- using R Under development (unstable) (2012-08-11 r60235)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘fpc/DESCRIPTION’ ... OK
- this is package ‘fpc’ version ‘2.0-3’
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
CRAN requires a NAMESPACE file for all submissions.
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking whether package ‘fpc’ 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 loading without being on the library search path ... 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 ... NOTE
File ‘fpc/R/fpc.R’:
.First.lib calls:
require(cluster)
require(MASS)
Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.
dip.pvalue: no visible binding for global variable ‘qDiptab’
- 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 examples ... [10s/10s] OK
- checking differences from ‘fpc-Ex.Rout’ to ‘fpc-Ex.Rout.save’ ...
2c2,6
< Package 'mclust' version 4.0
---
>
> by using mclust, invoked on its own or through another package,
> you accept the license agreement in the mclust LICENSE file
> and at http://www.stat.washington.edu/mclust/license.txt
>
135,137c139,141
< [1,] 1.0000000 9.987508e-01 1.00000e+00
< [2,] 0.9987508 1.000000e+00 1.78102e-11
< [3,] 1.0000000 1.781020e-11 1.00000e+00
---
> [1,] 1.0000000 9.987508e-01 1.000000e+00
> [2,] 0.9987508 1.000000e+00 1.781020e-11
> [3,] 1.0000000 1.781020e-11 1.000000e+00
318c322
< [1] 13.7291
---
> [1] 13.72910
747c751
< 0.193
---
> 0.686
750c754
< 0.139
---
> 0.412
754c758
< 0.571
---
> 0.736
892,894c896,898
< [1,] 0.84359426 -1.14608710 0.02209846
< [2,] -0.33649001 -0.27903245 0.01187219
< [3,] -0.06808816 -0.03965075 -1.00303099
---
> [1,] 0.84359426 1.14608710 0.02209846
> [2,] -0.33649001 0.27903245 0.01187219
> [3,] -0.06808816 0.03965075 -1.00303099
902,904c906,908
< [1,] -1.29527821 0.50007753 -0.33960121
< [2,] 0.65331636 0.05164296 -0.08010673
< [3,] -0.08051801 -0.66005066 -0.46509088
---
> [1,] -1.2952782 0.50007753 -0.33960121
> [2,] 0.6533164 0.05164296 -0.08010673
> [3,] -0.0805180 -0.66005066 -0.46509088
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< Sepal.Length 0.4364358 0.2255444 0.86784913 7.410413e-02
< Sepal.Width 0.6546537 0.5833044 -0.48081650 1.152417e-05
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< Petal.Width -0.4364358 0.5094192 0.02379441 7.412487e-01
---
> Sepal.Length 0.4364358 0.2255444 0.86784904 7.410527e-02
> Sepal.Width 0.6546537 0.5833044 -0.48081650 1.089355e-05
> Petal.Length -0.4364358 0.5910818 0.12283086 -6.671272e-01
> Petal.Width -0.4364358 0.5094192 0.02379343 7.412488e-01
1054,1057c1058,1061
< Sepal.Length 0.3685213 0.9175803 -0.0161054 0.1482532
< Sepal.Width -0.4237402 0.3056933 0.2672553 -0.8096731
< Petal.Length -0.7834017 0.2490473 -0.4429863 0.3577993
< Petal.Width -0.2663044 0.0507288 0.8556158 0.4409424
---
> Sepal.Length 0.3685213 0.9175803 -0.01610540 0.1482532
> Sepal.Width -0.4237402 0.3056933 0.26725530 -0.8096731
> Petal.Length -0.7834017 0.2490473 -0.44298628 0.3577993
> Petal.Width -0.2663044 0.0507288 0.85561579 0.4409424
1062,1065c1066,1069
< Sepal.Length 0.78842369 -0.1589992 -0.5596188 -0.1998354
< Sepal.Width 0.60787954 0.3492963 0.6715425 0.2398025
< Petal.Length 0.04212018 -0.4129676 0.4574837 -0.7863792
< Petal.Width 0.08424036 -0.8259353 0.1629913 0.5330744
---
> Sepal.Length 0.78842369 -0.1589992 -0.5613449 -0.1949340
> Sepal.Width 0.60787954 0.3492963 0.6736139 0.2339208
> Petal.Length 0.04212018 -0.4129676 0.4505895 -0.7903498
> Petal.Width 0.08424036 -0.8259353 0.1676467 0.5316287
1078,1081c1082,1085
< Sepal.Length 0.07550285 0.6328310 0.67278171 0.37575125
< Sepal.Width -0.17216644 0.4934753 0.03098703 -0.85198630
< Petal.Length -0.74300787 -0.4180672 0.51749754 -0.07318086
< Petal.Width -0.64233740 0.4257075 -0.52782655 0.35717629
---
> Sepal.Length 0.07550285 0.6328310 -0.7566467 0.1459795
> Sepal.Width -0.17216644 0.4934753 0.2375780 -0.8187781
> Petal.Length -0.74300787 -0.4180672 -0.4684942 -0.2316729
> Petal.Width -0.64233740 0.4257075 0.3893015 0.5045989
1094,1097c1098,1101
< Sepal.Length 0.7730041 -0.09914374 0.62452138 -0.0510699878
< Sepal.Width 0.4418583 0.79204432 -0.42122054 -0.0005715947
< Petal.Length -0.4416270 0.59416223 0.65375908 0.1566395315
< Petal.Width -0.1104150 0.09903318 0.07173123 -0.9863344193
---
> Sepal.Length 0.7730041 -0.09914374 0.6101968 -0.14246043
> Sepal.Width 0.4418583 0.79204432 -0.4167145 0.06145005
> Petal.Length -0.4416270 0.59416223 0.6696965 0.05868099
> Petal.Width -0.1104150 0.09903318 -0.0742664 -0.98614677
1262c1266
< Constant ca= 10.0701
---
> Constant ca= 10.07010
1270c1274
< Ratio to estimated expectation: 1.5872
---
> Ratio to estimated expectation: 1.587200
1279c1283
< Ratio to estimated expectation: 2.08242
---
> Ratio to estimated expectation: 2.082420
1351c1355
< Nonoptimal or repeated fit found in run 2
---
> k= 2 new best fit found in run 2
1355c1359
< k= 3 BIC= 1292.826
---
> k= 3 BIC= 1300.073
1366,1367c1370,1371
< Comp.1 0.506 48 100 0.48
< Comp.2 0.494 52 100 0.52
---
> Comp.1 0.527 51 100 0.51
> Comp.2 0.473 49 100 0.49
1374,1375c1378,1379
< [38] 2 2 1 2 1 1 2 2 1 1 2 2 2 1 2 1 1 2 2 1 2 2 2 1 2 1 1 2 1 1 2 2 2 1 2 2 1
< [75] 1 1 1 2 2 1 2 1 1 1 1 2 2 1 2 1 1 2 1 2 2 2 2 2 2 2
---
> [38] 2 2 1 2 1 1 2 2 1 1 2 1 2 1 2 1 1 2 2 1 2 2 2 1 2 1 1 2 1 1 2 2 1 1 2 2 1
> [75] 1 1 1 2 2 1 2 1 1 1 1 2 1 1 2 1 1 2 1 2 2 2 2 2 2 2
1380c1384
< [1] -0.06786994 -0.54104769
---
> [1] -0.06364726 -0.51088660
1384,1385c1388,1389
< [1,] 1.13052 0.000000
< [2,] 0.00000 1.091476
---
> [1,] 1.122126 0.000000
> [2,] 0.000000 1.096735
1389c1393
< [1] 0.27877309 0.22952064 0.14780796 0.30344389 0.04045442
---
> [1] 0.27279622 0.22617675 0.15713052 0.29791908 0.04597742
1392c1396
< [1] 0.1441872 0.1676908 0.5133395 0.1747825
---
> [1] 0.1490151 0.1719611 0.5061025 0.1729213
1400c1404
< [1] 0.2365028 0.4120134
---
> [1] 0.2462103 0.4234742
1404,1405c1408,1409
< [1,] 0.6873457 0.0000000
< [2,] 0.0000000 0.8517165
---
> [1,] 0.6738187 0.0000000
> [2,] 0.0000000 0.8547246
1409c1413
< [1] 0.09927107 0.16982896 0.27356225 0.05383639 0.40350133
---
> [1] 0.09744369 0.17073751 0.26910177 0.04818053 0.41453650
1412c1416
< [1] 0.27726281 0.41500389 0.06173992 0.24599338
---
> [1] 0.2781738 0.4219535 0.0484232 0.2514495
1489,1495d1492
<
< Attaching package: 'prabclus'
<
< The following object(s) are masked from 'package:fpc':
<
< con.comp
<
1496a1494
> [1] 11
1524,1525c1522,1523
< [1,] -0.4301944 0.1259479 -0.1113803 -0.1112671 0.103153 -0.129418 -0.1113858
< [2,] 3.2115590 6.8582670 5.3351123 5.3353299 6.953000 7.402776 5.3351018
---
> [1,] -0.4301944 0.1259479 -0.1113803 -0.1112671 0.1031530 -0.1294180 -0.1113858
> [2,] 3.2115590 6.8582670 5.3351123 5.3353299 6.9529995 7.4027761 5.3351018
1660,1665c1658,1663
< [,1] [,2] [,3] [,4] [,5] [,6] [,7]
< [1,] 0.3593477 0.3641063 -0.1113878 0.4429484 0.103153 -0.129418 -0.1113858
< [2,] 12.4801629 12.5943626 5.3350959 13.7169107 6.953000 7.402776 5.3351018
< [,8] [,9] [,10]
< [1,] -0.1115167 2.056731 -1.531638
< [2,] 5.3348502 17.205746 17.205554
---
> [,1] [,2] [,3] [,4] [,5] [,6]
> [1,] 0.3593477 0.3641063 -0.1113878 0.4429484 0.1031530 -0.1294180
> [2,] 12.4801629 12.5943626 5.3350959 13.7169107 6.9529995 7.4027761
> [,7] [,8] [,9] [,10]
> [1,] -0.1113858 -0.1115167 2.056731 -1.531638
> [2,] 5.3351018 5.3348502 17.205746 17.205554
1671,1672c1669,1670
< [1,] 3.520894 1.18919
< [2,] 1.189190 67.08240
---
> [1,] 3.520894 1.189190
> [2,] 1.189190 67.082397
2271,2274c2269,2272
< [1,] 0.069319855 0.0518654013 0.0046861756 0.0095378232
< [2,] 0.051865401 0.0431639712 0.0004953638 0.0007921612
< [3,] 0.004686176 0.0004953638 0.0032597388 0.0062255655
< [4,] 0.009537823 0.0007921612 0.0062255655 0.0124822565
---
> [1,] 0.069320616 0.0518644883 0.0046873868 0.009536685
> [2,] 0.051864488 0.0431650668 0.0004939104 0.000793527
> [3,] 0.004687387 0.0004939104 0.0032572771 0.006225948
> [4,] 0.009536685 0.0007935271 0.0062259484 0.012482862
2287,2290c2285,2288
< [1,] 0.0077020291 0.003885942 -0.01056405 -0.0009142804
< [2,] 0.0038859417 0.007498913 0.01063072 0.0157883091
< [3,] -0.0105640457 0.010630720 0.06416071 0.0496007520
< [4,] -0.0009142804 0.015788309 0.04960075 0.0488641667
---
> [1,] 0.007749167 0.003807059 -0.01056156 -0.000890472
> [2,] 0.003807059 0.007520730 0.01058065 0.015831108
> [3,] -0.010561560 0.010580649 0.06414171 0.049636441
> [4,] -0.000890472 0.015831108 0.04963644 0.048814211
2303,2306c2301,2304
< [1,] 0.066426726 0.036301977 -0.038563799 -0.009580652
< [2,] 0.036301977 0.032397906 -0.013662418 -0.004068082
< [3,] -0.038563799 -0.013662418 0.027805813 0.006407895
< [4,] -0.009580652 -0.004068082 0.006407895 0.001595376
---
> [1,] 0.066419771 0.036305431 -0.038563657 -0.009616086
> [2,] 0.036305431 0.032396421 -0.013663871 -0.004044032
> [3,] -0.038563657 -0.013663871 0.027814107 0.006369898
> [4,] -0.009616086 -0.004044032 0.006369898 0.001595522
2311,2330c2309,2328
< 122 1.000000e+00 0.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 42 1.000000e+00 1.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 45 7.431477e-78 7.431477e-78 1.0000000 0.000000e+00 0 0.0000000
< 86 1.000000e+00 0.000000e+00 0.0000000 1.027899e-264 0 0.0000000
< 70 1.074570e-19 0.000000e+00 0.0000000 1.000000e+00 0 0.0000000
< 137 4.297997e-134 0.000000e+00 0.0000000 0.000000e+00 1 0.0000000
< 37 9.430013e-103 9.430013e-103 1.0000000 0.000000e+00 0 0.0000000
< 46 1.000000e+00 1.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 134 0.000000e+00 0.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 88 0.000000e+00 0.000000e+00 0.0000000 0.000000e+00 0 1.0000000
< 72 2.878919e-90 0.000000e+00 0.0000000 1.000000e+00 0 0.0000000
< 123 0.000000e+00 0.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 1 8.836887e-28 8.836887e-28 1.0000000 0.000000e+00 0 0.0000000
< 147 1.422993e-288 0.000000e+00 0.0000000 0.000000e+00 0 1.0000000
< 51 0.000000e+00 0.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 120 0.000000e+00 0.000000e+00 0.0000000 0.000000e+00 0 0.9998512
< 9 1.000000e+00 1.000000e+00 0.0000000 0.000000e+00 0 0.0000000
< 18 3.526927e-03 3.526927e-03 0.9964731 0.000000e+00 0 0.0000000
< 28 8.360527e-61 8.360527e-61 1.0000000 0.000000e+00 0 0.0000000
< 54 2.602925e-34 0.000000e+00 0.0000000 1.000000e+00 0 0.0000000
---
> 122 1.000000e+00 0.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 42 1.000000e+00 1.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 45 7.431477e-78 7.431477e-78 1.000000 0.00000e+00 0 0.000000e+00
> 86 1.000000e+00 0.000000e+00 0.000000 7.61652e-267 0 0.000000e+00
> 70 1.074570e-19 0.000000e+00 0.000000 1.00000e+00 0 0.000000e+00
> 137 4.300906e-134 0.000000e+00 0.000000 0.00000e+00 1 0.000000e+00
> 37 9.430013e-103 9.430013e-103 1.000000 0.00000e+00 0 0.000000e+00
> 46 1.000000e+00 1.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 134 0.000000e+00 0.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 88 0.000000e+00 0.000000e+00 0.000000 0.00000e+00 0 1.000000e+00
> 72 2.877478e-90 0.000000e+00 0.000000 1.00000e+00 0 0.000000e+00
> 123 0.000000e+00 0.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 1 8.836887e-28 8.836887e-28 1.000000 0.00000e+00 0 0.000000e+00
> 147 1.424320e-288 0.000000e+00 0.000000 0.00000e+00 0 1.000000e+00
> 51 0.000000e+00 0.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 120 0.000000e+00 0.000000e+00 0.000000 0.00000e+00 0 9.998512e-01
> 9 1.000000e+00 1.000000e+00 0.000000 0.00000e+00 0 0.000000e+00
> 18 3.526927e-03 3.526927e-03 0.996473 0.00000e+00 0 0.000000e+00
> 28 8.360527e-61 8.360527e-61 1.000000 0.00000e+00 0 0.000000e+00
> 54 2.602855e-34 0.000000e+00 0.000000 1.00000e+00 0 1.825211e-292
2341c2339
< 88 0.000000e+00 7.026138e-62
---
> 88 0.000000e+00 4.085183e-80
2396c2394
< 93.1465719 138.3375500 119.1334177 117.5885785 168.8774326 150.4594812
---
> 93.1465719 138.3375499 119.1334177 117.5885785 168.8774326 150.4594812
2784,2790d2781
<
< Attaching package: 'prabclus'
<
< The following object(s) are masked from 'package:fpc':
<
< con.comp
<
OK
- checking for unstated dependencies in tests ... OK
- checking tests ... [17s/17s] OK
Running ‘fpctests.R’ [17s/17s]
Comparing ‘fpctests.Rout’ to ‘fpctests.Rout.save’ ...6c6,10
< Package 'mclust' version 4.0
---
>
> by using mclust, invoked on its own or through another package,
> you accept the license agreement in the mclust LICENSE file
> and at http://www.stat.washington.edu/mclust/license.txt
>
19,21c23,25
< [1,] -1.39122951 -0.30933547 0.10928950
< [2,] 0.62109134 -0.22334223 0.01643619
< [3,] -0.03130796 0.07485511 -0.80738843
---
> [1,] -1.39122951 -0.3093355 0.10928950
> [2,] 0.62109134 -0.2233422 0.01643619
> [3,] -0.03130796 0.0748551 -0.80738843
24,26c28,30
< [1,] 0.2153917 -0.33885087 -0.518856215
< [2,] -0.3702908 0.01439633 -0.008930009
< [3,] 0.1108281 0.79140767 -0.235742343
---
> [1,] 0.2153917 -0.33885087 -0.51885622
> [2,] -0.3702908 0.01439633 -0.00893001
> [3,] 0.1108281 0.79140767 -0.23574234
33c37
< 4 clusters 833.1691
---
> 4 clusters 833.169
88,90c92,94
< 12 13.9716414 13.677807 14.503586 13.94655 14.0084574 13.6015727 13.784232
< 34 0.3227397 0.459568 0.841392 1.21862 0.4964457 0.1656088 2.670075
< 50 14.6877989 15.036740 14.241074 15.09286 14.7181912 14.9490175 14.477326
---
> 12 13.9716414 13.677807 14.503586 13.946552 14.0084574 13.6015727 13.784232
> 34 0.3227397 0.459568 0.841392 1.218620 0.4964457 0.1656088 2.670075
> 50 14.6877989 15.036740 14.241074 15.092859 14.7181912 14.9490175 14.477326
588,594c592
<
< Attaching package: 'prabclus'
<
< The following object(s) are masked from 'package:fpc':
<
< con.comp
<
---
> [1] 5
669a668
> [1] 6
804,805c803,804
< [1] 4 4 4 3 4 3 3 1 5 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2
< [39] 2 2 2 1 1 1 1 1 5 5 5 5
---
> [1] 1 1 1 4 1 4 4 3 5 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2 2 2 2 2 2
> [39] 2 2 2 3 3 3 3 3 5 5 5 5
808,811c807,810
< 4 0.6842995 1.2614578
< 29 0.8974744 -1.0022315
< 24 -0.7193505 0.1440717
< 1 -0.4994704 -1.4250867
---
> 2 -0.4994704 -1.4250867
> 41 0.8974744 -1.0022315
> 11 0.6842995 1.2614578
> 15 -0.7193505 0.1440717
822c821
< [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
---
> [1] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
825c824
< [37] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE
---
> [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
836,839c835,838
< [1] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE
< [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
< [25] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE
< [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
---
> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
> [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
> [37] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE
843,845c842,844
< [1] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
< [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
< [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
---
> [1] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE
> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> [25] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE
858,859c857,858
< [1] 4 4 4 3 4 3 3 1 5 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2
< [39] 2 2 2 1 1 1 1 1 5 5 5 5
---
> [1] 1 1 1 4 1 4 4 3 5 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2 2 2 2 2 2
> [39] 2 2 2 3 3 3 3 3 5 5 5 5
900c899
< [1] 15.23
---
> [1] 15.23000
959a959
> [1] 10
1021c1021
< [1,] 8 0.13861386
---
> [1,] 8 0.17821782
- checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/fpc.Rcheck/00check.log’
for details.