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I've stumbled upon a problem affecting the Mac OS version of R 3.3.2 (and .3 too!) when using lme4 and lmerTest.
lmerTest produces an error:
Error in calculation of the Satterthwaite's approximation. The output of lme4 package is returned summary from lme4 is returned some computational error has occurred in lmerTest
The problem does not emerge with R 3.2 under MacOS and any R versions under Windows. However, this is not an installation problem, since I reproduced the error after reinstall of R and on also on a different Mac.
Here is the example code:
library(lme4)
#' start of data creation
mydat <-
structure(list(ID = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29,
1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29), sex = c(1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ROI = structure(c(4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L), .Label = c("calf",
"DSCAT", "KM", "neck", "SSCAT", "VAT"), class = "factor"),
value = c(0.674,
0.561, 0.543, 0.563, 0.697, 0.608, 0.56, 0.448, 0.626, 0.515,
0.568, 0.528, 0.587, 0.532, 0.547, 0.514, 0.587, 0.572, 0.559,
0.569, 0.462, 0.531, 0.477, 0.582, 0.583, 0.569, 0.563, 0.576,
0.84, 0.638, 0.69, 0.707, 0.704, 0.627, 0.769, 0.637, 0.515,
0.669, 0.699, 0.626, 0.59, 0.639, 0.501, 0.632, 0.624, 0.641,
0.669, 0.656, 0.556, 0.569, 0.633, 0.608, 0.616, 0.664, 0.666,
0.669, 0.545, 0.514, 0.45, 0.585, 0.547, 0.572, 0.577, 0.458,
0.47, 0.537, 0.532, 0.455, 0.62, 0.501, 0.506, 0.44, 0.499, 0.577,
0.457, 0.481, 0.522, 0.516, 0.513, 0.559, 0.571, 0.515, 0.575,
0.521, 0.44, 0.637, 0.521, 0.634, 0.552, 0.581, 0.55, 0.553,
0.522, 0.634, 0.631, 0.512, 0.603, 0.593, 0.58, 0.442, 0.53,
0.463, 0.587, 0.538, 0.48, 0.557, 0.482, 0.53, 0.592, 0.445,
0.526, 0.45, 0.551, 0.51, 0.678, 0.64, 0.599, 0.589, 0.627, 0.621,
0.601, 0.526, 0.619, 0.599, 0.668, 0.615, 0.621, 0.561, 0.532,
0.56, 0.578, 0.686, 0.57, 0.457, 0.563, 0.61, 0.513, 0.638, 0.594,
0.777, 0.562, 0.663, 0.538, 0.471, 0.518, 0.47, 0.535, 0.644,
0.605, 0.474, 0.468, 0.563, 0.539, 0.47, 0.538, 0.453, 0.494,
0.576, 0.418, 0.609, 0.528, 0.453, 0.569, 0.484, 0.486, 0.558,
0.621, 0.465, 0.691, 0.398, 0.539, 0.574), Alter = c(45, 47,
51, 44, 35, 26, 60, 44, 42, 50, 42, 51, 57, 23, 26, 29, 29, 50,
45, 61, 61, 58, 32, 27, 49, 45, 64, 28, 45, 47, 51, 44, 35, 26,
60, 44, 50, 42, 51, 57, 23, 26, 29, 29, 50, 45, 61, 61, 58, 32,
27, 49, 27, 45, 64, 28, 45, 47, 51, 44, 35, 26, 60, 44, 42, 50,
42, 51, 57, 23, 26, 29, 29, 50, 45, 61, 61, 58, 32, 27, 49, 27,
45, 64, 28, 45, 47, 51, 44, 35, 26, 60, 44, 42, 50, 42, 51, 57,
23, 26, 29, 29, 50, 45, 61, 61, 58, 32, 27, 49, 27, 45, 64, 28,
45, 47, 51, 44, 35, 26, 60, 44, 42, 50, 42, 51, 57, 23, 26, 29,
29, 50, 45, 61, 61, 58, 32, 27, 49, 27, 45, 64, 28, 45, 47, 51,
44, 35, 26, 60, 44, 42, 50, 42, 51, 57, 23, 26, 29, 29, 50, 45,
61, 61, 58, 32, 27, 49, 27, 45, 64, 28),
BMI = c(29.7506923675537,
28.8, 28.8385677337646, 41.48, 27.7186069488525, 29.54, 38.06,
35.8453826904297, 35.57, 31.77, 31.75, 32.78, 30.5336246490479,
29.1074104309082, 36.4690246582031, 31.7769088745117, 31.5393238067627,
31.5596752166748, 27.593786239624, 30.8192825317383, 27.0799140930176,
31.481481552124, 29.0328979492188, 24.52, 29.4029197692871, 35.6112785339355,
28.2401905059814, 28.8979587554932, 29.7506923675537, 28.8, 28.8385677337646,
41.48, 27.7186069488525, 29.54, 38.06, 35.8453826904297, 31.77,
31.75, 32.78, 30.5336246490479, 29.1074104309082, 36.4690246582031,
31.7769088745117, 31.5393238067627, 31.5596752166748, 27.593786239624,
30.8192825317383, 27.0799140930176, 31.481481552124, 29.0328979492188,
24.52, 29.4029197692871, 23.0956573486328, 35.6112785339355,
28.2401905059814, 28.8979587554932, 29.7506923675537, 28.8, 28.8385677337646,
41.48, 27.7186069488525, 29.54, 38.06, 35.8453826904297, 35.57,
31.77, 31.75, 32.78, 30.5336246490479, 29.1074104309082, 36.4690246582031,
31.7769088745117, 31.5393238067627, 31.5596752166748, 27.593786239624,
30.8192825317383, 27.0799140930176, 31.481481552124, 29.0328979492188,
24.52, 29.4029197692871, 23.0956573486328, 35.6112785339355,
28.2401905059814, 28.8979587554932, 29.7506923675537, 28.8, 28.8385677337646,
41.48, 27.7186069488525, 29.54, 38.06, 35.8453826904297, 35.57,
31.77, 31.75, 32.78, 30.5336246490479, 29.1074104309082, 36.4690246582031,
31.7769088745117, 31.5393238067627, 31.5596752166748, 27.593786239624,
30.8192825317383, 27.0799140930176, 31.481481552124, 29.0328979492188,
24.52, 29.4029197692871, 23.0956573486328, 35.6112785339355,
28.2401905059814, 28.8979587554932, 29.7506923675537, 28.8, 28.8385677337646,
41.48, 27.7186069488525, 29.54, 38.06, 35.8453826904297, 35.57,
31.77, 31.75, 32.78, 30.5336246490479, 29.1074104309082, 36.4690246582031,
31.7769088745117, 31.5393238067627, 31.5596752166748, 27.593786239624,
30.8192825317383, 27.0799140930176, 31.481481552124, 29.0328979492188,
24.52, 29.4029197692871, 23.0956573486328, 35.6112785339355,
28.2401905059814, 28.8979587554932, 29.7506923675537, 28.8, 28.8385677337646,
41.48, 27.7186069488525, 29.54, 38.06, 35.8453826904297, 35.57,
31.77, 31.75, 32.78, 30.5336246490479, 29.1074104309082, 36.4690246582031,
31.7769088745117, 31.5393238067627, 31.5596752166748, 27.593786239624,
30.8192825317383, 27.0799140930176, 31.481481552124, 29.0328979492188,
24.52, 29.4029197692871, 23.0956573486328, 35.6112785339355,
28.2401905059814, 28.8979587554932)), .Names = c("ID", "sex",
"ROI", "value", "Alter", "BMI"), row.names = c(NA, -172L), class = c("tbl_df","tbl", "data.frame"))
#' end of data creation
library(lmerTest)
mod <- lmer(value~Alter+ROI+BMI+(1|ID),data=mydat,REML=F)
summary(mod)
sessionInfo()
The system information is as follows:
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lmerTest_2.0-33 lme4_1.1-12 Matrix_1.2-8
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 Formula_1.2-1 knitr_1.15.1 magrittr_1.5 cluster_2.0.5 splines_3.3.3 MASS_7.3-45 munsell_0.4.3 [9] colorspace_1.3-2 lattice_0.20-34 minqa_1.2.4 stringr_1.1.0 plyr_1.8.4 tools_3.3.3 nnet_7.3-12 grid_3.3.3 [17] data.table_1.10.0 checkmate_1.8.2 htmlTable_1.8 gtable_0.2.0 nlme_3.1-131 latticeExtra_0.6-28 htmltools_0.3.5 digest_0.6.11 [25] survival_2.40-1 lazyeval_0.2.0 assertthat_0.1 tibble_1.2 gridExtra_2.2.1 RColorBrewer_1.1-2 nloptr_1.0.4 ggplot2_2.2.1 [33] base64enc_0.1-3 acepack_1.4.1 rpart_4.1-10 stringi_1.1.2 backports_1.0.4 scales_0.4.1 Hmisc_4.0-2 foreign_0.8-67
284
After a repeated attempt, the code worked under R3.3.3, although my system is unchanged. Was I dreaming? Kind of paranormal... I'm puzzled. Sorry for bothering.
R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.3
locale: [1] C
attached base packages: [1] stats graphics grDevices utils
datasets methods baseother attached packages: [1] lmerTest_2.0-33 lme4_1.1-12
Matrix_1.2-8loaded via a namespace (and not attached): [1] Rcpp_0.12.9
nloptr_1.0.4 RColorBrewer_1.1-2 plyr_1.8.4
base64enc_0.1-3 tools_3.3.3 rpart_4.1-10
digest_0.6.12 [9] tibble_1.2 nlme_3.1-131
gtable_0.2.0 htmlTable_1.9 checkmate_1.8.2
lattice_0.20-34 gridExtra_2.2.1 stringr_1.2.0 [17] cluster_2.0.5 knitr_1.15.1 htmlwidgets_0.8 grid_3.3.3 nnet_7.3-12 data.table_1.10.0 survival_2.40-1
foreign_0.8-67 [25] latticeExtra_0.6-28 minqa_1.2.4
Formula_1.2-1 ggplot2_2.2.1 magrittr_1.5
Hmisc_4.0-2 scales_0.4.1 backports_1.0.5 [33] htmltools_0.3.5 MASS_7.3-45 splines_3.3.3
assertthat_0.1 colorspace_1.3-2 stringi_1.1.2
acepack_1.4.1 lazyeval_0.2.0 [41] munsell_0.4.3
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