Running ‘agnes-ex.R’ [1s/2s]
  Comparing ‘agnes-ex.Rout’ to ‘agnes-ex.Rout.save’ ... OK
  Running ‘clara-NAs.R’ [0s/0s]
  Running ‘clara-ex.R’ [1s/2s]
  Comparing ‘clara-ex.Rout’ to ‘clara-ex.Rout.save’ ... OK
  Running ‘clara-gower.R’ [0s/0s]
  Running ‘clara.R’ [2s/3s]
  Comparing ‘clara.Rout’ to ‘clara.Rout.save’ ...
147,149d146
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
  Running ‘clusplot-out.R’ [1s/1s]
  Comparing ‘clusplot-out.Rout’ to ‘clusplot-out.Rout.save’ ...
42,48d41
< Warning messages:
< 1: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 2: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
95,103d87
< Warning messages:
< 1: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 2: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 4: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
119,121d102
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
  Running ‘daisy-ex.R’ [0s/0s]
  Comparing ‘daisy-ex.Rout’ to ‘daisy-ex.Rout.save’ ... OK
  Running ‘diana-boots.R’ [1s/1s]
  Running ‘diana-ex.R’ [0s/1s]
  Comparing ‘diana-ex.Rout’ to ‘diana-ex.Rout.save’ ... OK
  Running ‘ellipsoid-ex.R’ [0s/0s]
  Comparing ‘ellipsoid-ex.Rout’ to ‘ellipsoid-ex.Rout.save’ ... OK
  Running ‘fanny-ex.R’ [0s/1s]
  Comparing ‘fanny-ex.Rout’ to ‘fanny-ex.Rout.save’ ... OK
  Running ‘mona.R’ [0s/1s]
  Comparing ‘mona.Rout’ to ‘mona.Rout.save’ ... OK
  Running ‘pam.R’ [25s/30s]
  Comparing ‘pam.Rout’ to ‘pam.Rout.save’ ...
33,35d32
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
38,40d34
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
42,44d35
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
47,49d37
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
64,68d51
< Warning messages:
< 1: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 2: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
363,365d345
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
367,369d346
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
373,375d349
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
780,782d753
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
803,805d773
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
828,830d795
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
948,950d912
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
996,998d957
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1074,1076d1032
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1091,1093d1046
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1124,1126d1076
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1129,1131d1078
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1161,1163d1107
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1211,1213d1154
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1225,1227d1165
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1239,1241d1176
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1253,1255d1187
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1267,1269d1198
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1281,1283d1209
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1302,1304d1227
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1331,1333d1253
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1342,1344d1261
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1353,1355d1269
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1364,1366d1277
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1376,1378d1286
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1388,1390d1295
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1422,1424d1326
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1447,1449d1348
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1459,1461d1357
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1471,1473d1366
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1483,1485d1375
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1495,1497d1384
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1507,1509d1393
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1611,1613d1494
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1644,1646d1524
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1664,1666d1541
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1684,1686d1558
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1704,1706d1575
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1724,1726d1592
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1744,1746d1609
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
1863,1865d1725
< Warning message:
< In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
  Running ‘silhouette-default.R’ [2s/3s]
  Comparing ‘silhouette-default.Rout’ to ‘silhouette-default.Rout.save’ ...
554d553
< There were 39 warnings (use warnings() to see them)
615,627d613
< Warning messages:
< 1: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 2: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 3: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 4: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 5: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
< 6: In structure(res$obj, .Names = c("build", "swap")) :
<   Replacing special names '.Names' is deprecated; use 'names' instead.
  Running ‘sweep-ex.R’ [0s/1s]
Running the tests in ‘tests/clara-NAs.R’ failed.
Complete output:
  > library(cluster)
  > 
  > x <- cbind(c(0, -4, -22, -14, 0, NA, -28, 1, 10, -1,
  +              100 + c(13, 0, 2, 4, 7, 8, 1)),
  +            c(-5, -14, NA, -35, -30, NA, 7, 2, -18, 13,
  +              47, 64, 48, NA, NA, 44, 65))
  > x
        [,1] [,2]
   [1,]    0   -5
   [2,]   -4  -14
   [3,]  -22   NA
   [4,]  -14  -35
   [5,]    0  -30
   [6,]   NA   NA
   [7,]  -28    7
   [8,]    1    2
   [9,]   10  -18
  [10,]   -1   13
  [11,]  113   47
  [12,]  100   64
  [13,]  102   48
  [14,]  104   NA
  [15,]  107   NA
  [16,]  108   44
  [17,]  101   65
  > (d <- dist(x,'manhattan'))
       1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16
  2   13                                                            
  3   44  36                                                        
  4   44  31  16                                                    
  5   25  20  44  19                                                
  6   NA  NA  NA  NA  NA                                            
  7   40  45  12  56  65  NA                                        
  8    8  21  46  52  33  NA  34                                    
  9   23  18  64  41  22  NA  63  29                                
  10  19  30  42  61  44  NA  33  13  42                            
  11 165 178 270 209 190  NA 181 157 168 148                        
  12 169 182 244 213 194  NA 185 161 172 152  30                    
  13 155 168 248 199 180  NA 171 147 158 138  12  18                
  14 208 216 252 236 208  NA 264 206 188 210  18   8   4            
  15 214 222 258 242 214  NA 270 212 194 216  12  14  10   6        
  16 157 170 260 201 182  NA 173 149 160 140   8  28  10   8   2    
  17 171 184 246 215 196  NA 187 163 174 154  30   2  18   6  12  28
  > ## IGNORE_RDIFF_BEGIN
  > summary(d, na.rm = TRUE) # max = 270
     Min. 1st Qu.  Median    Mean 3rd Qu.    Max.     NAs 
     2.00   27.25  147.50  114.55  188.50  270.00      16 
  > ## IGNORE_RDIFF_END
  > ## First call with "trace" (seg.fault typically later ...):
  > try( clara(x, k=2, metric="manhattan", sampsize=10, trace = 3) )
  C clara(): (nsam,nran,n) = (10,5,17); 'large_sample',
  - clara sample  1  finding 1st... new k{ran}:
  .. kall: FALSE, 
  ... nrx [0:1]= 0 0 
  ... nsel[0:0]= 1 
   [ntt=7, nunfs=0] .. nsel[1:10]= 6 7 8 9 10 12 13 14 16 17  -> dysta2() gave dyst_toomany_NA --> new sample.
  - clara sample  2  finding 1st... new k{ran}:
  .. kall: FALSE, 
  ... nrx [0:1]= 0 0 
  ... nsel[0:0]= 3 
   [ntt=7, nunfs=1] .. nsel[1:10]= 1 4 7 9 11 12 13 15 16 17  -> dysta2();
   clara -> s:= max{dys[1..45]} = 270;
   bswap2(*, s=270), 1. BUILD:     new repr. 7
      new repr. 1
    after build: medoids are  1  7
    and min.dist dysma[1:n] are
        0     44     40     23     12     18      0     10     10     18
   --> sky = sum_j D_j= 175
     swp new 8 <-> 7 old; decreasing diss. by -18
    Last swap: new 8 <-> 7 old; decreasing diss. by 1
   end{bswap2}: sky = 157
   selec() -> 'NAfs' obj= 7.41176
  - clara sample  3  finding 1st... new k{ran}:
  .. kall: FALSE, 
  ... nrx [0:1]= 0 0 
  ... nsel[0:0]= 6 
   [ntt=7, nunfs=2] .. nsel[1:10]= 1 2 3 5 8 9 10 11 13 17  -> dysta2();
   clara -> s:= max{dys[1..45]} = 270;
   bswap2(*, s=270), 1. BUILD:     new repr. 5
      new repr. 9
    after build: medoids are  5  9
    and min.dist dysma[1:n] are
        8     21     46     33      0     29     13     12      0     18
   --> sky = sum_j D_j= 180
     swp new 1 <-> 5 old; decreasing diss. by -18
    Last swap: new 1 <-> 5 old; decreasing diss. by 1
   end{bswap2}: sky = 162
   selec() -> 'NAfs' obj= 7.41176
  - clara sample  4  finding 1st... new k{ran}:
  .. kall: FALSE, 
  ... nrx [0:1]= 0 0 
  ... nsel[0:0]= 5 
   [ntt=7, nunfs=3] .. nsel[1:10]= 1 2 3 4 7 8 9 10 13 14  -> dysta2();
   clara -> s:= max{dys[1..45]} = 264;
   bswap2(*, s=264), 1. BUILD:     new repr. 1
      new repr. 10
    after build: medoids are  1 10
    and min.dist dysma[1:n] are
        0     13     44     44     40      8     23     19      4      0
   --> sky = sum_j D_j= 195
    Last swap: new 9 <-> 10 old; decreasing diss. by 0
   end{bswap2}: sky = 195
   selec() -> 'NAfs' obj= 7.41176
  - clara sample  5  finding 1st... new k{ran}:
  .. kall: FALSE, 
  ... nrx [0:1]= 0 0 
  ... nsel[0:0]= 16 
   [ntt=7, nunfs=4] .. nsel[1:10]= 2 3 4 6 7 8 9 10 11 17  -> dysta2() gave dyst_toomany_NA --> new sample.
  C clara() -> best sample _found_ ; nbest[1:10] =
   c(0,0,0,0,0,0,0,0,0,0)
  Error in clara(x, k = 2, metric = "manhattan", sampsize = 10, trace = 3) : 
    Observation 6 has *only* NAs --> omit it for clustering
  In addition: Warning message:
  In clara(x, k = 2, metric = "manhattan", sampsize = 10, trace = 3) :*** buffer overflow detected ***: terminated
  Aborted