Check results for 'mlmRev'

using R version 3.0.1 (2013-05-16)
using platform: i686-pc-linux-gnu (32-bit)
using session charset: UTF-8
checking for file ‘mlmRev/DESCRIPTION’ ... OK
this is package ‘mlmRev’ version ‘1.0-1’
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 for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘mlmRev’ can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... 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 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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘myVignette.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
checking examples ... [9s/9s] OK
checking for unstated dependencies in tests ... OK
checking tests ... [39s/39s] OK
Running ‘guImmun.R’ [26s/26s]
Comparing ‘guImmun.Rout’ to ‘guImmun.Rout.save’ ...5,10d4
< Attaching package: 'lme4'
<
< The following object is masked from 'package:stats':
<
< AIC, BIC
<
24c18
< mom (Intercept) 1.288 1.1348
---
> mom (Intercept) 1.288 1.1349
31,32c25,26
< kid2pY 1.2815 0.1370 9.35 <2e-16 ***
< mom25pY -0.1284 0.1543 -0.83 0.4054
---
> kid2pY 1.2816 0.1370 9.35 <2e-16 ***
> mom25pY -0.1284 0.1543 -0.83 0.4055
34c28
< ord46 0.1741 0.1992 0.87 0.3821
---
> ord46 0.1740 0.1992 0.87 0.3822
36,37c30,31
< ethnN -0.1132 0.3125 -0.36 0.7172
< ethnS -0.0348 0.2321 -0.15 0.8810
---
> ethnN -0.1131 0.3125 -0.36 0.7173
> ethnS -0.0347 0.2322 -0.15 0.8810
42c36
< husEdU 0.0147 0.2296 0.06 0.9490
---
> husEdU 0.0146 0.2296 0.06 0.9492
79,80c73,74
< mom (Intercept) 1.2763 1.130
< comm (Intercept) 0.5227 0.723
---
> mom (Intercept) 1.2762 1.130
> comm (Intercept) 0.5228 0.723
85c79
< (Intercept) -0.6588 0.2927 -2.25 0.02439 *
---
> (Intercept) -0.6589 0.2927 -2.25 0.02438 *
87,92c81,86
< mom25pY -0.1360 0.1537 -0.88 0.37647
< ord23 -0.1375 0.1605 -0.86 0.39165
< ord46 0.1556 0.1977 0.79 0.43144
< ord7p 0.2404 0.2464 0.98 0.32912
< ethnN -0.2205 0.3095 -0.71 0.47622
< ethnS -0.0783 0.2311 -0.34 0.73461
---
> mom25pY -0.1359 0.1537 -0.88 0.37652
> ord23 -0.1375 0.1605 -0.86 0.39166
> ord46 0.1556 0.1977 0.79 0.43148
> ord7p 0.2404 0.2464 0.98 0.32913
> ethnN -0.2206 0.3095 -0.71 0.47600
> ethnS -0.0784 0.2311 -0.34 0.73438
94c88
< momEdS 0.3876 0.2766 1.40 0.16113
---
> momEdS 0.3876 0.2766 1.40 0.16115
96,97c90,91
< ruralY -0.6966 0.1945 -3.58 0.00034 ***
< pcInd81 -0.8355 0.3251 -2.57 0.01016 *
---
> ruralY -0.6965 0.1945 -3.58 0.00034 ***
> pcInd81 -0.8354 0.3251 -2.57 0.01018 *
111c105
< mom (Intercept) 1.2410 1.1140
---
> mom (Intercept) 1.2411 1.1140
118c112
< kid2pY 1.2680 0.1357 9.35 < 2e-16 ***
---
> kid2pY 1.2679 0.1357 9.35 < 2e-16 ***
120,124c114,118
< ethnN -0.2172 0.3068 -0.71 0.47899
< ethnS -0.0812 0.2294 -0.35 0.72327
< momEdP 0.3339 0.1366 2.44 0.01452 *
< momEdS 0.3266 0.2708 1.21 0.22776
< momWorkY 0.2538 0.1272 2.00 0.04590 *
---
> ethnN -0.2172 0.3068 -0.71 0.47896
> ethnS -0.0812 0.2294 -0.35 0.72324
> momEdP 0.3339 0.1366 2.44 0.01453 *
> momEdS 0.3266 0.2708 1.21 0.22778
> momWorkY 0.2538 0.1272 2.00 0.04592 *
Running ‘lmerTest.R’ [10s/10s]
Comparing ‘lmerTest.Rout’ to ‘lmerTest.Rout.save’ ...6,11d5
< Attaching package: 'lme4'
<
< The following object is masked from 'package:stats':
<
< AIC, BIC
<
171c165
< fm3 7 16519 16567 -8253 0.0 0 1
---
> fm3 7 16519 16567 -8253 0.0 0 <2e-16
212,213c206,207
< school (Intercept) 0.08583 0.293
< Residual 0.56253 0.750
---
> school (Intercept) 0.08583 0.2930
> Residual 0.56253 0.7500
297c291
< Subject (Intercept) 64.0346 8.0022
---
> Subject (Intercept) 64.0345 8.0022
354c348
< fm08 12 649.4 690.8 -312.7 0 0 1
---
> fm08 12 649.4 690.8 -312.7 1.68e-06 0 <2e-16
356c350
< + logLik(fm08, REML=FALSE), tol=1e-07))
---
> + logLik(fm08, REML=FALSE)))
365,368c359,362
< 2: 14869.120: 0.234540 0.0337760
< 3: 14868.448: 0.257104 0.0405383
< 4: 14868.361: 0.249359 0.0627849
< 5: 14868.329: 0.253832 0.0616947
---
> 2: 14869.120: 0.234540 0.0337758
> 3: 14868.448: 0.257104 0.0405381
> 4: 14868.361: 0.249359 0.0627845
> 5: 14868.329: 0.253832 0.0616944
371,372c365,366
< 8: 14868.325: 0.254282 0.0585649
< 9: 14868.325: 0.254614 0.0587517
---
> 8: 14868.325: 0.254282 0.0585648
> 9: 14868.325: 0.254614 0.0587516
444c438
< (Intercept) 5.92742 0.08660 68.4
---
> (Intercept) 5.92741 0.08660 68.4
446c440
< sexF 0.09844 0.11455 0.9
---
> sexF 0.09844 0.11454 0.9
Running ‘versions.R’ [3s/3s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [24s/24s] OK
checking re-building of vignette PDFs ... [19s/19s] OK
checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/home/hornik/tmp/R.check/r-release/Work/PKGS/mlmRev.Rcheck/00check.log’
for details.