@r-universe/webr 2023.6.11 → 2023.6.21

package/dist/vfs/usr/lib/R/tests/reg-tests-3.Rout.save

@@ -0,0 +1,1075 @@
+
+R version 4.3.0 beta (2023-04-12 r84234) -- "Already Tomorrow"
+Copyright (C) 2023 The R Foundation for Statistical Computing
+Platform: aarch64-apple-darwin22.4.0 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ### Regression tests for which the printed output is the issue
+> ### May fail.
+> ### Skipped on a Unix-alike without Recommended packages
+> 
+> pdf("reg-tests-3.pdf", encoding = "ISOLatin1.enc")
+> 
+> ## str() for character & factors with NA (levels), and for Surv objects:
+> ff <- factor(c(2:1,  NA),  exclude = NULL)
+> str(levels(ff))
+ chr [1:3] "1" "2" NA
+> str(ff)
+ Factor w/ 3 levels "1","2",NA: 2 1 3
+> str(ordered(ff, exclude=NULL))
+ Ord.factor w/ 3 levels "1"<"2"<NA: 2 1 3
+> if(require(survival)) {
++     (sa <- Surv(aml$time, aml$status))
++     str(sa)
++     detach("package:survival", unload = TRUE)
++ }
+Loading required package: survival
+ 'Surv' num [1:23, 1:2]   9   13   13+  18   23   28+  31   34   45+  48  ...
+ - attr(*, "dimnames")=List of 2
+  ..$ : NULL
+  ..$ : chr [1:2] "time" "status"
+ - attr(*, "type")= chr "right"
+> ## were different, the last one failed in 1.6.2 (at least)
+> 
+> 
+> ## lm.influence where hat[1] == 1
+> if(require(MASS)) {
++     fit <- lm(formula = 1000/MPG.city ~ Weight + Cylinders + Type + EngineSize + DriveTrain, data = Cars93)
++     print(lm.influence(fit))
++     ## row 57 should have hat = 1 and resid=0.
++     summary(influence.measures(fit))
++ }
+Loading required package: MASS
+$hat
+         1          2          3          4          5          6          7 
+0.09313909 0.07134091 0.19138434 0.08101081 0.24991662 0.10448752 0.12591828 
+         8          9         10         11         12         13         14 
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+        15         16         17         18         19         20         21 
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+        22         23         24         25         26         27         28 
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+        92         93 
+0.15864447 0.57312772 
+
+$coefficients
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+61  0.1520532649    0.0495057257  6.424741e-02 -0.1224729549 -0.0152320811
+62 -0.0675817916   -0.0375435877 -5.699613e-03 -0.0018561352 -0.0297646003
+63 -0.0124737319   -0.1163136988 -6.666660e-02  0.0045716898  0.0573650532
+64 -0.0495762572    0.0108982197  2.072756e-02  0.0311491661 -0.1744779053
+65  0.2450971786    0.1014330960  2.438442e-01  0.2322886433  0.1145616875
+66 -0.0137450945   -0.0933626778 -1.455145e-02 -0.0219051447  0.0210761620
+67 -0.5159902331   -0.3502832221  3.148977e-02 -0.1793660556  0.1719234355
+68  0.0601331294    0.0072908696  1.448763e-01  0.1417048477  0.1267967674
+69  0.0205395611   -0.0166707782 -6.624376e-02 -0.0877281099  0.0244232730
+70  0.2059222894   -0.1200505921  8.218720e-02  0.0002209106  0.0173235673
+71 -0.0312731330    0.0246836012  5.564636e-02  0.0035711688 -0.0041697238
+72 -0.0698149636   -0.0077907772 -5.798951e-02 -0.0404309294  0.0291804508
+73 -0.2461674520   -0.1792254003 -8.946335e-03 -0.0005023396 -0.1849210773
+74  0.2142676665    0.1219475973 -7.874021e-02 -0.0918428593 -0.2301439149
+75 -0.0028726461   -0.0993484475 -4.198827e-02 -0.0328695117  0.0082498333
+76  0.0016544356   -0.0670470508  3.751826e-02 -0.0342084452 -0.0003680573
+77 -0.0256147452    0.0156400843  4.086022e-02  0.0019511571 -0.0017546993
+78  0.2825081053    0.0902228220 -3.983641e-01 -0.4346234712 -0.6043441371
+79  0.0159835202   -0.0629476770  1.898330e-02  0.0085089202 -0.1077243741
+80 -0.8150304378   -0.7413746212  5.446384e-03  0.0101047426  0.0136845038
+81  0.0006315229    0.0011374665  5.007436e-05  0.0001020962  0.0003802979
+82 -0.1389697069   -0.2829444232  2.798773e-01  0.2855962270  0.2832007760
+83 -0.1199642681   -0.1139380335 -3.874836e-03 -0.0029066043  0.0054537971
+84 -0.4681723050   -0.3692610821 -6.915058e-02 -0.0611471408 -0.0286774399
+85  0.5868282269    0.6138842050 -4.618245e-02 -0.0093232438 -0.1687348360
+86 -0.0335385306   -0.0121341311  3.955944e-02  0.0530269621 -0.0049516790
+87 -0.1199323644   -0.0903358174  7.132870e-02  0.0441402079  0.0305846988
+88  0.3030076280    0.4897405972  2.110757e-02  0.0520618321  0.1828859889
+89 -0.1751107919   -0.2847075342 -1.578805e-02 -0.1009325245  0.0816716468
+90  0.0055450581   -0.2720115784 -2.803760e-01 -0.3305994053 -0.2254900027
+91  1.1629492149    0.1111057651 -3.399076e-01 -0.2295981894 -0.3032814817
+92  0.0465882510   -0.3782722178 -1.398749e-01 -0.2168631833 -0.2674612094
+93 -0.1751107919   -0.2847075342 -1.578805e-02 -0.1009325245  0.0816716468
+      TypeSporty       TypeVan    EngineSize DriveTrainFront DriveTrainRear
+1   0.0588316568 -0.1244451013 -0.0384310410    0.0770280182   0.0308309135
+2  -0.0008119071 -0.0929376586 -0.0169359479    0.0241959908  -0.0339336755
+3   0.1122278579  0.2291762722  0.0640824206   -0.0374592418  -0.0063680596
+4  -0.0076600464 -0.0180881612 -0.0224320460    0.0058289643  -0.0019669209
+5  -0.3020816254 -0.2058571702 -0.3622619462   -0.0332177591  -0.4896133013
+6   0.0174438088  0.1203009860  0.0149164277   -0.0095259785  -0.0123604155
+7   0.0006330938  0.0018693765  0.0107797571   -0.0019362039  -0.0134263631
+8   0.0888020681 -0.0981347691  0.5308561510   -0.0605205490   0.0622791836
+9   0.0084422208  0.0641063586 -0.1438112041    0.0132369251   0.1231952988
+10 -0.0453797315  0.1992829759  0.2094701125   -0.0711059699  -0.5860656544
+11  0.0248173290 -0.1726730349  0.0307556826    0.0513955297  -0.2418132557
+12  0.1493980797 -0.0158201826 -0.0533221135    0.0282944654   0.0228550025
+13  0.1994088698  0.1348657122 -0.0134379474   -0.0212986235   0.0103552709
+14  0.0454481137 -0.0247086389 -0.0005370853    0.0136434594   0.0759855468
+15  0.0737344548  0.0705529631 -0.0350342542    0.0366749177   0.0023334058
+16 -0.0098606591 -0.6464182823 -0.1570311735   -0.3099924798  -0.2432841941
+17 -0.0121432263  0.2179211370  0.2426878264   -0.2268810389  -0.3003526507
+18 -0.0012645247  0.0023497958 -0.0011648194   -0.0007816983   0.0031588791
+19 -0.0601680504 -0.0271883474 -0.1686877849    0.0224897952   0.0378443211
+20 -0.0039938145  0.0181201352  0.0439331331   -0.0137111692   0.0000888560
+21  0.1294650212  0.2558709492 -0.1869157355   -0.0403252374   0.1039524785
+22 -0.0110221099  0.0377992374  0.0616023114   -0.0236300001  -0.0027554274
+23  0.0036748958 -0.0109040520  0.0047056340   -0.0027760031  -0.0075815300
+24  0.1217218160 -0.2001221968  0.1453646196    0.1092627610  -0.0419265979
+25 -0.0473791084 -0.0661671214  0.0174623161    0.0138168014  -0.0113597498
+26  0.0343625250 -0.1263789642  0.0185185704    0.0899765460   0.0628671160
+27  0.0521314845  0.1121866729  0.0452354145    0.0036741989  -0.0328558430
+28 -0.1357733641  0.3598998278  0.0635427842    0.1408150632   0.2289697825
+29  0.0032709010 -0.0102098982  0.0072097840   -0.0046929662  -0.0097593036
+30 -0.0031503060  0.0096427335  0.0191501496   -0.0072782279   0.0183269440
+31  0.0124966732 -0.0309659093 -0.0029315971    0.0080704811  -0.0032291174
+32  0.0842166724 -0.1426179532 -0.0047149618    0.1266243473   0.0488025203
+33 -0.2007361705 -0.0700394295  0.0650345678   -0.0076553978  -0.0323613407
+34  0.1985477388  0.1317049456 -0.0379303148    0.0476640032   0.2557928936
+35 -0.0241684660 -0.0063797023  0.0015970165   -0.0082742198  -0.0012845847
+36 -0.2213615898  0.8328871713 -0.1490208173   -0.6045260895  -0.4274997860
+37  0.0832688361  0.0526955171  0.0412992657    0.0057199017   0.0750539814
+38  0.0381452581 -0.0364723376  0.1718996509   -0.0083216767  -0.1711269654
+39  0.0126715370 -0.1319040895  0.0157246728   -0.1238552960  -0.1433995801
+40 -0.6152814178 -0.4391609078  0.1925710081   -0.1848270831  -0.1257923223
+41 -0.2136693396 -0.0102756220 -0.0187378955   -0.0760535877   0.0079050473
+42  0.0115250441 -0.0626784733  0.1853115582   -0.1341403576  -0.1937539975
+43  0.1223234350  0.2339351557  0.0477222207   -0.0703208756  -0.0131810299
+44  0.0012062101 -0.0056275300  0.0138113326   -0.0099328213  -0.0147138005
+45  0.1593529911 -0.3154119193 -0.0734215883    0.2186169305   0.0863564493
+46 -0.0178306744 -0.0229394143  0.0050172709   -0.0032569785  -0.0040140299
+47  0.0870826598  0.5764940782 -0.0661850124   -0.0160346100   0.0058237374
+48  0.0351028466  0.0519540796  0.0730561863   -0.0117874040  -0.0875600533
+49 -0.0118615751 -0.1170935139 -0.0664392527    0.0351943834  -0.0256500862
+50 -0.0881348868  0.0099122018 -0.1427997802   -0.0154102445   0.2834351261
+51  0.0341259919 -0.1980471170  0.1301931475    0.0329557292  -0.1390726822
+52  0.0198930304  0.0233944834  0.2437424291   -0.0398986993  -0.2216521963
+53  0.0026357380 -0.0124859669  0.0032736381   -0.0076038099  -0.0111780184
+54 -0.0052948316  0.0043390590 -0.0062558306   -0.0100922249  -0.0036764450
+55  0.3245941919  0.4533108376 -0.1196342985   -0.0946588832   0.0778256270
+56  0.1438282891 -0.5411631576  0.0968253310    0.3927869929   0.2777652749
+57  0.0000000000  0.0000000000  0.0000000000    0.0000000000   0.0000000000
+58 -0.5770947483 -0.1184054962 -0.1740228604   -0.0285545091   0.7693037902
+59  0.0412280879 -0.0075198458  0.0438882586    0.0121450418  -0.1252262379
+60  0.3533541160  0.2760694598 -0.1036620689    0.1001975219   0.0703124944
+61  0.0813382295 -0.0073739718 -0.0680618001    0.0531536577  -0.2332865147
+62  0.0032709010 -0.0102098982  0.0072097840   -0.0046929662  -0.0097593036
+63  0.0180571278 -0.1370722536 -0.0731027259    0.0500357603  -0.0039945662
+64 -0.0280219408  0.0596353403  0.0485330769   -0.0523499513  -0.0380625252
+65  0.1445564205  0.2773146947 -0.0044527086   -0.0739571632   0.0145722623
+66  0.0147554787  0.0493296285 -0.0390174812    0.0705967740   0.0634638159
+67  0.1109162662 -0.0476703926 -0.0101172134    0.0463473545   0.0838855959
+68  0.1228600624  0.1417644316 -0.0078297996   -0.0320462976   0.0093214403
+69 -0.0117468402 -0.0753433644 -0.0087753330    0.0054190284   0.0076171833
+70 -0.0098606591 -0.6464182823 -0.1570311735   -0.3099924798  -0.2432841941
+71  0.0006330938  0.0018693765  0.0107797571   -0.0019362039  -0.0134263631
+72 -0.0675185509  0.0151499809 -0.0006299133    0.1444639061   0.1463776010
+73  0.0024427576 -0.0249870886  0.0183259078   -0.0314868930  -0.0391504393
+74 -0.1684498617 -0.0211344382  0.0051450670   -0.0108665177  -0.0006733384
+75  0.0454481137 -0.0247086389 -0.0005370853    0.0136434594   0.0759855468
+76  0.0087561990  0.0294347022 -0.0243866906    0.0001777584   0.0361467380
+77  0.0011372964 -0.0003003688  0.0071919929   -0.0007018973  -0.0096901840
+78 -0.4998716808 -0.3342094594 -0.0381922269    0.0632770184   0.0098092574
+79 -0.0142230621  0.0179025413 -0.0175009156   -0.0191510694  -0.0015333501
+80 -0.0247650968 -0.1469466395  0.0130804686   -0.2728976699  -0.2592164502
+81 -0.0001483293 -0.0004719821  0.0001778419   -0.0011917350  -0.0011218042
+82  0.3679140434  0.7422456267  0.0018768183    0.7508948030   0.7730015531
+83  0.0043841507  0.0024787823  0.0002320259    0.0183666140   0.0145190633
+84  0.0640691059 -0.1711824885 -0.0312673044    0.0349340607  -0.0192550330
+85 -0.4756750417  0.0452676883  0.0298336291   -0.1959168864  -0.0136381614
+86  0.0135669048  0.0363260497 -0.0012178976    0.0026468538  -0.0024799878
+87  0.0376963721  0.1229412256 -0.0225447495   -0.0488081493  -0.0417831082
+88 -0.0360445039  0.1399780291  0.1137882315   -0.0178410448  -0.0105132722
+89  0.0609817970  0.1720567027 -0.0724262979    0.1875627215   0.1892070773
+90 -0.2273870236 -0.3709143259 -0.1506696521    0.1197628934   0.0586023325
+91  0.4164006880 -0.1004183249  0.0323442452    0.1231599812  -0.1040204060
+92 -0.2996222296 -0.1090340253 -0.1173564279    0.0035664196   0.4305799574
+93  0.0609817970  0.1720567027 -0.0724262979    0.1875627215   0.1892070773
+
+$sigma
+       1        2        3        4        5        6        7        8 
+3.591432 3.594883 3.598562 3.600558 3.522694 3.598166 3.600799 3.582363 
+       9       10       11       12       13       14       15       16 
+3.590729 3.528259 3.589350 3.596037 3.584177 3.600028 3.593696 3.580547 
+      17       18       19       20       21       22       23       24 
+3.590040 3.601220 3.599441 3.598460 3.584656 3.597078 3.600671 3.553725 
+      25       26       27       28       29       30       31       32 
+3.599688 3.599193 3.595214 3.598433 3.600406 3.596419 3.601044 3.518649 
+      33       34       35       36       37       38       39       40 
+3.587115 3.592663 3.601139 3.501762 3.560763 3.588001 3.592963 3.514670 
+      41       42       43       44       45       46       47       48 
+3.595497 3.334292 3.589110 3.599718 3.471882 3.601133 3.521852 3.594122 
+      49       50       51       52       53       54       55       56 
+3.588734 3.589710 3.583459 3.581755 3.599157 3.599895 3.528075 3.559578 
+      57       58       59       60       61       62       63       64 
+3.601231 3.523963 3.598459 3.571771 3.582319 3.600406 3.596626 3.592960 
+      65       66       67       68       69       70       71       72 
+3.583325 3.600828 3.569987 3.592482 3.599979 3.580547 3.600799 3.599768 
+      73       74       75       76       77       78       79       80 
+3.579302 3.593475 3.600028 3.598895 3.600991 3.495965 3.597794 3.594229 
+      81       82       83       84       85       86       87       88 
+3.601231 3.563077 3.601124 3.585986 3.575773 3.600658 3.599786 3.563954 
+      89       90       91       92       93 
+3.594056 3.566216 3.484273 3.578056 3.594056 
+
+$wt.res
+            1             2             3             4             5 
+  2.218439708   1.807326787  -1.093991760   0.585986462  -5.684589270 
+            6             7             8             9            10 
+  1.233522386   0.457950438   2.515990067  -2.287803728   5.535960625 
+           11            12            13            14            15 
+  2.178905651  -1.596117514  -2.967297860   0.745175851   1.933882824 
+           16            17            18            19            20 
+ -3.035594591   2.195009903   0.072527577  -0.753360641  -1.155059621 
+           21            22            23            24            25 
+ -2.847828869  -1.410703414  -0.540252474   4.877197398   0.890715640 
+           26            27            28            29            30 
+ -0.968642103   1.731771561  -0.993218102  -0.656454198  -1.529950693 
+           31            32            33            34            35 
+ -0.298424469   6.510112647   2.683267748   1.992954455  -0.214079423 
+           36            37            38            39            40 
+  6.735053083  -4.545792145  -2.399183444  -1.714795692  -6.472930954 
+           41            42            43            44            45 
+ -1.671169308 -11.585332803  -2.485888781  -0.888857647   8.068071025 
+           46            47            48            49            50 
+ -0.216046323   6.246829383  -1.747619081   2.530823032   2.314106628 
+           51            52            53            54            55 
+  2.974532942  -2.887230686  -1.041442666  -0.835536301  -6.102291353 
+           56            57            58            59            60 
+ -4.376058028   0.000000000   5.966190371  -1.147443467   3.788198306 
+           61            62            63            64            65 
+ -3.015807719  -0.656454198   1.508247858  -2.064017840  -3.023462268 
+           66            67            68            69            70 
+  0.407243898  -3.964783523  -2.127186213  -0.789242889  -3.035594591 
+           71            72            73            74            75 
+  0.457950438  -0.797900840  -3.382338495   1.978150290   0.745175851 
+           76            77            78            79            80 
+ -1.096455031   0.341748714   7.324729228  -1.336726492   1.519313995 
+           81            82            83            84            85 
+  0.005901292  -4.095330927   0.195481697  -2.773676266  -3.487375439 
+           86            87            88            89            90 
+  0.536312040   0.775871729   4.379791779   1.302710701   4.213228761 
+           91            92            93 
+  7.334576566   3.283113507  -1.302710701 
+
+Potentially influential observations of
+	 lm(formula = 1000/MPG.city ~ Weight + Cylinders + Type + EngineSize +      DriveTrain, data = Cars93) :
+
+   dfb.1_ dfb.Wght dfb.Cyl4 dfb.Cyl5 dfb.Cyl6 dfb.Cyl8 dfb.Cyln dfb.TypL
+8  -0.16   0.00    -0.10    -0.07    -0.24    -0.44     0.01     0.12   
+19 -0.03   0.09    -0.01    -0.03     0.00    -0.01    -0.03     0.08   
+28  0.11  -0.15     0.04     0.02     0.02     0.02     0.04     0.07   
+39 -0.19   0.05     0.34     0.21     0.25     0.18     0.18    -0.01   
+42  0.12  -0.04    -0.30    -0.17    -0.28    -0.26    -0.11    -0.03   
+57  0.00   0.00     0.00     0.00     0.00     0.00     0.00     0.00   
+66 -0.03   0.04    -0.02    -0.03    -0.01     0.00    -0.02    -0.01   
+80  0.18   0.00    -0.31    -0.17    -0.24    -0.19    -0.15     0.00   
+83  0.01   0.01    -0.04    -0.03    -0.04    -0.03    -0.02     0.00   
+87 -0.03   0.04    -0.01    -0.04    -0.04    -0.03    -0.02     0.04   
+89 -0.11   0.11    -0.05     0.28    -0.06    -0.04    -0.06    -0.01   
+93 -0.11   0.11    -0.05    -0.45    -0.06    -0.04    -0.06    -0.01   
+   dfb.TypM dfb.TypSm dfb.TypSp dfb.TypV dfb.EngS dfb.DrTF dfb.DrTR dffit
+8   0.00     0.21      0.06     -0.04     0.47    -0.04     0.03     0.73
+19  0.01     0.00     -0.04     -0.01    -0.15     0.01     0.02    -0.24
+28  0.08    -0.08     -0.09      0.16     0.06     0.09     0.12    -0.26
+39 -0.01     0.04      0.01     -0.06     0.01    -0.08    -0.08    -0.44
+42  0.01    -0.42      0.01     -0.03     0.18    -0.10    -0.11    -0.89
+57  0.00     0.00      0.00      0.00     0.00     0.00     0.00      NaN
+66 -0.02     0.01      0.01      0.02    -0.03     0.05     0.03     0.08
+80  0.01     0.01     -0.02     -0.07     0.01    -0.18    -0.14     0.45
+83  0.00     0.00      0.00      0.00     0.00     0.01     0.01     0.05
+87  0.03     0.02      0.03      0.06    -0.02    -0.03    -0.02     0.14
+89 -0.07     0.05      0.04      0.08    -0.06     0.12     0.10     0.64
+93 -0.07     0.05      0.04      0.08    -0.06     0.12     0.10    -0.64
+   cov.r   cook.d hat    
+8   1.71_*  0.04   0.39  
+19  2.09_*  0.00   0.43  
+28  1.86_*  0.00   0.36  
+39  1.76_*  0.01   0.36  
+42  0.13_*  0.05   0.06  
+57   NaN     NaN   1.00_*
+66  1.63_*  0.00   0.26  
+80  1.92_*  0.01   0.40  
+83  1.88_*  0.00   0.36  
+87  1.60_*  0.00   0.25  
+89  2.68_*  0.03   0.57_*
+93  2.68_*  0.03   0.57_*
+> ## only last two cols in row 57 should be influential
+> 
+> 
+> ## PR#6640  Zero weights in plot.lm
+> if(require(MASS)) {
++     fm1 <- lm(time~dist, data=hills, weights=c(0,0,rep(1,33)))
++     plot(fm1)
++ }
+> ## gave warnings in 1.8.1
+> 
+> 
+> ## PR#7829 model.tables & replications
+> if(require(MASS)) {
++     oats.aov <- aov(Y ~ B + V + N + V:N, data=oats[-1,])
++     model.tables(oats.aov, "means", cterms=c("N", "V:N"))
++ }
+Tables of means
+Grand mean
+         
+103.8732 
+
+ N 
+    0.0cwt 0.2cwt 0.4cwt 0.6cwt
+     78.74  98.51  113.8    123
+rep  17.00  18.00   18.0     18
+
+ V:N 
+             N
+V             0.0cwt 0.2cwt 0.4cwt 0.6cwt
+  Golden.rain  79.53  98.03 114.20 124.37
+  rep           6.00   6.00   6.00   6.00
+  Marvellous   86.20 108.03 116.70 126.37
+  rep           6.00   6.00   6.00   6.00
+  Victory      69.77  89.20 110.37 118.03
+  rep           5.00   6.00   6.00   6.00
+> ## wrong printed output in 2.1.0
+> 
+> 
+> ## drop1 on weighted lm() fits
+> if(require(MASS)) {
++     hills.lm <- lm(time ~ 0 + dist + climb, data=hills, weights=1/dist^2)
++     print(drop1(hills.lm))
++     print(stats:::drop1.default(hills.lm))
++     hills.lm2 <- lm(time/dist ~ 1 + I(climb/dist), data=hills)
++     drop1(hills.lm2)
++ }
+Single term deletions
+
+Model:
+time ~ 0 + dist + climb
+       Df Sum of Sq    RSS     AIC
+<none>              442.22  92.776
+dist    1    330.92 773.14 110.329
+climb   1      9.73 451.95  91.538
+Single term deletions
+
+Model:
+time ~ 0 + dist + climb
+       Df     AIC
+<none>     92.776
+dist    1 110.329
+climb   1  91.538
+Single term deletions
+
+Model:
+time/dist ~ 1 + I(climb/dist)
+              Df Sum of Sq    RSS    AIC
+<none>                     442.22 92.776
+I(climb/dist)  1    9.7331 451.95 91.538
+> ## quoted unweighted RSS etc in 2.2.1
+> 
+> 
+> ## tests of ISO C99 compliance (Windows fails without a workaround)
+> sprintf("%g", 123456789)
+[1] "1.23457e+08"
+> sprintf("%8g", 123456789)
+[1] "1.23457e+08"
+> sprintf("%9.7g", 123456789)
+[1] "1.234568e+08"
+> sprintf("%10.9g", 123456789)
+[1] " 123456789"
+> sprintf("%g", 12345.6789)
+[1] "12345.7"
+> sprintf("%10.9g", 12345.6789)
+[1] "12345.6789"
+> sprintf("%10.7g", 12345.6789)
+[1] "  12345.68"
+> sprintf("%.7g", 12345.6789)
+[1] "12345.68"
+> sprintf("%.5g", 12345.6789)
+[1] "12346"
+> sprintf("%.4g", 12345.6789)
+[1] "1.235e+04"
+> sprintf("%9.4g", 12345.6789)
+[1] "1.235e+04"
+> sprintf("%10.4g", 12345.6789)
+[1] " 1.235e+04"
+> ## Windows used e+008 etc prior to 2.3.0
+> 
+> 
+> ## weighted glm() fits
+> if(require(MASS)) {
++     hills.glm <- glm(time ~ 0 + dist + climb, data=hills, weights=1/dist^2)
++     print(AIC(hills.glm))
++     print(extractAIC(hills.glm))
++     print(drop1(hills.glm))
++     stats:::drop1.default(hills.glm)
++ }
+[1] 322.2318
+[1]   2.0000 322.2318
+Single term deletions
+
+Model:
+time ~ 0 + dist + climb
+       Df Deviance    AIC
+<none>      442.22 322.23
+dist    1   773.14 339.78
+climb   1   451.95 320.99
+Single term deletions
+
+Model:
+time ~ 0 + dist + climb
+       Df    AIC
+<none>    322.23
+dist    1 339.78
+climb   1 320.99
+> ## wrong AIC() and drop1 prior to 2.3.0.
+> 
+> ## calculating no of signif digits
+> print(1.001, digits=16)
+[1] 1.001
+> ## 2.4.1 gave  1.001000000000000
+> ## 2.5.0 errs on the side of caution.
+> 
+> 
+> ## as.matrix.data.frame with coercion
+> if(require("survival")) {
++     soa <- Surv(1:5, c(0, 0, 1, 0, 1))
++     df.soa <- data.frame(soa)
++     print(as.matrix(df.soa)) # numeric result
++     df.soac <- data.frame(soa, letters[1:5])
++     print(as.matrix(df.soac)) # character result
++     detach("package:survival", unload = TRUE)
++ }
+Loading required package: survival
+     soa.time soa.status
+[1,]        1          0
+[2,]        2          0
+[3,]        3          1
+[4,]        4          0
+[5,]        5          1
+     soa  letters.1.5.
+[1,] "1+" "a"         
+[2,] "2+" "b"         
+[3,] "3 " "c"         
+[4,] "4+" "d"         
+[5,] "5 " "e"         
+> ## failed in 2.8.1
+> 
+> ## wish of PR#13505
+> npk.aov <- aov(yield ~ block + N * P + K, npk)
+> foo <- proj(npk.aov)
+> cbind(npk, foo)
+   block N P K yield (Intercept)  block         N          P         K
+1      1 0 1 1  49.5      54.875 -0.850 -2.808333 -0.5916667 -1.991667
+2      1 1 1 0  62.8      54.875 -0.850  2.808333 -0.5916667  1.991667
+3      1 0 0 0  46.8      54.875 -0.850 -2.808333  0.5916667  1.991667
+4      1 1 0 1  57.0      54.875 -0.850  2.808333  0.5916667 -1.991667
+5      2 1 0 0  59.8      54.875  2.575  2.808333  0.5916667  1.991667
+6      2 1 1 1  58.5      54.875  2.575  2.808333 -0.5916667 -1.991667
+7      2 0 0 1  55.5      54.875  2.575 -2.808333  0.5916667 -1.991667
+8      2 0 1 0  56.0      54.875  2.575 -2.808333 -0.5916667  1.991667
+9      3 0 1 0  62.8      54.875  5.900 -2.808333 -0.5916667  1.991667
+10     3 1 1 1  55.8      54.875  5.900  2.808333 -0.5916667 -1.991667
+11     3 1 0 0  69.5      54.875  5.900  2.808333  0.5916667  1.991667
+12     3 0 0 1  55.0      54.875  5.900 -2.808333  0.5916667 -1.991667
+13     4 1 0 0  62.0      54.875 -4.750  2.808333  0.5916667  1.991667
+14     4 1 1 1  48.8      54.875 -4.750  2.808333 -0.5916667 -1.991667
+15     4 0 0 1  45.5      54.875 -4.750 -2.808333  0.5916667 -1.991667
+16     4 0 1 0  44.2      54.875 -4.750 -2.808333 -0.5916667  1.991667
+17     5 1 1 0  52.0      54.875 -4.350  2.808333 -0.5916667  1.991667
+18     5 0 0 0  51.5      54.875 -4.350 -2.808333  0.5916667  1.991667
+19     5 1 0 1  49.8      54.875 -4.350  2.808333  0.5916667 -1.991667
+20     5 0 1 1  48.8      54.875 -4.350 -2.808333 -0.5916667 -1.991667
+21     6 1 0 1  57.2      54.875  1.475  2.808333  0.5916667 -1.991667
+22     6 1 1 0  59.0      54.875  1.475  2.808333 -0.5916667  1.991667
+23     6 0 1 1  53.2      54.875  1.475 -2.808333 -0.5916667 -1.991667
+24     6 0 0 0  56.0      54.875  1.475 -2.808333  0.5916667  1.991667
+          N:P  Residuals
+1   0.9416667 -0.0750000
+2  -0.9416667  5.5083333
+3  -0.9416667 -6.0583333
+4   0.9416667  0.6250000
+5   0.9416667 -3.9833333
+6  -0.9416667  1.7666667
+7  -0.9416667  3.2000000
+8   0.9416667 -0.9833333
+9   0.9416667  2.4916667
+10 -0.9416667 -4.2583333
+11  0.9416667  2.3916667
+12 -0.9416667 -0.6250000
+13  0.9416667  5.5416667
+14 -0.9416667 -0.6083333
+15 -0.9416667  0.5250000
+16  0.9416667 -5.4583333
+17 -0.9416667 -1.7916667
+18 -0.9416667  2.1416667
+19  0.9416667 -3.0750000
+20  0.9416667  2.7250000
+21  0.9416667 -1.5000000
+22 -0.9416667 -0.6166667
+23  0.9416667  1.3000000
+24 -0.9416667  0.8166667
+> ## failed in R < 2.10.0
+> 
+> 
+> if(suppressMessages(require("Matrix"))) {
++   print(cS. <- contr.SAS(5, sparse = TRUE))
++   stopifnot(all(contr.SAS(5) == cS.),
++ 	    all(contr.helmert(5, sparse = TRUE) == contr.helmert(5)))
++ 
++   x1 <- x2 <- c('a','b','a','b','c')
++   x3 <- x2; x3[4:5] <- x2[5:4]
++   print(xtabs(~ x1 + x2, sparse= TRUE, exclude = 'c'))
++   print(xtabs(~ x1 + x3, sparse= TRUE, exclude = 'c'))
++   detach("package:Matrix")
++   ## failed in R <= 2.13.1
++ }
+5 x 4 sparse Matrix of class "dgCMatrix"
+  1 2 3 4
+1 1 . . .
+2 . 1 . .
+3 . . 1 .
+4 . . . 1
+5 . . . .
+2 x 2 sparse Matrix of class "dgCMatrix"
+   x2
+x1  a b
+  a 2 .
+  b . 2
+2 x 2 sparse Matrix of class "dgCMatrix"
+   x3
+x1  a b
+  a 2 .
+  b . 1
+> 
+> ## regression tests for dimnames (broken on 2009-07-31)
+> contr.sum(4)
+  [,1] [,2] [,3]
+1    1    0    0
+2    0    1    0
+3    0    0    1
+4   -1   -1   -1
+> contr.helmert(4)
+  [,1] [,2] [,3]
+1   -1   -1   -1
+2    1   -1   -1
+3    0    2   -1
+4    0    0    3
+> contr.sum(2) # needed drop=FALSE at one point.
+  [,1]
+1    1
+2   -1
+> 
+> ## xtabs did not exclude levels from factors
+> x1 <- c('a','b','a','b','c', NA)
+> x2 <- factor(x1, exclude=NULL)
+> print(xtabs(~ x1 + x2, na.action = na.pass))
+   x2
+x1  a b c <NA>
+  a 2 0 0    0
+  b 0 2 0    0
+  c 0 0 1    0
+> print(xtabs(~ x1 + x2, exclude = 'c', na.action = na.pass))
+      x2
+x1     a b <NA>
+  a    2 0    0
+  b    0 2    0
+  <NA> 0 0    1
+> 
+> 
+> ## median should work by default for a suitable S4 class.
+> ## adapted from adaptsmoFMRI
+> if(suppressMessages(require("Matrix"))) {
++     x <- matrix(c(1,2,3,4))
++     print(median(x))
++     print(median(as(x, "dgeMatrix")))
++     detach("package:Matrix")
++ }
+[1] 2.5
+'as(<matrix>, "dgeMatrix")' is deprecated.
+Use 'as(as(as(., "dMatrix"), "generalMatrix"), "unpackedMatrix")' instead.
+See help("Deprecated") and help("Matrix-deprecated").
+[1] 2.5
+> 
+> ## Various arguments were not duplicated:  PR#15352 to 15354
+> x <- 5
+> y <- 2
+> f <- function (y) x
+> numericDeriv(f(y),"y")
+[1] 5
+attr(,"gradient")
+     [,1]
+[1,]    0
+> x
+[1] 5
+> 
+> a<-list(1,2)
+> b<-rep.int(a,c(2,2))
+> b[[1]][1]<-9
+> a[[1]]
+[1] 1
+> 
+> a <- numeric(1)
+> x <- mget("a",as.environment(1))
+> x
+$a
+[1] 0
+
+> a[1] <- 9
+> x
+$a
+[1] 0
+
+> 
+> 
+> ## needs MASS installed
+> ## PR#2586 labelling in alias()
+> if(require("MASS")) {
++     Y <- c(0,1,2)
++     X1 <- c(0,1,0)
++     X2 <- c(0,1,0)
++     X3 <- c(0,0,1)
++     print(res <- alias(lm(Y ~ X1 + X2 + X3)))
++     stopifnot(identical(rownames(res[[2]]), "X2"))
++ }
+Model :
+Y ~ X1 + X2 + X3
+
+Complete :
+   (Intercept) X1 X3
+X2 0           1  0 
+
+> ## the error was in lm.(w)fit
+> 
+> if(require("Matrix")) {
++  m1 <- m2 <- m <- matrix(1:12, 3,4)
++  dimnames(m2) <- list(LETTERS[1:3],
++                       letters[1:4])
++  dimnames(m1) <- list(NULL,letters[1:4])
++  M  <- Matrix(m)
++  M1 <- Matrix(m1)
++  M2 <- Matrix(m2)
++  ## Now, with a new ideal cbind(), rbind():
++  print(cbind(M, M1))
++  stopifnot(identical(cbind (M, M1),
++                      cbind2(M, M1)))
++  rm(M,M1,M2)
++  detach("package:Matrix", unload=TRUE)
++ }##{Matrix}
+Loading required package: Matrix
+3 x 8 Matrix of class "dgeMatrix"
+              a b c  d
+[1,] 1 4 7 10 1 4 7 10
+[2,] 2 5 8 11 2 5 8 11
+[3,] 3 6 9 12 3 6 9 12
+> 
+> 
+> ## Invalid UTF-8 strings
+> x <- c("Jetz", "no", "chli", "z\xc3\xbcrit\xc3\xbc\xc3\xbctsch:",
++        "(noch", "ein", "bi\xc3\x9fchen", "Z\xc3\xbc", "deutsch)",
++        "\xfa\xb4\xbf\xbf\x9f")
+> lapply(x, utf8ToInt)
+[[1]]
+[1]  74 101 116 122
+
+[[2]]
+[1] 110 111
+
+[[3]]
+[1]  99 104 108 105
+
+[[4]]
+ [1] 122 252 114 105 116 252 252 116 115  99 104  58
+
+[[5]]
+[1]  40 110 111  99 104
+
+[[6]]
+[1] 101 105 110
+
+[[7]]
+[1]  98 105 223  99 104 101 110
+
+[[8]]
+[1]  90 252
+
+[[9]]
+[1] 100 101 117 116 115  99 104  41
+
+[[10]]
+[1] NA
+
+> Encoding(x) <- "UTF-8"
+> nchar(x, "b")
+ [1]  4  2  4 15  5  3  8  3  8  5
+> try(nchar(x, "c"))
+Error in nchar(x, "c") : invalid multibyte string, element 10
+> try(nchar(x, "w"))
+Error in nchar(x, "w") : invalid multibyte string, element 10
+> nchar(x, "c", allowNA = TRUE)
+ [1]  4  2  4 12  5  3  7  2  8 NA
+> nchar(x, "w", allowNA = TRUE)
+ [1]  4  2  4 12  5  3  7  2  8 NA
+> ## Results differed by platform, but some gave incorrect results on string 10.
+> 
+> 
+> ## str() on large strings
+> if (l10n_info()$"UTF-8" || l10n_info()$"Latin-1") {
++   cc <- "J\xf6reskog" # valid in "latin-1"; invalid multibyte string in UTF-8
++   .tmp <- capture.output(
++   str(cc) # failed in some R-devel versions
++   )
++   stopifnot(grepl("chr \"J.*reskog\"", .tmp))
++ 
++   print(nchar(L <- strrep(paste(LETTERS, collapse="."), 100000), type="b")) # 5.1 M
++   print(str(L))
++ }
+> 
+> if(require("Matrix", .Library)) {
++     M <- Matrix(diag(1:10), sparse=TRUE) # a "ddiMatrix"
++     setClass("TestM", slots = c(M='numeric'))
++     setMethod("+", c("TestM","TestM"), function(e1,e2) {
++         e1@M + e2@M
++     })
++     M+M # works the first time
++     M+M # was error   "object '.Generic' not found"
++     ##
++     as.Matrix <- if(packageVersion("Matrix", .Library) >= "1.4.2") {
++                      as.matrix
++                  } else function(x) `dimnames<-`(as.matrix(x), list(NULL,NULL))
++     stopifnot(exprs = {
++         identical(pmin(2,M), pmin(2, as.matrix(M)))
++         identical(as.matrix(pmax(M, 7)),
++                   pmax(as.Matrix(M), 7))
++     })
++     rm(M)
++ 
++     ## show(<S4 generic>) from base
++     show(chol2inv) # last line now has .. showMethods(chol2inv) ..
++ 
++     detach("package:Matrix", unload=TRUE)
++ }##{Matrix}
+Loading required package: Matrix
+<sparse>[ <logic> ]: .M.sub.i.logical() maybe inefficient
+standardGeneric for "chol2inv" defined from package "base"
+
+function (x, ...) 
+standardGeneric("chol2inv")
+<bytecode: 0x11e3f50e0>
+<environment: 0x11e3f0458>
+Methods may be defined for arguments: x
+Use  showMethods(chol2inv)  for currently available ones.
+> 
+> ## citation() / bibentry: year will change but check is sloppy
+> options(width=88) # format.bibentry() using strwrap()
+> print(c1 <- citation())
+To cite R in publications use:
+
+  R Core Team (2023). _R: A Language and Environment for Statistical
+  Computing_. R Foundation for Statistical Computing, Vienna, Austria.
+  <https://www.R-project.org/>.
+
+A BibTeX entry for LaTeX users is
+
+  @Manual{,
+    title = {R: A Language and Environment for Statistical Computing},
+    author = {{R Core Team}},
+    organization = {R Foundation for Statistical Computing},
+    address = {Vienna, Austria},
+    year = {2023},
+    url = {https://www.R-project.org/},
+  }
+
+We have invested a lot of time and effort in creating R, please cite it when
+using it for data analysis. See also 'citation("pkgname")' for citing R
+packages.
+> fc1B <- format(c1)
+> fc1N <- format(c1, bibtex=FALSE)
+> stopifnot(exprs = {
++     identical(fc1B[-2], fc1N[-2])
++     (b2 <- fc1B[2]) != (n2 <- fc1N[2]) # bibtex left away (at end of line 2)
++     startsWith(b2, n2)
++ })
+> 
+> pkg <- "nlme"
+> (hasME <- requireNamespace(pkg, quietly=TRUE, lib.loc = .Library))
+[1] TRUE
+> if(hasME) withAutoprint({
++     c2 <- citation(package=pkg)
++     ## avoid spurious diffs:
++     c2$author[[1]]$given[[1]] <- "J."
++     c2$year[[1]] <- "9999"
++     c2$note[[1]] <- sub("3.1-[0-9]*$", "3.1-999", c2$note[[1]])
++     print(c2)
++     print(c2, bibtex=FALSE) # no final message
++     print(c2, bibtex=TRUE)  # w/ two bibTeX
++     stopifnot(length(c2) >= 2)
++     f2N <- format(c2) # -> format.bibentry(*, style="citation")
++     f2B <- format(c2, bibtex=TRUE)
++     stopifnot(exprs = {
++         print(n <- length(f2N)) == length(f2B)
++         identical(f2N[1], f2B[1])
++         grepl("see these entries in BibTeX",       f2N[n], fixed=TRUE)
++         grepl("'format(<citation>, bibtex=TRUE)'", f2N[n], fixed=TRUE) # "format(..)" was "print(..)"
++         f2B[n] == ""
++         (ie <- -c(1,n)) < 0
++         grepl("A BibTeX entry ", f2B[ie], fixed=TRUE)
++         grepl(" @[A-Z]", f2B[ie]) # @Book etc
++        !grepl(" @[A-Z]", f2N[ie]) # *not* there
++         nchar(f2N[ie]) < nchar(f2B[ie])
++         startsWith(f2B[ie], f2N[ie])
++       })
++ })
+> c2 <- citation(package = pkg)
+> c2$author[[1]]$given[[1]] <- "J."
+> c2$year[[1]] <- "9999"
+> c2$note[[1]] <- sub("3.1-[0-9]*$", "3.1-999", c2$note[[1]])
+> print(c2)
+To cite package 'nlme' in publications use:
+
+  Pinheiro J, Bates D, R Core Team (9999). _nlme: Linear and Nonlinear Mixed
+  Effects Models_. R package version 3.1-999,
+  <https://CRAN.R-project.org/package=nlme>.
+
+  Pinheiro JC, Bates DM (2000). _Mixed-Effects Models in S and S-PLUS_.
+  Springer, New York. doi:10.1007/b98882 <https://doi.org/10.1007/b98882>.
+
+To see these entries in BibTeX format, use 'print(<citation>, bibtex=TRUE)',
+'toBibtex(.)', or set 'options(citation.bibtex.max=999)'.
+> print(c2, bibtex = FALSE)
+To cite package 'nlme' in publications use:
+
+  Pinheiro J, Bates D, R Core Team (9999). _nlme: Linear and Nonlinear Mixed
+  Effects Models_. R package version 3.1-999,
+  <https://CRAN.R-project.org/package=nlme>.
+
+  Pinheiro JC, Bates DM (2000). _Mixed-Effects Models in S and S-PLUS_.
+  Springer, New York. doi:10.1007/b98882 <https://doi.org/10.1007/b98882>.
+> print(c2, bibtex = TRUE)
+To cite package 'nlme' in publications use:
+
+  Pinheiro J, Bates D, R Core Team (9999). _nlme: Linear and Nonlinear Mixed
+  Effects Models_. R package version 3.1-999,
+  <https://CRAN.R-project.org/package=nlme>.
+
+A BibTeX entry for LaTeX users is
+
+  @Manual{,
+    title = {nlme: Linear and Nonlinear Mixed Effects Models},
+    author = {J. Pinheiro and Douglas Bates and {R Core Team}},
+    year = {9999},
+    note = {R package version 3.1-999},
+    url = {https://CRAN.R-project.org/package=nlme},
+  }
+
+  Pinheiro JC, Bates DM (2000). _Mixed-Effects Models in S and S-PLUS_.
+  Springer, New York. doi:10.1007/b98882 <https://doi.org/10.1007/b98882>.
+
+A BibTeX entry for LaTeX users is
+
+  @Book{,
+    title = {Mixed-Effects Models in S and S-PLUS},
+    author = {Jos<U+00E9> C. Pinheiro and Douglas M. Bates},
+    year = {2000},
+    publisher = {Springer},
+    address = {New York},
+    doi = {10.1007/b98882},
+  }
+> stopifnot(length(c2) >= 2)
+> f2N <- format(c2)
+> f2B <- format(c2, bibtex = TRUE)
+> stopifnot(exprs = {
++     print(n <- length(f2N)) == length(f2B)
++     identical(f2N[1], f2B[1])
++     grepl("see these entries in BibTeX", f2N[n], fixed = TRUE)
++     grepl("'format(<citation>, bibtex=TRUE)'", f2N[n], fixed = TRUE)
++     f2B[n] == ""
++     (ie <- -c(1, n)) < 0
++     grepl("A BibTeX entry ", f2B[ie], fixed = TRUE)
++     grepl(" @[A-Z]", f2B[ie])
++     !grepl(" @[A-Z]", f2N[ie])
++     nchar(f2N[ie]) < nchar(f2B[ie])
++     startsWith(f2B[ie], f2N[ie])
++ })
+[1] 4
+> 
+> cat('Time elapsed: ', proc.time(),'\n')
+Time elapsed:  1.467 0.085 1.559 0.001 0.003 
+>