘startvals2.Rout.save’ ...
165,171d164
< Warning messages:
< 1: In structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(c(34L, 57L, 77L, 114L, 115L, 116L, 117L, 125L, 141L, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(list(TOTCONES = c(19, 42, 40, 68, 5, 0, 21, 114, 37, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘test-relist1.R’ [2s/3s]
Comparing ‘test-relist1.Rout’ to ‘test-relist1.Rout.save’ ... OK
Running ‘testbounds.R’ [2s/3s]
Comparing ‘testbounds.Rout’ to ‘testbounds.Rout.save’ ... OK
Running ‘testderiv.R’ [2s/3s]
Comparing ‘testderiv.Rout’ to ‘testderiv.Rout.save’ ... OK
Running ‘testenv.R’ [2s/4s]
Comparing ‘testenv.Rout’ to ‘testenv.Rout.save’ ... OK
Running ‘testparpred.R’ [2s/3s]
Comparing ‘testparpred.Rout’ to ‘testparpred.Rout.save’ ... OK
Running ‘tmptest.R’ [2s/3s]
Comparing ‘tmptest.Rout’ to ‘tmptest.Rout.save’ ... OK
Running ‘update.R’ [2s/2s]
Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.25.1
Check: tests
Result: NOTE
Running ‘BIC.R’
Comparing ‘BIC.Rout’ to ‘BIC.Rout.save’ ... OK
Running ‘ICtab.R’
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’
Running ‘binomtest1.R’
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ...
12,14d11
< Warning message:
< In structure(list(Initial = as.integer(c(5, 5, 10, 10, 15, 15, 20, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘boundstest.R’
Running ‘controleval.R’
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘eval.R’
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ...
29,31d28
< Warning message:
< In structure(list(TBL = as.integer(c(9, 9, 9, 12, 12, 12, 21, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
335,341d331
< Warning messages:
< 1: In structure(as.integer(c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(15, 15, 15, 15, 15, 15, 15, 15, 15, 15, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(exper = as.integer(c(1, 1, 1, 1, 1, 1, 1, 1, 1, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘glmcomp.R’
Comparing ‘glmcomp.Rout’ to ‘glmcomp.Rout.save’ ... OK
Running ‘gradient_vecpar_profile.R’ [17s/20s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ... OK
Running ‘impsamp.R’
Running ‘methods.R’
Comparing ‘methods.Rout’ to ‘methods.Rout.save’ ... OK
Running ‘mortanal.R’
Comparing ‘mortanal.Rout’ to ‘mortanal.Rout.save’ ...
48,54d47
< Warning messages:
< 1: In structure(as.integer(c(20, 77, 79, 21, 33, 40, 11, 28, 43, 85, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(indiv = structure(as.integer(c(20, 77, 79, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘optimize.R’
Comparing ‘optimize.Rout’ to ‘optimize.Rout.save’ ... OK
Running ‘optimizers.R’
Comparing ‘optimizers.Rout’ to ‘optimizers.Rout.save’ ... OK
Running ‘optimx.R’ [13s/16s]
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ... OK
Running ‘order.R’
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’
Comparing ‘parscale.Rout’ to ‘parscale.Rout.save’ ... OK
Running ‘predict.R’
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘prof_newmin.R’
Running ‘prof_spec.R’
Running ‘profbound.R’
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ... OK
Running ‘richards.R’ [18s/23s]
Comparing ‘richards.Rout’ to ‘richards.Rout.save’ ... OK
Running ‘startvals.R’
Comparing ‘startvals.Rout’ to ‘startvals.Rout.save’ ... OK
Running ‘startvals2.R’
Comparing ‘startvals2.Rout’ to ‘startvals2.Rout.save’ ...
165,171d164
< Warning messages:
< 1: In structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(c(34L, 57L, 77L, 114L, 115L, 116L, 117L, 125L, 141L, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(list(TOTCONES = c(19, 42, 40, 68, 5, 0, 21, 114, 37, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘test-relist1.R’
Comparing ‘test-relist1.Rout’ to ‘test-relist1.Rout.save’ ... OK
Running ‘testbounds.R’
Comparing ‘testbounds.Rout’ to ‘testbounds.Rout.save’ ... OK
Running ‘testderiv.R’
Comparing ‘testderiv.Rout’ to ‘testderiv.Rout.save’ ... OK
Running ‘testenv.R’
Comparing ‘testenv.Rout’ to ‘testenv.Rout.save’ ... OK
Running ‘testparpred.R’
Comparing ‘testparpred.Rout’ to ‘testparpred.Rout.save’ ... OK
Running ‘tmptest.R’
Comparing ‘tmptest.Rout’ to ‘tmptest.Rout.save’ ... OK
Running ‘update.R’
Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.25.1
Check: tests
Result: ERROR
Running ‘BIC.R’
Comparing ‘BIC.Rout’ to ‘BIC.Rout.save’ ... OK
Running ‘ICtab.R’
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’
Running ‘binomtest1.R’
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ...
12,14d11
< Warning message:
< In structure(list(Initial = as.integer(c(5, 5, 10, 10, 15, 15, 20, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘boundstest.R’
Running ‘controleval.R’
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘eval.R’
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ...
29,31d28
< Warning message:
< In structure(list(TBL = as.integer(c(9, 9, 9, 12, 12, 12, 21, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
335,341d331
< Warning messages:
< 1: In structure(as.integer(c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(15, 15, 15, 15, 15, 15, 15, 15, 15, 15, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(exper = as.integer(c(1, 1, 1, 1, 1, 1, 1, 1, 1, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘glmcomp.R’
Comparing ‘glmcomp.Rout’ to ‘glmcomp.Rout.save’ ... OK
Running ‘gradient_vecpar_profile.R’ [11s/12s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ... OK
Running ‘impsamp.R’
Running ‘methods.R’
Comparing ‘methods.Rout’ to ‘methods.Rout.save’ ... OK
Running ‘mortanal.R’
Comparing ‘mortanal.Rout’ to ‘mortanal.Rout.save’ ...
48,54d47
< Warning messages:
< 1: In structure(as.integer(c(20, 77, 79, 21, 33, 40, 11, 28, 43, 85, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(indiv = structure(as.integer(c(20, 77, 79, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘optimize.R’
Comparing ‘optimize.Rout’ to ‘optimize.Rout.save’ ... OK
Running ‘optimizers.R’
Comparing ‘optimizers.Rout’ to ‘optimizers.Rout.save’ ... OK
Running ‘optimx.R’
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ... OK
Running ‘order.R’
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’
Running ‘predict.R’
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘prof_newmin.R’
Running ‘prof_spec.R’
Running ‘profbound.R’
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ... OK
Running ‘richards.R’ [9s/11s]
Comparing ‘richards.Rout’ to ‘richards.Rout.save’ ... OK
Running ‘startvals.R’
Comparing ‘startvals.Rout’ to ‘startvals.Rout.save’ ... OK
Running ‘startvals2.R’
Comparing ‘startvals2.Rout’ to ‘startvals2.Rout.save’ ...
165,171d164
< Warning messages:
< 1: In structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(c(34L, 57L, 77L, 114L, 115L, 116L, 117L, 125L, 141L, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(list(TOTCONES = c(19, 42, 40, 68, 5, 0, 21, 114, 37, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running ‘test-relist1.R’
Comparing ‘test-relist1.Rout’ to ‘test-relist1.Rout.save’ ... OK
Running ‘testbounds.R’
Comparing ‘testbounds.Rout’ to ‘testbounds.Rout.save’ ... OK
Running ‘testderiv.R’
Comparing ‘testderiv.Rout’ to ‘testderiv.Rout.save’ ... OK
Running ‘testenv.R’
Comparing ‘testenv.Rout’ to ‘testenv.Rout.save’ ... OK
Running ‘testparpred.R’
Comparing ‘testparpred.Rout’ to ‘testparpred.Rout.save’ ... OK
Running ‘tmptest.R’
Comparing ‘tmptest.Rout’ to ‘tmptest.Rout.save’ ... OK
Running ‘update.R’
Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
Running the tests in ‘tests/parscale.R’ failed.
Complete output:
> library(bbmle)
Loading required package: stats4
> old_opt <- options(digits=3)
> tracelevel <- 0
>
> ## source("~/lib/R/pkgs/bbmle/pkg/R/mle.R
>
> set.seed(1002)
> X <- rexp(1000, rate = 0.0001)
> f <- function(X, rate) {
+ if (tracelevel>0 && rate<0) cat("rate<0: ",rate,"\n")
+ -sum(dexp(X, rate = rate, log = TRUE))
+ }
> if (FALSE) {
+ ## L-BFGS-B violates bounds, and gets stuck at lower bound
+ m <- mle2(minuslogl = f,
+ data = list(X = X),
+ start = list(rate = 0.01),
+ method = "L-BFGS-B",
+ control = list(trace = tracelevel,
+ parscale = 1e-4),
+ lower = c(rate = 1e-9))
+
+ profile(m, std.err=0.0001) ## finds new optimum
+
+ fsc <- function(X, rate) {
+ -sum(dexp(X, rate = rate*1e-4, log = TRUE))
+ }
+ msc <- mle2(minuslogl = fsc,
+ data = list(X = X),
+ start = list(rate = 100),
+ method = "L-BFGS-B",
+ control = list(trace = tracelevel),
+ lower = c(rate = 1e-5))
+
+ ## does it work if we scale by hand?
+ ## no, identical problem
+ }
>
> ## works fine with a better starting point
> m <- mle2(minuslogl = f,
+ data = list(X = X),
+ start = list(rate = 0.001),
+ method = "L-BFGS-B",
+ control = list(trace = tracelevel,
+ parscale=1e-4),
+ lower = c(rate = 1e-9))
> vcov(m)
rate
rate 1.05e-11
> confint(m)
2.5 % 97.5 %
9.61e-05 1.09e-04
>
>
> ## works OK despite warnings about 1-dimensional opt. with N-M
> (m0 <- mle2(minuslogl = f,
+ data = list(X = X),
+ start = list(rate = 0.01),
+ method = "Nelder-Mead",
+ control = list(trace = tracelevel, parscale = 1e-4)))
Call:
mle2(minuslogl = f, start = list(rate = 0.01), method = "Nelder-Mead",
data = list(X = X), control = list(trace = tracelevel, parscale = 1e-04))
Coefficients:
rate
0.000102
Log-likelihood: -10188
Warning message:
In optim(par = c(rate = 0.01), fn = function (p) :*** buffer overflow detected ***: terminated
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.25.1
Check: tests
Result: NOTE
Running 'BIC.R' [2s]
Comparing 'BIC.Rout' to 'BIC.Rout.save' ... OK
Running 'ICtab.R' [2s]
Comparing 'ICtab.Rout' to 'ICtab.Rout.save' ... OK
Running 'RUnit-tests.R' [0s]
Running 'binomtest1.R' [2s]
Comparing 'binomtest1.Rout' to 'binomtest1.Rout.save' ...
12,14d11
< Warning message:
< In structure(list(Initial = as.integer(c(5, 5, 10, 10, 15, 15, 20, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running 'boundstest.R' [0s]
Running 'controleval.R' [2s]
Comparing 'controleval.Rout' to 'controleval.Rout.save' ... OK
Running 'eval.R' [2s]
Comparing 'eval.Rout' to 'eval.Rout.save' ... OK
Running 'formulatest.R' [3s]
Comparing 'formulatest.Rout' to 'formulatest.Rout.save' ...
29,31d28
< Warning message:
< In structure(list(TBL = as.integer(c(9, 9, 9, 12, 12, 12, 21, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
335,341d331
< Warning messages:
< 1: In structure(as.integer(c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(15, 15, 15, 15, 15, 15, 15, 15, 15, 15, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(exper = as.integer(c(1, 1, 1, 1, 1, 1, 1, 1, 1, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running 'glmcomp.R' [3s]
Comparing 'glmcomp.Rout' to 'glmcomp.Rout.save' ... OK
Running 'gradient_vecpar_profile.R' [11s]
Comparing 'gradient_vecpar_profile.Rout' to 'gradient_vecpar_profile.Rout.save' ... OK
Running 'grtest1.R' [2s]
Comparing 'grtest1.Rout' to 'grtest1.Rout.save' ... OK
Running 'impsamp.R' [2s]
Running 'methods.R' [2s]
Comparing 'methods.Rout' to 'methods.Rout.save' ... OK
Running 'mortanal.R' [3s]
Comparing 'mortanal.Rout' to 'mortanal.Rout.save' ...
48,54d47
< Warning messages:
< 1: In structure(as.integer(c(20, 77, 79, 21, 33, 40, 11, 28, 43, 85, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(as.integer(c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 3: In structure(list(indiv = structure(as.integer(c(20, 77, 79, 21, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running 'optimize.R' [3s]
Comparing 'optimize.Rout' to 'optimize.Rout.save' ... OK
Running 'optimizers.R' [2s]
Comparing 'optimizers.Rout' to 'optimizers.Rout.save' ... OK
Running 'optimx.R' [9s]
Comparing 'optimx.Rout' to 'optimx.Rout.save' ... OK
Running 'order.R' [2s]
Comparing 'order.Rout' to 'order.Rout.save' ... OK
Running 'parscale.R' [2s]
Comparing 'parscale.Rout' to 'parscale.Rout.save' ... OK
Running 'predict.R' [2s]
Comparing 'predict.Rout' to 'predict.Rout.save' ... OK
Running 'prof_newmin.R' [2s]
Running 'prof_spec.R' [2s]
Running 'profbound.R' [3s]
Comparing 'profbound.Rout' to 'profbound.Rout.save' ... OK
Running 'richards.R' [11s]
Comparing 'richards.Rout' to 'richards.Rout.save' ... OK
Running 'startvals.R' [2s]
Comparing 'startvals.Rout' to 'startvals.Rout.save' ... OK
Running 'startvals2.R' [2s]
Comparing 'startvals2.Rout' to 'startvals2.Rout.save' ...
165,171d164
< Warning messages:
< 1: In structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, :
< Replacing special names '.Label' is deprecated; use 'levels' instead.
< 2: In structure(c(34L, 57L, 77L, 114L, 115L, 116L, 117L, 125L, 141L, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(list(TOTCONES = c(19, 42, 40, 68, 5, 0, 21, 114, 37, :
< Replacing special names '.Names' is deprecated; use 'names' instead.
Running 'test-relist1.R' [2s]
Comparing 'test-relist1.Rout' to 'test-relist1.Rout.save' ... OK
Running 'testbounds.R' [2s]
Comparing 'testbounds.Rout' to 'testbounds.Rout.save' ... OK
Running 'testderiv.R' [2s]
Comparing 'testderiv.Rout' to 'testderiv.Rout.save' ... OK
Running 'testenv.R' [2s]
Comparing 'testenv.Rout' to 'testenv.Rout.save' ... OK
Running 'testparpred.R' [2s]
Comparing 'testparpred.Rout' to 'testparpred.Rout.save' ... OK
Running 'tmptest.R' [2s]
Comparing 'tmptest.Rout' to 'tmptest.Rout.save' ... OK
Running 'update.R' [2s]
Comparing 'update.Rout' to 'update.Rout.save' ... OK
Flavor: r-devel-windows-x86_64
Version: 1.0.25.1
Check: tests
Result: NOTE
Running ‘BIC.R’ [1s/1s]
Comparing ‘BIC.Rout’ to ‘BIC.Rout.save’ ... OK
Running ‘ICtab.R’ [1s/1s]
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’ [0s/0s]
Running ‘binomtest1.R’ [1s/1s]
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ... OK
Running ‘boundstest.R’ [0s/0s]
Running ‘controleval.R’ [1s/1s]
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘eval.R’ [1s/1s]
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’ [1s/1s]
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ... OK
Running ‘glmcomp.R’ [1s/1s]
Comparing ‘glmcomp.Rout’ to ‘glmcomp.Rout.save’ ... OK
Running ‘gradient_vecpar_profile.R’ [4s/4s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’ [1s/1s]
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ... OK
Running ‘impsamp.R’ [1s/1s]
Running ‘methods.R’ [1s/1s]
Comparing ‘methods.Rout’ to ‘methods.Rout.save’ ... OK
Running ‘mortanal.R’ [1s/1s]
Comparing ‘mortanal.Rout’ to ‘mortanal.Rout.save’ ... OK
Running ‘optimize.R’ [1s/1s]
Comparing ‘optimize.Rout’ to ‘optimize.Rout.save’ ... OK
Running ‘optimizers.R’ [1s/1s]
Comparing ‘optimizers.Rout’ to ‘optimizers.Rout.save’ ... OK
Running ‘optimx.R’ [3s/3s]
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ... OK
Running ‘order.R’ [1s/1s]
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’ [1s/1s]
Comparing ‘parscale.Rout’ to ‘parscale.Rout.save’ ... OK
Running ‘predict.R’ [1s/1s]
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘prof_newmin.R’ [1s/1s]
Running ‘prof_spec.R’ [1s/1s]
Running ‘profbound.R’ [1s/1s]
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ...
36,38d35
< Warning message:
< In mle2(minuslogl = function (a = NULL, b = NULL) :
< convergence failure: code=52 (ERROR: ABNORMAL_TERMINATION_IN_LNSRCH)
Running ‘richards.R’ [3s/3s]
Comparing ‘richards.Rout’ to ‘richards.Rout.save’ ... OK
Running ‘startvals.R’ [1s/1s]
Comparing ‘startvals.Rout’ to ‘startvals.Rout.save’ ... OK
Running ‘startvals2.R’ [1s/1s]
Comparing ‘startvals2.Rout’ to ‘startvals2.Rout.save’ ... OK
Running ‘test-relist1.R’ [1s/1s]
Comparing ‘test-relist1.Rout’ to ‘test-relist1.Rout.save’ ... OK
Running ‘testbounds.R’ [1s/1s]
Comparing ‘testbounds.Rout’ to ‘testbounds.Rout.save’ ... OK
Running ‘testderiv.R’ [1s/1s]
Comparing ‘testderiv.Rout’ to ‘testderiv.Rout.save’ ... OK
Running ‘testenv.R’ [1s/1s]
Comparing ‘testenv.Rout’ to ‘testenv.Rout.save’ ... OK
Running ‘testparpred.R’ [1s/1s]
Comparing ‘testparpred.Rout’ to ‘testparpred.Rout.save’ ... OK
Running ‘tmptest.R’ [1s/1s]
Comparing ‘tmptest.Rout’ to ‘tmptest.Rout.save’ ... OK
Running ‘update.R’ [1s/1s]
Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
Flavor: r-release-macos-arm64
Version: 1.0.25.1
Check: tests
Result: NOTE
Running ‘BIC.R’ [1s/1s]
Comparing ‘BIC.Rout’ to ‘BIC.Rout.save’ ... OK
Running ‘ICtab.R’ [1s/1s]
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’ [0s/0s]
Running ‘binomtest1.R’ [1s/2s]
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ... OK
Running ‘boundstest.R’ [0s/0s]
Running ‘controleval.R’ [1s/1s]
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘eval.R’ [1s/1s]
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’ [1s/2s]
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ... OK
Running ‘glmcomp.R’ [1s/2s]
Comparing ‘glmcomp.Rout’ to ‘glmcomp.Rout.save’ ... OK
Running ‘gradient_vecpar_profile.R’ [6s/9s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’ [1s/2s]
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ... OK
Running ‘impsamp.R’ [1s/2s]
Running ‘methods.R’ [1s/2s]
Comparing ‘methods.Rout’ to ‘methods.Rout.save’ ... OK
Running ‘mortanal.R’ [1s/2s]
Comparing ‘mortanal.Rout’ to ‘mortanal.Rout.save’ ... OK
Running ‘optimize.R’ [1s/2s]
Comparing ‘optimize.Rout’ to ‘optimize.Rout.save’ ... OK
Running ‘optimizers.R’ [1s/2s]
Comparing ‘optimizers.Rout’ to ‘optimizers.Rout.save’ ... OK
Running ‘optimx.R’ [4s/6s]
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ... OK
Running ‘order.R’ [1s/1s]
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’ [1s/1s]
Comparing ‘parscale.Rout’ to ‘parscale.Rout.save’ ... OK
Running ‘predict.R’ [1s/1s]
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘prof_newmin.R’ [1s/1s]
Running ‘prof_spec.R’ [1s/1s]
Running ‘profbound.R’ [1s/1s]
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ...36,38d35
< Warning message:
< In mle2(minuslogl = function (a = NULL, b = NULL) :
< convergence failure: code=52 (ERROR: ABNORMAL_TERMINATION_IN_LNSRCH)
Running ‘richards.R’ [5s/6s]
Comparing ‘richards.Rout’ to ‘richards.Rout.save’ ... OK
Running ‘startvals.R’ [1s/1s]
Comparing ‘startvals.Rout’ to ‘startvals.Rout.save’ ... OK
Running ‘startvals2.R’ [1s/1s]
Comparing ‘startvals2.Rout’ to ‘startvals2.Rout.save’ ... OK
Running ‘test-relist1.R’ [1s/1s]
Comparing ‘test-relist1.Rout’ to ‘test-relist1.Rout.save’ ... OK
Running ‘testbounds.R’ [1s/1s]
Comparing ‘testbounds.Rout’ to ‘testbounds.Rout.save’ ... OK
Running ‘testderiv.R’ [1s/1s]
Comparing ‘testderiv.Rout’ to ‘testderiv.Rout.save’ ... OK
Running ‘testenv.R’ [1s/1s]
Comparing ‘testenv.Rout’ to ‘testenv.Rout.save’ ... OK
Running ‘testparpred.R’ [1s/2s]
Comparing ‘testparpred.Rout’ to ‘testparpred.Rout.save’ ... OK
Running ‘tmptest.R’ [1s/1s]
Comparing ‘tmptest.Rout’ to ‘tmptest.Rout.save’ ... OK
Running ‘update.R’ [1s/1s]
Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
Flavor: r-oldrel-macos-arm64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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