I am trying to run phangorn and I am running into a problem with the NJ command.

The R “chunk” that terminates in the NJ call is as follows:

1. # First align the sequences
2. library(DECIPHER)
3. seqs <- getSequences(st)
4.  
5. # This next command will allow propagation of sequence names to the tip labels of the tree
6. names(seqs) <- seqs
7. alignment <- AlignSeqs(DNAStringSet(seqs), anchor=NA)
8.  
9. # Now create the tree
10.  
11. library(phangorn)
12.  
13. # Construct the tree
14. phang.align <- phyDat(as(alignment, "matrix"), type="DNA")
15. dm <- dist.ml(phang.align)
16. treeNJ <- NJ(dm) # Tip order will not equal sequence order

The result of this chunk, terminating in the error is as follows:

1. Loading required package: Biostrings
2. Loading required package: BiocGenerics
3. Loading required package: parallel
4.  
5. Attaching package: ‘BiocGenerics’
6.  
7. The following objects are masked from ‘package:parallel’:
8.  
9.     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
10.     clusterExport, clusterMap, parApply, parCapply, parLapply,
11.     parLapplyLB, parRapply, parSapply, parSapplyLB
12.  
13. The following object is masked from ‘package:gridExtra’:
14.  
15.     combine
16.  
17. The following objects are masked from ‘package:stats’:
18.  
19.     IQR, mad, sd, var, xtabs
20.  
21. The following objects are masked from ‘package:base’:
22.  
23.     anyDuplicated, append, as.data.frame, cbind, colMeans,
24.     colnames, colSums, do.call, duplicated, eval, evalq, Filter,
25.     Find, get, grep, grepl, intersect, is.unsorted, lapply,
26.     lengths, Map, mapply, match, mget, order, paste, pmax,
27.     pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
28.     rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
29.     tapply, union, unique, unsplit, which, which.max, which.min
30.  
31. Loading required package: S4Vectors
32. Loading required package: stats4
33.  
34. Attaching package: ‘S4Vectors’
35.  
36. The following object is masked from ‘package:base’:
37.  
38.     expand.grid
39.  
40. Loading required package: IRanges
41.  
42. Attaching package: ‘IRanges’
43.  
44. The following object is masked from ‘package:phyloseq’:
45.  
46.     distance
47.  
48. Loading required package: XVector
49.  
50. Attaching package: ‘Biostrings’
51.  
52. The following object is masked from ‘package:base’:
53.  
54.     strsplit
55.  
56. Loading required package: RSQLite
57. Determining distance matrix based on shared 7-mers:
58.   |================================================================| 100%
59.  
60. Time difference of 3.85 secs
61.  
62. Clustering into groups by similarity:
63.   |================================================================| 100%
64.  
65. Time difference of 1.62 secs
66.  
67. Aligning Sequences:
68.   |================================================================| 100%
69.  
70. Time difference of 5.07 secs
71.  
72. Determining distance matrix based on alignment:
73.   |================================================================| 100%
74.  
75. Time difference of 1.93 secs
76.  
77. Reclustering into groups by similarity:
78.   |================================================================| 100%
79.  
80. Time difference of 2.3 secs
81.  
82. Realigning Sequences:
83.   |================================================================| 100%
84.  
85. Time difference of 4.21 secs
86.  
87. Loading required package: ape
88.  
89. Attaching package: ‘ape’
90.  
91. The following object is masked from ‘package:Biostrings’:
92.  
93.     complement
94.  
95.  Hide Traceback
96. Error in nj(x) : object 'C_nj' not found
97.  
98.  

The session.info is as follows:

1. R version 3.4.0 (2017-04-21)
2. Platform: x86_64-apple-darwin15.6.0 (64-bit)
3. Running under: macOS Sierra 10.12.5
4.  
5. Matrix products: default
6. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
7. LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
8.  
9. locale:
10. [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
11.  
12. attached base packages:
13. [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods 
14. [9] base    
15.  
16. other attached packages:
17. [1] phangorn_2.2.0       ape_4.1              DECIPHER_2.4.0     
18.  [4] RSQLite_2.0          Biostrings_2.44.1    XVector_0.16.0      
19.  [7] IRanges_2.10.2       S4Vectors_0.14.3     BiocGenerics_0.22.0
20. [10] gridExtra_2.2.1      RColorBrewer_1.1-2   ggplot2_2.2.1      
21. [13] phyloseq_1.20.0      dada2_1.4.0          Rcpp_0.12.11       
22. [16] BiocInstaller_1.26.0
23.  
24. loaded via a namespace (and not attached):
25. [1] lattice_0.20-35            Rsamtools_1.28.0         
26.  [3] digest_0.6.12              foreach_1.4.3            
27.  [5] GenomeInfoDb_1.12.2        plyr_1.8.4               
28.  [7] ShortRead_1.34.0           zlibbioc_1.22.0           
29.  [9] rlang_0.1.1                lazyeval_0.2.0           
30. [11] data.table_1.10.4          vegan_2.4-3              
31. [13] blob_1.1.0                 Matrix_1.2-10            
32. [15] labeling_0.3               splines_3.4.0            
33. [17] BiocParallel_1.10.1        stringr_1.2.0            
34. [19] igraph_1.0.1               RCurl_1.95-4.8           
35. [21] bit_1.1-12                 munsell_0.4.3            
36. [23] DelayedArray_0.2.7         compiler_3.4.0           
37. [25] multtest_2.32.0            mgcv_1.8-17              
38. [27] biomformat_1.4.0           SummarizedExperiment_1.6.3
39. [29] tibble_1.3.3               GenomeInfoDbData_0.99.0  
40. [31] quadprog_1.5-5             codetools_0.2-15         
41. [33] matrixStats_0.52.2         permute_0.9-4            
42. [35] GenomicAlignments_1.12.1   MASS_7.3-47              
43. [37] bitops_1.0-6               grid_3.4.0               
44. [39] nlme_3.1-131               jsonlite_1.5             
45. [41] gtable_0.2.0               DBI_0.7                   
46. [43] magrittr_1.5               scales_0.4.1             
47. [45] RcppParallel_4.3.20        stringi_1.1.5            
48. [47] hwriter_1.3.2              reshape2_1.4.2           
49. [49] latticeExtra_0.6-28        fastmatch_1.1-0          
50. [51] iterators_1.0.8            tools_3.4.0              
51. [53] ade4_1.7-6                 bit64_0.9-7              
52. [55] Biobase_2.36.2             survival_2.41-3          
53. [57] colorspace_1.3-2           rhdf5_2.20.0             
54. [59] cluster_2.0.6              GenomicRanges_1.28.3     
55. [61] memoise_1.1.0              knitr_1.16

Can you please advise – what am I doing wrong, how can I fix this?