Check results for 'bbmle'

using R version 2.15.3 (2013-03-01)
using platform: i386-w64-mingw32 (32-bit)
using session charset: ISO8859-1
checking for file 'bbmle/DESCRIPTION' ... OK
this is package 'bbmle' version '1.0.5.2'
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking whether package 'bbmle' can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking for portable file names ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
checking for unstated dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... OK
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking sizes of PDF files under 'inst/doc' ... OK
checking installed files from 'inst/doc' ... OK
checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
checking for unstated dependencies in tests ... OK
checking tests ...
** running tests for arch 'i386' OK
Running 'BIC.R'
Comparing 'BIC.Rout' to 'BIC.Rout.save' ...9c9
< > BIC(fit)
---
> > BIC(fit,nobs=length(x))
11,14c11,14
< > BIC(fit,fit2)
< df BIC
< fit 2 62.0039
< fit2 1 228.2046
---
> > BIC(fit,fit2,nobs=length(x))
> BIC df
> 1 62.0039 2
> 2 228.2046 1
Running 'ICtab.R'
Comparing 'ICtab.Rout' to 'ICtab.Rout.save' ... OK
Running 'RUnit-tests.R'
Comparing 'RUnit-tests.Rout' to 'RUnit-tests.Rout.save' ... OK
Running 'binomtest1.R'
Comparing 'binomtest1.Rout' to 'binomtest1.Rout.save' ...34,38c34,38
< 1 -4.2047554 0.294897783 -0.002923583
< 2 -3.1552212 0.341178865 0.002585989
< 3 -2.2351135 0.387459947 0.007009784
< 4 -1.4145492 0.433741029 0.010694588
< 5 -0.6726288 0.480022111 0.013859290
---
> 1 -4.2047344 0.294898645 -0.002923466
> 2 -3.1552066 0.341179554 0.002586064
> 3 -2.2351038 0.387460464 0.007009828
> 4 -1.4145435 0.433741374 0.010694613
> 5 -0.6726261 0.480022283 0.013859302
40,46c40,46
< 7 0.6321760 0.572584274 0.019113315
< 8 1.2156093 0.618865356 0.021399166
< 9 1.7630665 0.665146438 0.023494944
< 10 2.2805003 0.711427520 0.025475127
< 11 2.7729234 0.757708602 0.027355982
< 12 3.2447829 0.803989684 0.029170797
< 13 3.7001640 0.850270766 0.030945320
---
> 7 0.6321738 0.572584102 0.019113307
> 8 1.2156051 0.618865012 0.021399150
> 9 1.7630606 0.665145921 0.023494921
> 10 2.2804928 0.711426831 0.025475099
> 11 2.7729144 0.757707740 0.027355948
> 12 3.2447726 0.803988650 0.029170757
> 13 3.7001523 0.850269559 0.030945274
50,62c50,62
< 1 -3.7637734 0.326856388 -0.002427473
< 2 -3.1748492 0.354263260 0.000751042
< 3 -2.5644575 0.384375345 0.003929557
< 4 -1.9359501 0.417048930 0.007108072
< 5 -1.2938816 0.451955213 0.010286586
< 6 -0.6437628 0.488599955 0.013465101
< 7 0.0000000 0.526303193 0.016643616
< 8 0.6563208 0.564651420 0.019822131
< 9 1.2951093 0.602851644 0.023000645
< 10 1.9201322 0.640513395 0.026179160
< 11 2.5281144 0.677306100 0.029357675
< 12 3.1168399 0.713018494 0.032536190
< 13 3.6850068 0.747543285 0.035714705
---
> 1 -3.7637543 0.3268572493 -0.0024273676
> 2 -3.1748327 0.3542640536 0.0007511297
> 3 -2.5644438 0.3843760379 0.0039296269
> 4 -1.9359396 0.4170494900 0.0071081242
> 5 -1.2938745 0.4519556085 0.0102866214
> 6 -0.6437592 0.4886001613 0.0134651187
> 7 0.0000000 0.5263031926 0.0166436159
> 8 0.6563173 0.5646512092 0.0198221132
> 9 1.2951023 0.6028512247 0.0230006104
> 10 1.9201220 0.6405127788 0.0261791077
> 11 2.5281012 0.6773052997 0.0293576049
> 12 3.1168240 0.7130175259 0.0325361022
> 13 3.6849884 0.7475421634 0.0357145994
66c66
< a 0.402495806 0.68249529
---
> a 0.402495803 0.68249529
87c87
< a 0.402495806 0.68249529
---
> a 0.402495803 0.68249529
Running 'controleval.R'
Comparing 'controleval.Rout' to 'controleval.Rout.save' ... OK
Running 'doRUnit.R'
Comparing 'doRUnit.Rout' to 'doRUnit.Rout.save' ...72c72
< [1] "d:/Rcompile/CRANpkg/local/2.15/bbmle.Rcheck/tests_i386"
---
> [1] "/mnt/hgfs/bolker/Documents/R/pkgs/bbmle/pkg/tests"
75c75
< [1] "D:/temp/Rtmpkl6Rwt/RLIBS_2a044fcc644/bbmle/unitTests"
---
> [1] "/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/bbmle/unitTests"
79c79
< RUNIT TEST PROTOCOL -- Sat May 18 08:14:55 2013
---
> RUNIT TEST PROTOCOL -- Sun Jul 29 14:00:37 2012
Running 'eval.R'
Comparing 'eval.Rout' to 'eval.Rout.save' ... OK
Running 'formulatest.R'
Comparing 'formulatest.Rout' to 'formulatest.Rout.save' ...22c22
< 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(30.4960429004192, :
---
> 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(30.4960310771523, :
24c24
< 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2466899047813, :
---
> 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.246672169881, :
26c26
< 3: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(35.9973369091434, :
---
> 3: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(35.9973132626097, :
28c28
< 4: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(38.7479839135055, :
---
> 4: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(38.7479543553384, :
30c30
< 5: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.4986309178676, :
---
> 5: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.4985954480671, :
32c32
< 6: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.4986309178676, :
---
> 6: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.4985954480671, :
34c34
< 7: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492779222298, :
---
> 7: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492365407958, :
36c36
< 8: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492779222298, :
---
> 8: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492365407958, :
Running 'glmcomp.R'
Comparing 'glmcomp.Rout' to 'glmcomp.Rout.save' ... OK
Running 'gradient_vecpar_profile.R'
Comparing 'gradient_vecpar_profile.Rout' to 'gradient_vecpar_profile.Rout.save' ... OK
Running 'grtest1.R'
Comparing 'grtest1.Rout' to 'grtest1.Rout.save' ... OK
Running 'methods.R'
Comparing 'methods.Rout' to 'methods.Rout.save' ... OK
Running 'mortanal.R'
Comparing 'mortanal.Rout' to 'mortanal.Rout.save' ... OK
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' ...16c16,36
< There were 11 warnings (use warnings() to see them)
---
>
> Attaching package: 'Rcgmin'
>
> The following object(s) are masked from 'package:optimx':
>
> optansout
>
>
> Attaching package: 'Rvmmin'
>
> The following object(s) are masked from 'package:Rcgmin':
>
> optansout
>
> The following object(s) are masked from 'package:optimx':
>
> optansout
>
> Warning message:
> In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(37.7033783803611, :
> NaNs produced
18,20d37
< > ## FIXME!! fails (although not with an error, because
< > ## errors are caught by profiling) due to npar now
< > ## being restricted to >1 in optimx 2012.05.24 ...
26,29c43,46
< 1 -3.3769595 13.992604 9.990240
< 2 -2.3408105 16.743630 6.538601
< 3 -1.4582079 19.494656 4.793141
< 4 -0.6872020 22.245682 3.747887
---
> 1 -3.3769529 13.992620 9.990210
> 2 -2.3408063 16.743642 6.538591
> 3 -1.4582055 19.494664 4.793137
> 4 -0.6872010 22.245686 3.747885
31,37c48,54
< 6 0.6199922 27.747734 2.567514
< 7 1.1878573 30.498760 2.205221
< 8 1.7126030 33.249786 1.926961
< 9 2.2014985 36.000812 1.707196
< 10 2.6601415 38.751839 1.529683
< 11 3.0929245 41.502865 1.383619
< 12 3.5033512 44.253891 1.261548
---
> 6 0.6199914 27.747730 2.567515
> 7 1.1878557 30.498752 2.205222
> 8 1.7126008 33.249774 1.926962
> 9 2.2014957 36.000796 1.707197
> 10 2.6601382 38.751818 1.529684
> 11 3.0929208 41.502840 1.383620
> 12 3.5033471 44.253863 1.261549
41,45c58,62
< 1 -3.6930686 41.342754 1.035623
< 2 -2.6386115 36.082841 1.372416
< 3 -1.8618297 32.494510 1.709210
< 4 -1.2549256 29.876418 2.046003
< 5 -0.7619506 27.873802 2.382796
---
> 1 -3.6930563 41.342691 1.035627
> 2 -2.6386042 36.082806 1.372419
> 3 -1.8618252 32.494490 1.709212
> 4 -1.2549229 29.876407 2.046004
> 5 -0.7619491 27.873796 2.382797
47,61c64,78
< 7 0.5712035 23.018946 3.729968
< 8 1.0191671 21.567785 4.403554
< 9 1.3826771 20.454242 5.077140
< 10 1.6849402 19.570757 5.750726
< 11 1.9410491 18.851518 6.424312
< 12 2.1613333 18.253878 7.097898
< 13 2.3531475 17.748924 7.771484
< 14 2.5218967 17.316327 8.445070
< 15 2.6716577 16.941353 9.118656
< 16 2.8055726 16.613055 9.792242
< 17 2.9261080 16.323116 10.465828
< 18 3.0352309 16.065103 11.139414
< 19 3.1345319 15.833957 11.813000
< 20 3.2253126 15.625643 12.486586
< 21 3.3086496 15.436902 13.160172
---
> 7 0.5712027 23.018949 3.729967
> 8 1.0191658 21.567789 4.403552
> 9 1.3826755 20.454247 5.077137
> 10 1.6849383 19.570763 5.750721
> 11 1.9410472 18.851524 6.424306
> 12 2.1613313 18.253883 7.097891
> 13 2.3531454 17.748929 7.771476
> 14 2.5218946 17.316332 8.445061
> 15 2.6716557 16.941359 9.118646
> 16 2.8055706 16.613060 9.792231
> 17 2.9261059 16.323121 10.465816
> 18 3.0352289 16.065108 11.139401
> 19 3.1345299 15.833962 11.812986
> 20 3.2253106 15.625647 12.486571
> 21 3.3086476 15.436906 13.160156
63c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 14 warnings (use warnings() to see them)
Running 'order.R'
Comparing 'order.Rout' to 'order.Rout.save' ... OK
Running 'parscale.R'
Comparing 'parscale.Rout' to 'parscale.Rout.save' ...44a45
> iter 0 value 12490.509482
49c50
< rate 1.045665e-11
---
> rate 1.045669e-11
105c106
< rate 1.046425e-11
---
> rate 1.046414e-11
112c113
< 9.595473e-05 1.086351e-04
---
> 9.595477e-05 1.086351e-04
146c147
< rate 1.407192e-11
---
> rate 1.407176e-11
Running 'predict.R'
Comparing 'predict.Rout' to 'predict.Rout.save' ... OK
Running 'profbound.R'
Comparing 'profbound.Rout' to 'profbound.Rout.save' ...19c19
< a 2.814052 3.35794623
---
> a 2.814052 3.35794624
Running 'richards.R'
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' ... OK
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' ...21,26c21,26
< 1 -5.4686715 2.5585125 27.2089012
< 2 -3.2038301 2.6685692 2.2247873
< 3 -2.5686060 2.7786259 1.9643696
< 4 -1.9314577 2.8886826 1.7291893
< 5 -1.2916426 2.9987393 1.5123047
< 6 -0.6482126 3.1087960 1.3092610
---
> 1 -5.4686774 2.5585146 27.2088421
> 2 -3.2038200 2.6685710 2.2247829
> 3 -2.5685978 2.7786273 1.9643664
> 4 -1.9314516 2.8886836 1.7291871
> 5 -1.2916385 2.9987400 1.5123034
> 6 -0.6482105 3.1087963 1.3092604
28,32c28,32
< 8 0.6543908 3.3289094 0.9335200
< 9 1.3165901 3.4389660 0.7571495
< 10 1.9884556 3.5490227 0.5870933
< 11 2.6720631 3.6590794 0.4223483
< 12 3.3696881 3.7691361 0.2626576
---
> 8 0.6543886 3.3289090 0.9335206
> 9 1.3165858 3.4389653 0.7571506
> 10 1.9884490 3.5490217 0.5870949
> 11 2.6720542 3.6590780 0.4223504
> 12 3.3696768 3.7691343 0.2626602
36,40c36,40
< 1 -3.7697981 3.73162778 0.01516639
< 2 -2.9354303 3.62491273 0.23554003
< 3 -2.1408129 3.51907972 0.45591368
< 4 -1.3862373 3.41538652 0.67628733
< 5 -0.6722988 3.31497396 0.89666097
---
> 1 -3.7697805 3.73162558 0.01517093
> 2 -2.9354168 3.62491097 0.23554367
> 3 -2.1408033 3.51907842 0.45591641
> 4 -1.3862312 3.41538568 0.67628915
> 5 -0.6722959 3.31497356 0.89666188
42,48c42,48
< 7 0.6292999 3.12788864 1.33740827
< 8 1.2140464 3.04279596 1.55778191
< 9 1.7527507 2.96412468 1.77815556
< 10 2.2442653 2.89224839 1.99852921
< 11 2.6880438 2.82736253 2.21890285
< 12 3.0843314 2.76948254 2.43927650
< 13 3.4342608 2.71845380 2.65965015
---
> 7 0.6292974 3.12788901 1.33740736
> 8 1.2140418 3.04279663 1.55778009
> 9 1.7527443 2.96412561 1.77815283
> 10 2.2442576 2.89224952 1.99852557
> 11 2.6880351 2.82736380 2.21889831
> 12 3.0843222 2.76948388 2.43927104
> 13 3.4342513 2.71845517 2.65964378
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 tests for arch 'x64' OK
Running 'BIC.R'
Comparing 'BIC.Rout' to 'BIC.Rout.save' ...9c9
< > BIC(fit)
---
> > BIC(fit,nobs=length(x))
11,14c11,14
< > BIC(fit,fit2)
< df BIC
< fit 2 62.0039
< fit2 1 228.2046
---
> > BIC(fit,fit2,nobs=length(x))
> BIC df
> 1 62.0039 2
> 2 228.2046 1
Running 'ICtab.R'
Comparing 'ICtab.Rout' to 'ICtab.Rout.save' ... OK
Running 'RUnit-tests.R'
Comparing 'RUnit-tests.Rout' to 'RUnit-tests.Rout.save' ... OK
Running 'binomtest1.R'
Comparing 'binomtest1.Rout' to 'binomtest1.Rout.save' ...34,38c34,38
< 1 -4.2047554 0.294897783 -0.002923583
< 2 -3.1552212 0.341178865 0.002585989
< 3 -2.2351135 0.387459947 0.007009784
< 4 -1.4145492 0.433741029 0.010694588
< 5 -0.6726288 0.480022111 0.013859290
---
> 1 -4.2047344 0.294898645 -0.002923466
> 2 -3.1552066 0.341179554 0.002586064
> 3 -2.2351038 0.387460464 0.007009828
> 4 -1.4145435 0.433741374 0.010694613
> 5 -0.6726261 0.480022283 0.013859302
40,46c40,46
< 7 0.6321760 0.572584274 0.019113315
< 8 1.2156093 0.618865356 0.021399166
< 9 1.7630665 0.665146438 0.023494944
< 10 2.2805003 0.711427520 0.025475127
< 11 2.7729234 0.757708602 0.027355982
< 12 3.2447829 0.803989684 0.029170797
< 13 3.7001640 0.850270766 0.030945320
---
> 7 0.6321738 0.572584102 0.019113307
> 8 1.2156051 0.618865012 0.021399150
> 9 1.7630606 0.665145921 0.023494921
> 10 2.2804928 0.711426831 0.025475099
> 11 2.7729144 0.757707740 0.027355948
> 12 3.2447726 0.803988650 0.029170757
> 13 3.7001523 0.850269559 0.030945274
50,62c50,62
< 1 -3.7637734 0.326856388 -0.002427473
< 2 -3.1748492 0.354263260 0.000751042
< 3 -2.5644575 0.384375345 0.003929557
< 4 -1.9359501 0.417048930 0.007108072
< 5 -1.2938816 0.451955213 0.010286586
< 6 -0.6437628 0.488599955 0.013465101
< 7 0.0000000 0.526303193 0.016643616
< 8 0.6563208 0.564651420 0.019822131
< 9 1.2951093 0.602851644 0.023000645
< 10 1.9201322 0.640513395 0.026179160
< 11 2.5281144 0.677306100 0.029357675
< 12 3.1168399 0.713018494 0.032536190
< 13 3.6850068 0.747543285 0.035714705
---
> 1 -3.7637543 0.3268572493 -0.0024273676
> 2 -3.1748327 0.3542640536 0.0007511297
> 3 -2.5644438 0.3843760379 0.0039296269
> 4 -1.9359396 0.4170494900 0.0071081242
> 5 -1.2938745 0.4519556085 0.0102866214
> 6 -0.6437592 0.4886001613 0.0134651187
> 7 0.0000000 0.5263031926 0.0166436159
> 8 0.6563173 0.5646512092 0.0198221132
> 9 1.2951023 0.6028512247 0.0230006104
> 10 1.9201220 0.6405127788 0.0261791077
> 11 2.5281012 0.6773052997 0.0293576049
> 12 3.1168240 0.7130175259 0.0325361022
> 13 3.6849884 0.7475421634 0.0357145994
66c66
< a 0.402495806 0.68249529
---
> a 0.402495803 0.68249529
87c87
< a 0.402495806 0.68249529
---
> a 0.402495803 0.68249529
Running 'controleval.R'
Comparing 'controleval.Rout' to 'controleval.Rout.save' ... OK
Running 'doRUnit.R'
Comparing 'doRUnit.Rout' to 'doRUnit.Rout.save' ...72c72
< [1] "d:/Rcompile/CRANpkg/local/2.15/bbmle.Rcheck/tests_x64"
---
> [1] "/mnt/hgfs/bolker/Documents/R/pkgs/bbmle/pkg/tests"
75c75
< [1] "D:/temp/Rtmpkl6Rwt/RLIBS_2a044fcc644/bbmle/unitTests"
---
> [1] "/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/bbmle/unitTests"
79c79
< RUNIT TEST PROTOCOL -- Sat May 18 08:15:37 2013
---
> RUNIT TEST PROTOCOL -- Sun Jul 29 14:00:37 2012
Running 'eval.R'
Comparing 'eval.Rout' to 'eval.Rout.save' ... OK
Running 'formulatest.R'
Comparing 'formulatest.Rout' to 'formulatest.Rout.save' ...15c15
< 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(15.9069797540562, :
---
> 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(15.9069797530336, :
17c17
< 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2333275658228, :
---
> 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2333275647578, :
22c22
< 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(30.4960429002996, :
---
> 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(30.4960310771523, :
24c24
< 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2466899046504, :
---
> 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.246672169881, :
26c26
< 3: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(35.9973369090013, :
---
> 3: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(35.9973132626097, :
28c28
< 4: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(38.7479839133521, :
---
> 4: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(38.7479543553384, :
30c30
< 5: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.498630917703, :
---
> 5: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.4985954480671, :
32c32
< 6: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.498630917703, :
---
> 6: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(41.4985954480671, :
34c34
< 7: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492779220538, :
---
> 7: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492365407958, :
36c36
< 8: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492779220538, :
---
> 8: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(44.2492365407958, :
42c42
< 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(15.9069797540562, :
---
> 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(15.9069797530336, :
44c44
< 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2333275658228, :
---
> 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2333275647578, :
Running 'glmcomp.R'
Comparing 'glmcomp.Rout' to 'glmcomp.Rout.save' ...18c18
< -1.354668e-09
---
> -2.709339e-10
20c20
< 'log Lik.' 1.421085e-14 (df=1)
---
> 'log Lik.' 7.105427e-15 (df=1)
31c31
< [7] -0.7491345 -1.0434374 -1.9263460 -2.2206488 -1.0434374
---
> [7] -0.7491346 -1.0434374 -1.9263460 -2.2206488 -1.0434374
Running 'gradient_vecpar_profile.R'
Comparing 'gradient_vecpar_profile.Rout' to 'gradient_vecpar_profile.Rout.save' ... OK
Running 'grtest1.R'
Comparing 'grtest1.Rout' to 'grtest1.Rout.save' ...15c15
< 1.090239e-13 1.000000e+00
---
> 1.092459e-13 1.000000e+00
Running 'methods.R'
Comparing 'methods.Rout' to 'methods.Rout.save' ...19c19
< [7] -0.7491345 -1.0434374 -1.9263460 -2.2206488 -1.0434374
---
> [7] -0.7491346 -1.0434374 -1.9263460 -2.2206488 -1.0434374
Running 'mortanal.R'
Comparing 'mortanal.Rout' to 'mortanal.Rout.save' ... OK
Running 'optimize.R'
Comparing 'optimize.Rout' to 'optimize.Rout.save' ... OK
Running 'optimizers.R'
Comparing 'optimizers.Rout' to 'optimizers.Rout.save' ...13c13
< 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(31.4659915609388, :
---
> 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(31.4659916032255, :
Running 'optimx.R'
Comparing 'optimx.Rout' to 'optimx.Rout.save' ...16c16,36
< There were 11 warnings (use warnings() to see them)
---
>
> Attaching package: 'Rcgmin'
>
> The following object(s) are masked from 'package:optimx':
>
> optansout
>
>
> Attaching package: 'Rvmmin'
>
> The following object(s) are masked from 'package:Rcgmin':
>
> optansout
>
> The following object(s) are masked from 'package:optimx':
>
> optansout
>
> Warning message:
> In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(37.7033783803611, :
> NaNs produced
18,20d37
< > ## FIXME!! fails (although not with an error, because
< > ## errors are caught by profiling) due to npar now
< > ## being restricted to >1 in optimx 2012.05.24 ...
26,29c43,46
< 1 -3.3769595 13.992604 9.990240
< 2 -2.3408105 16.743630 6.538601
< 3 -1.4582079 19.494656 4.793141
< 4 -0.6872020 22.245682 3.747887
---
> 1 -3.3769529 13.992620 9.990210
> 2 -2.3408063 16.743642 6.538591
> 3 -1.4582055 19.494664 4.793137
> 4 -0.6872010 22.245686 3.747885
31,37c48,54
< 6 0.6199922 27.747734 2.567514
< 7 1.1878573 30.498760 2.205221
< 8 1.7126030 33.249786 1.926961
< 9 2.2014985 36.000812 1.707196
< 10 2.6601415 38.751839 1.529683
< 11 3.0929245 41.502865 1.383619
< 12 3.5033512 44.253891 1.261548
---
> 6 0.6199914 27.747730 2.567515
> 7 1.1878557 30.498752 2.205222
> 8 1.7126008 33.249774 1.926962
> 9 2.2014957 36.000796 1.707197
> 10 2.6601382 38.751818 1.529684
> 11 3.0929208 41.502840 1.383620
> 12 3.5033471 44.253863 1.261549
41,45c58,62
< 1 -3.6930686 41.342754 1.035623
< 2 -2.6386115 36.082841 1.372416
< 3 -1.8618297 32.494510 1.709210
< 4 -1.2549256 29.876418 2.046003
< 5 -0.7619506 27.873802 2.382796
---
> 1 -3.6930563 41.342691 1.035627
> 2 -2.6386042 36.082806 1.372419
> 3 -1.8618252 32.494490 1.709212
> 4 -1.2549229 29.876407 2.046004
> 5 -0.7619491 27.873796 2.382797
47,61c64,78
< 7 0.5712035 23.018946 3.729968
< 8 1.0191671 21.567785 4.403554
< 9 1.3826771 20.454242 5.077140
< 10 1.6849402 19.570757 5.750726
< 11 1.9410491 18.851518 6.424312
< 12 2.1613333 18.253877 7.097898
< 13 2.3531475 17.748924 7.771484
< 14 2.5218967 17.316327 8.445070
< 15 2.6716577 16.941353 9.118656
< 16 2.8055726 16.613055 9.792242
< 17 2.9261080 16.323116 10.465828
< 18 3.0352309 16.065103 11.139414
< 19 3.1345319 15.833957 11.813000
< 20 3.2253126 15.625642 12.486586
< 21 3.3086496 15.436902 13.160172
---
> 7 0.5712027 23.018949 3.729967
> 8 1.0191658 21.567789 4.403552
> 9 1.3826755 20.454247 5.077137
> 10 1.6849383 19.570763 5.750721
> 11 1.9410472 18.851524 6.424306
> 12 2.1613313 18.253883 7.097891
> 13 2.3531454 17.748929 7.771476
> 14 2.5218946 17.316332 8.445061
> 15 2.6716557 16.941359 9.118646
> 16 2.8055706 16.613060 9.792231
> 17 2.9261059 16.323121 10.465816
> 18 3.0352289 16.065108 11.139401
> 19 3.1345299 15.833962 11.812986
> 20 3.2253106 15.625647 12.486571
> 21 3.3086476 15.436906 13.160156
63c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 14 warnings (use warnings() to see them)
Running 'order.R'
Comparing 'order.Rout' to 'order.Rout.save' ... OK
Running 'parscale.R'
Comparing 'parscale.Rout' to 'parscale.Rout.save' ...44a45
> iter 0 value 12490.509482
49c50
< rate 1.045665e-11
---
> rate 1.045669e-11
105c106
< rate 1.046425e-11
---
> rate 1.046414e-11
112c113
< 9.595473e-05 1.086351e-04
---
> 9.595477e-05 1.086351e-04
146c147
< rate 1.407192e-11
---
> rate 1.407176e-11
Running 'predict.R'
Comparing 'predict.Rout' to 'predict.Rout.save' ... OK
Running 'profbound.R'
Comparing 'profbound.Rout' to 'profbound.Rout.save' ...19c19
< a 2.814052 3.35794623
---
> a 2.814052 3.35794624
Running 'richards.R'
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' ... OK
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' ...21,26c21,26
< 1 -5.4686715 2.5585125 27.2089012
< 2 -3.2038301 2.6685692 2.2247873
< 3 -2.5686060 2.7786259 1.9643696
< 4 -1.9314577 2.8886826 1.7291893
< 5 -1.2916426 2.9987393 1.5123047
< 6 -0.6482126 3.1087960 1.3092610
---
> 1 -5.4686774 2.5585146 27.2088421
> 2 -3.2038200 2.6685710 2.2247829
> 3 -2.5685978 2.7786273 1.9643664
> 4 -1.9314516 2.8886836 1.7291871
> 5 -1.2916385 2.9987400 1.5123034
> 6 -0.6482105 3.1087963 1.3092604
28,32c28,32
< 8 0.6543908 3.3289094 0.9335200
< 9 1.3165901 3.4389660 0.7571495
< 10 1.9884556 3.5490227 0.5870933
< 11 2.6720631 3.6590794 0.4223483
< 12 3.3696881 3.7691361 0.2626576
---
> 8 0.6543886 3.3289090 0.9335206
> 9 1.3165858 3.4389653 0.7571506
> 10 1.9884490 3.5490217 0.5870949
> 11 2.6720542 3.6590780 0.4223504
> 12 3.3696768 3.7691343 0.2626602
36,40c36,40
< 1 -3.7697981 3.73162778 0.01516639
< 2 -2.9354303 3.62491273 0.23554003
< 3 -2.1408129 3.51907972 0.45591368
< 4 -1.3862373 3.41538652 0.67628733
< 5 -0.6722988 3.31497396 0.89666097
---
> 1 -3.7697805 3.73162558 0.01517093
> 2 -2.9354168 3.62491097 0.23554367
> 3 -2.1408033 3.51907842 0.45591641
> 4 -1.3862312 3.41538568 0.67628915
> 5 -0.6722959 3.31497356 0.89666188
42,48c42,48
< 7 0.6292999 3.12788864 1.33740827
< 8 1.2140464 3.04279596 1.55778191
< 9 1.7527507 2.96412468 1.77815556
< 10 2.2442653 2.89224839 1.99852921
< 11 2.6880438 2.82736253 2.21890285
< 12 3.0843314 2.76948254 2.43927650
< 13 3.4342608 2.71845380 2.65965015
---
> 7 0.6292974 3.12788901 1.33740736
> 8 1.2140418 3.04279663 1.55778009
> 9 1.7527443 2.96412561 1.77815283
> 10 2.2442576 2.89224952 1.99852557
> 11 2.6880351 2.82736380 2.21889831
> 12 3.0843222 2.76948388 2.43927104
> 13 3.4342513 2.71845517 2.65964378
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' ...11c11
< 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(15.9069797540562, :
---
> 1: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(15.9069797530336, :
13c13
< 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2333275658228, :
---
> 2: In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(33.2333275647578, :
checking for unstated dependencies in vignettes ... OK
checking package vignettes in 'inst/doc' ... OK
checking running R code from vignettes ... OK
checking re-building of vignette PDFs ... OK
checking PDF version of manual ... OK