• using R version 2.15.1 (2012-06-22)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• 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 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 installed files from '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' ...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 -4.2047663 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'
  Comparing 'doRUnit.Rout' to 'doRUnit.Rout.save' ...72c72
  < [1] "/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/bbmle.Rcheck/tests"
  ---
  > [1] "/mnt/hgfs/bolker/Documents/R/pkgs/bbmle/pkg/tests"
  75c75
  < [1] "/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/bbmle.Rcheck/bbmle/unitTests"
  ---
  > [1] "/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/bbmle/unitTests"
  79c79
  < RUNIT TEST PROTOCOL -- Wed Aug 1 03:19:29 2012
  ---
  > 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(30.4960450512455, :
  ---
  > 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(33.2466931310693, :
  ---
  > 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(35.9973412108931, :
  ---
  > 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(38.747989290717, :
  ---
  > 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(41.4986373705408, :
  ---
  > 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(41.4986373705408, :
  ---
  > 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(44.2492854503646, :
  ---
  > 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(44.2492854503646, :
  ---
  > 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(31.4659916367342, :
  ---
  > 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' ...35c35
  < In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(37.7033783775527, :
  ---
  > In dpois(x = c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8), lambda = c(37.7033783803611, :
  38,40d37
  < > ## 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 ...
  46,49c43,46
  < 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
  51,57c48,54
  < 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
  61,65c58,62
  < 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
  67,81c64,78
  < 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 '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 -5.4686708 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' ...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
• elapsed time (check, wall clock): 2:01