• 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