- 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 ‘multcomp/DESCRIPTION’ ... OK
- this is package ‘multcomp’ version ‘1.2-9’
- 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 ‘multcomp’ 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking examples ... OK
- checking differences from ‘multcomp-Ex.Rout’ to ‘multcomp-Ex.Rout.save’ ...
43c43
< F-statistic: 89.57 on 1 and 48 DF, p-value: 1.49e-12
---
> F-statistic: 89.57 on 1 and 48 DF, p-value: 1.490e-12
274,290d273
<
< Attaching package: 'bdsmatrix'
<
< The following object(s) are masked from 'package:base':
<
< backsolve
<
<
< Attaching package: 'Matrix'
<
< The following object(s) are masked from 'package:base':
<
< det
<
< Warning: replacing previous import 'diag' when loading 'Matrix'
< Warning in Ops.factor(1, center) : | not meaningful for factors
< Warning in Ops.factor(1, center) : | not meaningful for factors
292,293c275,276
< trt2 - trt1 1.551055 1.184063 Inf
< trt3 - trt1 1.396362 1.068776 Inf
---
> trt2 - trt1 1.551157 1.184130 Inf
> trt3 - trt1 1.396387 1.068788 Inf
299,300c282
< detaching 'package:coxme', 'package:Matrix', 'package:lattice',
< 'package:nlme', 'package:bdsmatrix'
---
> detaching 'package:coxme', 'package:bdsmatrix'
453c435
< Quantile = 3.0638
---
> Quantile = 3.0631
459,468c441,450
< B - A == 0 -2.1333 -4.7925 0.5259
< C - A == 0 3.6000 0.9408 6.2592
< D - A == 0 2.2000 -0.4592 4.8592
< E - A == 0 -4.3333 -6.9925 -1.6741
< C - B == 0 5.7333 3.0741 8.3925
< D - B == 0 4.3333 1.6741 6.9925
< E - B == 0 -2.2000 -4.8592 0.4592
< D - C == 0 -1.4000 -4.0592 1.2592
< E - C == 0 -7.9333 -10.5925 -5.2741
< E - D == 0 -6.5333 -9.1925 -3.8741
---
> B - A == 0 -2.1333 -4.7920 0.5253
> C - A == 0 3.6000 0.9414 6.2586
> D - A == 0 2.2000 -0.4586 4.8586
> E - A == 0 -4.3333 -6.9920 -1.6747
> C - B == 0 5.7333 3.0747 8.3920
> D - B == 0 4.3333 1.6747 6.9920
> E - B == 0 -2.2000 -4.8586 0.4586
> D - C == 0 -1.4000 -4.0586 1.2586
> E - C == 0 -7.9333 -10.5920 -5.2747
> E - D == 0 -6.5333 -9.1920 -3.8747
513c495
< D - B == 0 4.3333 0.8679 4.993 0.000531 ***
---
> D - B == 0 4.3333 0.8679 4.993 0.000398 ***
534c516
< C - A == 0 3.6000 0.8679 4.148 0.00275 **
---
> C - A == 0 3.6000 0.8679 4.148 0.00266 **
580,586d561
< Attaching package: 'zoo'
<
< The following object(s) are masked from 'package:base':
<
< as.Date, as.Date.numeric
<
<
594c569
< Quantile = 2.8942
---
> Quantile = 2.8941
600c575
< PE4 - PE3 == 0 -0.012820 -0.114108 0.088468
---
> PE4 - PE3 == 0 -0.012820 -0.114107 0.088468
602,607c577,582
< PE6 - PE3 == 0 0.019286 -0.084210 0.122781
< PE7 - PE3 == 0 -0.010048 -0.120043 0.099948
< PE9 - PE3 == 0 0.075536 -0.028027 0.179098
< PE5 - PE4 == 0 -0.071579 -0.128779 -0.014379
< PE6 - PE4 == 0 0.032105 -0.034133 0.098344
< PE7 - PE4 == 0 0.002772 -0.073223 0.078767
---
> PE6 - PE3 == 0 0.019286 -0.084209 0.122780
> PE7 - PE3 == 0 -0.010048 -0.120042 0.099947
> PE9 - PE3 == 0 0.075536 -0.028026 0.179098
> PE5 - PE4 == 0 -0.071579 -0.128778 -0.014380
> PE6 - PE4 == 0 0.032105 -0.034133 0.098343
> PE7 - PE4 == 0 0.002772 -0.073222 0.078766
609,610c584,585
< PE6 - PE5 == 0 0.103684 0.042661 0.164707
< PE7 - PE5 == 0 0.074351 0.002856 0.145845
---
> PE6 - PE5 == 0 0.103684 0.042662 0.164707
> PE7 - PE5 == 0 0.074351 0.002857 0.145845
614c589
< PE9 - PE7 == 0 0.085583 0.006582 0.164584
---
> PE9 - PE7 == 0 0.085583 0.006583 0.164584
946,947c921,922
< otrend >= 0 -3.4821 2.0867 -1.669 0.2185
< atrend >= 0 -314.7324 408.9901 -0.770 0.6625
---
> otrend >= 0 -3.4821 2.0867 -1.669 0.2182
> atrend >= 0 -314.7324 408.9901 -0.770 0.6621
989c964
< Quantile = 2.4159
---
> Quantile = 2.416
995,997c970,972
< M - L == 0 -10.0000 -19.3552 -0.6448
< H - L == 0 -14.7222 -24.0774 -5.3670
< H - M == 0 -4.7222 -14.0774 4.6330
---
> M - L == 0 -10.0000 -19.3557 -0.6443
> H - L == 0 -14.7222 -24.0779 -5.3665
> H - M == 0 -4.7222 -14.0779 4.6335
1026,1028c1001,1003
< M - L == 0 -10.000 3.872 -2.582 0.03370 *
< H - L == 0 -14.722 3.872 -3.802 0.00115 **
< H - M == 0 -4.722 3.872 -1.219 0.44743
---
> M - L == 0 -10.000 3.872 -2.582 0.03365 *
> H - L == 0 -14.722 3.872 -3.802 0.00111 **
> H - M == 0 -4.722 3.872 -1.219 0.44745
1134c1109
< Quantile = 1.8433
---
> Quantile = 1.843
1140,1142c1115,1117
< V2 - V1 >= 0 -2.13330 -Inf 0.82288
< V3 - V1 >= 0 -7.46670 -Inf -4.51052
< V4 - V1 >= 0 -1.66670 -Inf -0.03584
---
> V2 - V1 >= 0 -2.13330 -Inf 0.82253
> V3 - V1 >= 0 -7.46670 -Inf -4.51087
> V4 - V1 >= 0 -1.66670 -Inf -0.03604
1258c1233
< VarCorr, lmList
---
> BIC, VarCorr, lmList
1262c1237
< AIC, BIC
---
> AIC
1303c1278
< Quantile = 1.8433
---
> Quantile = 1.843
1309,1311c1284,1286
< b1 - b0 >= 0 -2.13333 -Inf 0.82285
< b2 - b0 >= 0 -7.46667 -Inf -4.51048
< b3 - b0 >= 0 -1.66667 -Inf -0.03581
---
> b1 - b0 >= 0 -2.1333 -Inf 0.8225
> b2 - b0 >= 0 -7.4667 -Inf -4.5108
> b3 - b0 >= 0 -1.6667 -Inf -0.0360
1327c1302
< Quantile = 1.8429
---
> Quantile = 1.8432
1333,1335c1308,1310
< b1 - b0 >= 0 -2.13333 -Inf 0.82222
< b2 - b0 >= 0 -7.46667 -Inf -4.51112
< b3 - b0 >= 0 -1.66667 -Inf -0.03616
---
> b1 - b0 >= 0 -2.13333 -Inf 0.82281
> b2 - b0 >= 0 -7.46667 -Inf -4.51052
> b3 - b0 >= 0 -1.66667 -Inf -0.03583
1457c1432
< Quantile = 2.5984
---
> Quantile = 2.5986
1463,1465c1438,1440
< low - high == 0 -2.0150 -3.2745 -0.7555
< medium - high == 0 -2.2560 -3.5155 -0.9965
< medium - low == 0 -0.2410 -1.5005 1.0185
---
> low - high == 0 -2.0150 -3.2746 -0.7554
> medium - high == 0 -2.2560 -3.5156 -0.9964
> medium - low == 0 -0.2410 -1.5006 1.0186
OK
- checking for unstated dependencies in tests ... OK
- checking tests ... OK
Running ‘bugfix.R’
Comparing ‘bugfix.Rout’ to ‘bugfix.Rout.save’ ...124,125c124,125
< [1] 1.380883e-01 3.524764e-04 3.563710e-07 2.897682e-14 2.050268e-01
< [6] 9.917862e-04 6.540452e-10 2.512705e-01 3.447725e-06 3.042641e-03
---
> [1] 1.380883e-01 3.524764e-04 9.394029e-07 2.897682e-14 2.050268e-01
> [6] 9.917862e-04 6.540450e-10 2.512705e-01 3.447725e-06 3.042641e-03
163c163
< 2: In glht.matrix(model = list(coefficients = c(14.4166666666667, -5.83333333333334, :
---
> 2: In glht.matrix(model = list(coefficients = c(14.4166666666667, -5.83333333333333, :
181c181
< 2: In glht.matrix(model = list(coefficients = c(14.4166666666667, -5.83333333333334, :
---
> 2: In glht.matrix(model = list(coefficients = c(14.4166666666667, -5.83333333333333, :
202c202
< 2: In glht.matrix(model = list(coefficients = c(14.4166666666667, -5.83333333333334, :
---
> 2: In glht.matrix(model = list(coefficients = c(14.4166666666667, -5.83333333333333, :
Running ‘regtest-Tukey.R’
Comparing ‘regtest-Tukey.Rout’ to ‘regtest-Tukey.Rout.save’ ... OK
Running ‘regtest-anova.R’
Comparing ‘regtest-anova.Rout’ to ‘regtest-anova.Rout.save’ ...47,53d46
<
< Attaching package: 'zoo'
<
< The following object(s) are masked from 'package:base':
<
< as.Date, as.Date.numeric
<
Running ‘regtest-interface.R’
Comparing ‘regtest-interface.Rout’ to ‘regtest-interface.Rout.save’ ... OK
Running ‘regtest-lme.R’
Comparing ‘regtest-lme.Rout’ to ‘regtest-lme.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