- using R Under development (unstable) (2012-08-11 r60235)
- 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 ‘1.0.5.2’
- 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 for hidden files and directories ... 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 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 ... [7s/8s] OK
- checking for unstated dependencies in tests ... OK
- checking tests ... [44s/44s] OK
Running ‘BIC.R’ [1s/1s]
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’ [1s/1s]
Comparing ‘ICtab.Rout’ to ‘ICtab.Rout.save’ ... OK
Running ‘RUnit-tests.R’ [0s/0s]
Comparing ‘RUnit-tests.Rout’ to ‘RUnit-tests.Rout.save’ ... OK
Running ‘binomtest1.R’ [2s/2s]
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’ [1s/1s]
Comparing ‘controleval.Rout’ to ‘controleval.Rout.save’ ... OK
Running ‘doRUnit.R’ [1s/1s]
Comparing ‘doRUnit.Rout’ to ‘doRUnit.Rout.save’ ...72c72
< [1] "/home/hornik/tmp/R.check/r-devel/Work/PKGS/bbmle.Rcheck/tests"
---
> [1] "/mnt/hgfs/bolker/Documents/R/pkgs/bbmle/pkg/tests"
75c75
< [1] "/tmp/RtmpYGN1Qc/RLIBS_1c0a948935f/bbmle/unitTests"
---
> [1] "/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/bbmle/unitTests"
79c79
< RUNIT TEST PROTOCOL -- Tue Aug 14 02:34:52 2012
---
> RUNIT TEST PROTOCOL -- Sun Jul 29 14:00:37 2012
Running ‘eval.R’ [1s/1s]
Comparing ‘eval.Rout’ to ‘eval.Rout.save’ ... OK
Running ‘formulatest.R’ [2s/3s]
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(30.4960450568859, :
---
> 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(33.2466931395299, :
---
> 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(35.9973412221739, :
---
> 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(38.7479893048179, :
---
> 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(41.4986373874619, :
---
> 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(41.4986373874619, :
---
> 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(44.2492854701059, :
---
> 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(44.2492854701059, :
---
> 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, :
98c98
< 1: In dpois(x = c(16L, 8L, 6L, 6L, 8L, 0L, 2L, 3L, 5L, 3L, 1L, 5L, :
---
> 1: In dpois(x = c(16, 8, 6, 6, 8, 0, 2, 3, 5, 3, 1, 5, 3, 2, 5, 1, :
100c100
< 2: In dpois(x = c(16L, 8L, 6L, 6L, 8L, 0L, 2L, 3L, 5L, 3L, 1L, 5L, :
---
> 2: In dpois(x = c(16, 8, 6, 6, 8, 0, 2, 3, 5, 3, 1, 5, 3, 2, 5, 1, :
Running ‘glmcomp.R’ [1s/1s]
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’ [1s/1s]
Comparing ‘gradient_vecpar_profile.Rout’ to ‘gradient_vecpar_profile.Rout.save’ ... OK
Running ‘grtest1.R’ [1s/1s]
Comparing ‘grtest1.Rout’ to ‘grtest1.Rout.save’ ...15c15
< 1.090239e-13 1.000000e+00
---
> 1.092459e-13 1.000000e+00
Running ‘methods.R’ [1s/1s]
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’ [2s/2s]
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’ ...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’ [5s/5s]
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 -3.3769515 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
31,37c48,54
< 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
41,45c58,62
< 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
47,61c64,78
< 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
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’ [1s/1s]
Comparing ‘order.Rout’ to ‘order.Rout.save’ ... OK
Running ‘parscale.R’ [1s/1s]
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’ [1s/1s]
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘profbound.R’ [1s/1s]
Comparing ‘profbound.Rout’ to ‘profbound.Rout.save’ ...19c19
< a 2.814052 3.35794623
---
> a 2.814052 3.35794624
Running ‘richards.R’ [7s/7s]
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’ ...32c32
< 1: In dbinom(x = c(7L, 4L, 4L, 4L, 4L, 6L, 1L, 2L, 3L, 5L, 4L, 2L, :
---
> 1: In dbinom(x = c(7, 4, 4, 4, 4, 6, 1, 2, 3, 5, 4, 2, 6, 4, 3, 6, :
34c34
< 2: In dbinom(x = c(7L, 4L, 4L, 4L, 4L, 6L, 1L, 2L, 3L, 5L, 4L, 2L, :
---
> 2: In dbinom(x = c(7, 4, 4, 4, 4, 6, 1, 2, 3, 5, 4, 2, 6, 4, 3, 6, :
36c36
< 3: In dbinom(x = c(7L, 4L, 4L, 4L, 4L, 6L, 1L, 2L, 3L, 5L, 4L, 2L, :
---
> 3: In dbinom(x = c(7, 4, 4, 4, 4, 6, 1, 2, 3, 5, 4, 2, 6, 4, 3, 6, :
38c38
< 4: In dbinom(x = c(7L, 4L, 4L, 4L, 4L, 6L, 1L, 2L, 3L, 5L, 4L, 2L, :
---
> 4: In dbinom(x = c(7, 4, 4, 4, 4, 6, 1, 2, 3, 5, 4, 2, 6, 4, 3, 6, :
Running ‘testenv.R’ [1s/1s]
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’ [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’ ...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 ... [20s/20s] OK
- checking re-building of vignette PDFs ... [19s/19s] OK
- checking PDF version of manual ... OK