- using R version 2.14.1 Patched (2012-02-07 r58290)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘bbmle/DESCRIPTION’ ... OK
- this is package ‘bbmle’ version ‘1.0.4.1’
- 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 for executable files ... 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 for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level 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
- 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 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 examples ... OK
- checking for unstated dependencies in tests ... OK
- checking tests ... OK
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’
Comparing ‘RUnit-tests.Rout’ to ‘RUnit-tests.Rout.save’ ... OK
Running ‘binomtest1.R’
Comparing ‘binomtest1.Rout’ to ‘binomtest1.Rout.save’ ...34,38c34,38
< 1 -4.2047663 0.294897333 -0.002923644
< 2 -3.1552288 0.341178505 0.002585950
< 3 -2.2351185 0.387459677 0.007009760
< 4 -1.4145523 0.433740849 0.010694574
< 5 -0.6726301 0.480022021 0.013859285
---
> 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 0.6321772 0.572584365 0.019113320
< 8 1.2156115 0.618865537 0.021399174
< 9 1.7630696 0.665146709 0.023494956
< 10 2.2805042 0.711427881 0.025475142
< 11 2.7729280 0.757709053 0.027356000
< 12 3.2447883 0.803990224 0.029170818
< 13 3.7001701 0.850271396 0.030945344
---
> 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
50,55c50,55
< 1 -3.7637857 0.3268558330 -0.0024275405
< 2 -3.1748599 0.3542627493 0.0007509856
< 3 -2.5644663 0.3843748979 0.0039295116
< 4 -1.9359569 0.4170485690 0.0071080377
< 5 -1.2938862 0.4519549579 0.0102865638
< 6 -0.6437651 0.4885998229 0.0134650899
---
> 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
57,62c57,62
< 8 0.6563231 0.5646515566 0.0198221420
< 9 1.2951138 0.6028519138 0.0230006681
< 10 1.9201388 0.6405137927 0.0261791941
< 11 2.5281229 0.6773066155 0.0293577202
< 12 3.1168502 0.7130191185 0.0325362463
< 13 3.6850187 0.7475440084 0.0357147724
---
> 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 0.402495808 0.68249529
---
> a 0.402495803 0.68249529
87c87
< a 0.402495808 0.68249529
---
> a 0.402495803 0.68249529
Running ‘controleval.R’
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘doRUnit.R’
Running ‘eval.R’
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’
Comparing ‘formulatest.Rout’ to ‘formulatest.Rout.save’ ... OK
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 ‘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’ ... OK
Running ‘optimx.R’
Comparing ‘optimx.Rout’ to ‘optimx.Rout.save’ ...42,45c42,45
< 1 -3.3769515 13.992623 9.990204
< 2 -2.3408055 16.743644 6.538589
< 3 -1.4582050 19.494666 4.793137
< 4 -0.6872008 22.245687 3.747885
---
> 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
47,53c47,53
< 6 0.6199912 27.747729 2.567515
< 7 1.1878554 30.498751 2.205222
< 8 1.7126003 33.249772 1.926963
< 9 2.2014952 36.000793 1.707197
< 10 2.6601376 38.751814 1.529684
< 11 3.0929200 41.502836 1.383620
< 12 3.5033462 44.253857 1.261549
---
> 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
57,61c57,61
< 1 -3.6930532 41.342674 1.035628
< 2 -2.6386023 36.082797 1.372420
< 3 -1.8618241 32.494485 1.709212
< 4 -1.2549222 29.876404 2.046005
< 5 -0.7619487 27.873795 2.382797
---
> 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
63,77c63,77
< 7 0.5712025 23.018950 3.729966
< 8 1.0191654 21.567790 4.403551
< 9 1.3826750 20.454248 5.077136
< 10 1.6849379 19.570764 5.750720
< 11 1.9410467 18.851525 6.424305
< 12 2.1613308 18.253884 7.097890
< 13 2.3531449 17.748930 7.771474
< 14 2.5218941 17.316333 8.445059
< 15 2.6716551 16.941360 9.118644
< 16 2.8055700 16.613061 9.792228
< 17 2.9261054 16.323122 10.465813
< 18 3.0352283 16.065109 11.139398
< 19 3.1345294 15.833963 11.812982
< 20 3.2253101 15.625648 12.486567
< 21 3.3086471 15.436908 13.160152
---
> 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
Running ‘order.R’
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’
Comparing ‘parscale.Rout’ to ‘parscale.Rout.save’ ...50c50
< rate 1.045704e-11
---
> rate 1.045669e-11
147c147
< rate 1.407221e-11
---
> rate 1.407176e-11
Running ‘predict.R’
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
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 -5.4686708 2.5585122 27.2089090
< 2 -3.2038315 2.6685690 2.2247879
< 3 -2.5686071 2.7786257 1.9643700
< 4 -1.9314586 2.8886824 1.7291895
< 5 -1.2916431 2.9987392 1.5123049
< 6 -0.6482128 3.1087959 1.3092611
---
> 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 0.6543910 3.3289094 0.9335199
< 9 1.3165907 3.4389661 0.7571493
< 10 1.9884564 3.5490229 0.5870931
< 11 2.6720642 3.6590796 0.4223480
< 12 3.3696896 3.7691363 0.2626573
---
> 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
36,48c36,48
< 1 -3.7698011 3.7316282 0.0151656
< 2 -2.9354326 3.6249130 0.2355394
< 3 -2.1408145 3.5190799 0.4559132
< 4 -1.3862383 3.4153867 0.6762870
< 5 -0.6722993 3.3149740 0.8966608
< 6 0.0000000 3.2188527 1.1170346
< 7 0.6293003 3.1278886 1.3374084
< 8 1.2140472 3.0427958 1.5577822
< 9 1.7527518 2.9641245 1.7781560
< 10 2.2442667 2.8922482 1.9985298
< 11 2.6880452 2.8273623 2.2189036
< 12 3.0843330 2.7694823 2.4392774
< 13 3.4342624 2.7184536 2.6596512
---
> 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
> 6 0.0000000 3.21885266 1.11703462
> 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
- 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