Running examples in ‘SeqFeatR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getfreqs
> ### Title: Get frequencies for amino acids/nucleotides in alignment window
> ###   (epitope)
> ### Aliases: getfreqs
> 
> ### ** Examples
> 
> #Input files
> 	fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
> 	consensus_input <- system.file("extdata", "Example_Consensus_aa.fasta", package="SeqFeatR")
> 	
> #Usage
> getfreqs(
+ 	path_to_file_sequence_alignment=fasta_input,
+ 	save_csv="getfreqs_result.csv",
+ 	save_png="getfreqs_result.png",
+ 	epitope_position_start=1,
+ 	epitope_position_end=40,
+ 	path_to_file_consensus=consensus_input,
+ 	patnum_threshold=1,
+ 	A11=10,
+ 	A12=11,
+ 	A21=13,
+ 	A22=14,
+ 	B11=17,
+ 	B12=18,
+ 	B21=20,
+ 	B22=21,
+ 	one_feature=FALSE)
allel:  1 
allel:  2 
allel:  3 
allel:  4 
allel:  5 
allel:  6 
allel:  7 
allel:  8 
    Allels letter I_abs      kind
1       A1    1_I     6     allel
2       A1    2_P     1     allel
3       A1    3_D     0     allel
4       A1    4_T     6     allel
5       A1    5_N     6     allel
6       A1    6_G     4     allel
7       A1    7_C     7     allel
8       A1    8_T     6     allel
9       A1    9_C     5     allel
10      A1   10_G     7     allel
11      A1   11_I     6     allel
12      A1   12_Q     7     allel
13      A1   13_Q     5     allel
14      A1   14_A     5     allel
15      A1   15_L     5     allel
16      A1   16_I     5     allel
17      A1   17_W     7     allel
18      A1   18_W     7     allel
19      A1   19_G     6     allel
20      A1   20_G     5     allel
21      A1   21_H     6     allel
22      A1   22_E     6     allel
23      A1   23_H     5     allel
24      A1   24_M     7     allel
25      A1   25_I     6     allel
26      A1   26_K     7     allel
27      A1   27_Q     0     allel
28      A1   28_L     5     allel
29      A1   29_L     5     allel
30      A1   30_C     6     allel
31      A1   31_I     6     allel
32      A1   32_V     5     allel
33      A1   33_H     5     allel
34      A1   34_I     6     allel
35      A1   35_C     6     allel
36      A1   36_G     6     allel
37      A1   37_E     7     allel
38      A1   38_C     7     allel
39      A1   39_N     5     allel
40      A1   40_W     5     allel
41      A2    1_I     2     allel
42      A2    2_P     1     allel
43      A2    3_D     0     allel
44      A2    4_T     3     allel
45      A2    5_N     3     allel
46      A2    6_G     2     allel
47      A2    7_C     3     allel
48      A2    8_T     3     allel
49      A2    9_C     2     allel
50      A2   10_G     3     allel
51      A2   11_I     2     allel
52      A2   12_Q     3     allel
53      A2   13_Q     2     allel
54      A2   14_A     3     allel
55      A2   15_L     2     allel
56      A2   16_I     3     allel
57      A2   17_W     3     allel
58      A2   18_W     3     allel
59      A2   19_G     3     allel
60      A2   20_G     2     allel
61      A2   21_H     3     allel
62      A2   22_E     3     allel
63      A2   23_H     1     allel
64      A2   24_M     3     allel
65      A2   25_I     3     allel
66      A2   26_K     3     allel
67      A2   27_Q     0     allel
68      A2   28_L     1     allel
69      A2   29_L     3     allel
70      A2   30_C     3     allel
71      A2   31_I     2     allel
72      A2   32_V     3     allel
73      A2   33_H     3     allel
74      A2   34_I     3     allel
75      A2   35_C     3     allel
76      A2   36_G     2     allel
77      A2   37_E     3     allel
78      A2   38_C     3     allel
79      A2   39_N     3     allel
80      A2   40_W     2     allel
81      A3    1_I     6     allel
82      A3    2_P     6     allel
83      A3    3_D     7     allel
84      A3    4_T     0     allel
85      A3    5_N     6     allel
86      A3    6_G     6     allel
87      A3    7_C     5     allel
88      A3    8_T     5     allel
89      A3    9_C     5     allel
90      A3   10_G     5     allel
91      A3   11_I     5     allel
92      A3   12_Q     4     allel
93      A3   13_Q     6     allel
94      A3   14_A     7     allel
95      A3   15_L     5     allel
96      A3   16_I     6     allel
97      A3   17_W     4     allel
98      A3   18_W     5     allel
99      A3   19_G     5     allel
100     A3   20_G     7     allel
101     A3   21_H     6     allel
102     A3   22_E     6     allel
103     A3   23_H     5     allel
104     A3   24_M     5     allel
105     A3   25_I     5     allel
106     A3   26_K     4     allel
107     A3   27_Q     7     allel
108     A3   28_L     5     allel
109     A3   29_L     6     allel
110     A3   30_C     6     allel
111     A3   31_I     5     allel
112     A3   32_V     7     allel
113     A3   33_H     6     allel
114     A3   34_I     5     allel
115     A3   35_C     5     allel
116     A3   36_G     5     allel
117     A3   37_E     5     allel
118     A3   38_C     5     allel
119     A3   39_N     6     allel
120     A3   40_W     6     allel
121     A4    1_I     6     allel
122     A4    2_P     6     allel
123     A4    3_D     7     allel
124     A4    4_T     0     allel
125     A4    5_N     6     allel
126     A4    6_G     6     allel
127     A4    7_C     5     allel
128     A4    8_T     5     allel
129     A4    9_C     5     allel
130     A4   10_G     5     allel
131     A4   11_I     5     allel
132     A4   12_Q     4     allel
133     A4   13_Q     6     allel
134     A4   14_A     7     allel
135     A4   15_L     5     allel
136     A4   16_I     6     allel
137     A4   17_W     4     allel
138     A4   18_W     5     allel
139     A4   19_G     5     allel
140     A4   20_G     7     allel
141     A4   21_H     6     allel
142     A4   22_E     6     allel
143     A4   23_H     5     allel
144     A4   24_M     5     allel
145     A4   25_I     5     allel
146     A4   26_K     4     allel
147     A4   27_Q     7     allel
148     A4   28_L     5     allel
149     A4   29_L     6     allel
150     A4   30_C     6     allel
151     A4   31_I     5     allel
152     A4   32_V     7     allel
153     A4   33_H     6     allel
154     A4   34_I     5     allel
155     A4   35_C     5     allel
156     A4   36_G     5     allel
157     A4   37_E     5     allel
158     A4   38_C     5     allel
159     A4   39_N     6     allel
160     A4   40_W     6     allel
161     B1    1_I     6     allel
162     B1    2_P     1     allel
163     B1    3_D     0     allel
164     B1    4_T     6     allel
165     B1    5_N     6     allel
166     B1    6_G     4     allel
167     B1    7_C     7     allel
168     B1    8_T     6     allel
169     B1    9_C     5     allel
170     B1   10_G     7     allel
171     B1   11_I     6     allel
172     B1   12_Q     7     allel
173     B1   13_Q     5     allel
174     B1   14_A     5     allel
175     B1   15_L     5     allel
176     B1   16_I     5     allel
177     B1   17_W     7     allel
178     B1   18_W     7     allel
179     B1   19_G     6     allel
180     B1   20_G     5     allel
181     B1   21_H     6     allel
182     B1   22_E     6     allel
183     B1   23_H     5     allel
184     B1   24_M     7     allel
185     B1   25_I     6     allel
186     B1   26_K     7     allel
187     B1   27_Q     0     allel
188     B1   28_L     5     allel
189     B1   29_L     5     allel
190     B1   30_C     6     allel
191     B1   31_I     6     allel
192     B1   32_V     5     allel
193     B1   33_H     5     allel
194     B1   34_I     6     allel
195     B1   35_C     6     allel
196     B1   36_G     6     allel
197     B1   37_E     7     allel
198     B1   38_C     7     allel
199     B1   39_N     5     allel
200     B1   40_W     5     allel
201     B2    1_I     6     allel
202     B2    2_P     1     allel
203     B2    3_D     0     allel
204     B2    4_T     6     allel
205     B2    5_N     6     allel
206     B2    6_G     4     allel
207     B2    7_C     7     allel
208     B2    8_T     6     allel
209     B2    9_C     5     allel
210     B2   10_G     7     allel
211     B2   11_I     6     allel
212     B2   12_Q     7     allel
213     B2   13_Q     5     allel
214     B2   14_A     5     allel
215     B2   15_L     5     allel
216     B2   16_I     5     allel
217     B2   17_W     7     allel
218     B2   18_W     7     allel
219     B2   19_G     6     allel
220     B2   20_G     5     allel
221     B2   21_H     6     allel
222     B2   22_E     6     allel
223     B2   23_H     5     allel
224     B2   24_M     7     allel
225     B2   25_I     6     allel
226     B2   26_K     7     allel
227     B2   27_Q     0     allel
228     B2   28_L     5     allel
229     B2   29_L     5     allel
230     B2   30_C     6     allel
231     B2   31_I     6     allel
232     B2   32_V     5     allel
233     B2   33_H     5     allel
234     B2   34_I     6     allel
235     B2   35_C     6     allel
236     B2   36_G     6     allel
237     B2   37_E     7     allel
238     B2   38_C     7     allel
239     B2   39_N     5     allel
240     B2   40_W     5     allel
241     B3    1_I     5     allel
242     B3    2_P     4     allel
243     B3    3_D     5     allel
244     B3    4_T     0     allel
245     B3    5_N     4     allel
246     B3    6_G     4     allel
247     B3    7_C     4     allel
248     B3    8_T     3     allel
249     B3    9_C     5     allel
250     B3   10_G     3     allel
251     B3   11_I     4     allel
252     B3   12_Q     2     allel
253     B3   13_Q     5     allel
254     B3   14_A     5     allel
255     B3   15_L     3     allel
256     B3   16_I     5     allel
257     B3   17_W     3     allel
258     B3   18_W     5     allel
259     B3   19_G     3     allel
260     B3   20_G     5     allel
261     B3   21_H     5     allel
262     B3   22_E     4     allel
263     B3   23_H     4     allel
264     B3   24_M     4     allel
265     B3   25_I     4     allel
266     B3   26_K     2     allel
267     B3   27_Q     5     allel
268     B3   28_L     3     allel
269     B3   29_L     4     allel
270     B3   30_C     4     allel
271     B3   31_I     3     allel
272     B3   32_V     5     allel
273     B3   33_H     4     allel
274     B3   34_I     3     allel
275     B3   35_C     4     allel
276     B3   36_G     3     allel
277     B3   37_E     3     allel
278     B3   38_C     3     allel
279     B3   39_N     4     allel
280     B3   40_W     4     allel
281     B4    1_I     6     allel
282     B4    2_P     6     allel
283     B4    3_D     7     allel
284     B4    4_T     0     allel
285     B4    5_N     6     allel
286     B4    6_G     6     allel
287     B4    7_C     5     allel
288     B4    8_T     5     allel
289     B4    9_C     5     allel
290     B4   10_G     5     allel
291     B4   11_I     5     allel
292     B4   12_Q     4     allel
293     B4   13_Q     6     allel
294     B4   14_A     7     allel
295     B4   15_L     5     allel
296     B4   16_I     6     allel
297     B4   17_W     4     allel
298     B4   18_W     5     allel
299     B4   19_G     5     allel
300     B4   20_G     7     allel
301     B4   21_H     6     allel
302     B4   22_E     6     allel
303     B4   23_H     5     allel
304     B4   24_M     5     allel
305     B4   25_I     5     allel
306     B4   26_K     4     allel
307     B4   27_Q     7     allel
308     B4   28_L     5     allel
309     B4   29_L     6     allel
310     B4   30_C     6     allel
311     B4   31_I     5     allel
312     B4   32_V     7     allel
313     B4   33_H     6     allel
314     B4   34_I     5     allel
315     B4   35_C     5     allel
316     B4   36_G     5     allel
317     B4   37_E     5     allel
318     B4   38_C     5     allel
319     B4   39_N     6     allel
320     B4   40_W     6     allel
321     A1    1_I     6 not allel
322     A1    2_P     6 not allel
323     A1    3_D     7 not allel
324     A1    4_T     0 not allel
325     A1    5_N     6 not allel
326     A1    6_G     6 not allel
327     A1    7_C     5 not allel
328     A1    8_T     5 not allel
329     A1    9_C     5 not allel
330     A1   10_G     5 not allel
331     A1   11_I     5 not allel
332     A1   12_Q     4 not allel
333     A1   13_Q     6 not allel
334     A1   14_A     7 not allel
335     A1   15_L     5 not allel
336     A1   16_I     6 not allel
337     A1   17_W     4 not allel
338     A1   18_W     5 not allel
339     A1   19_G     5 not allel
340     A1   20_G     7 not allel
341     A1   21_H     6 not allel
342     A1   22_E     6 not allel
343     A1   23_H     5 not allel
344     A1   24_M     5 not allel
345     A1   25_I     5 not allel
346     A1   26_K     4 not allel
347     A1   27_Q     7 not allel
348     A1   28_L     5 not allel
349     A1   29_L     6 not allel
350     A1   30_C     6 not allel
351     A1   31_I     5 not allel
352     A1   32_V     7 not allel
353     A1   33_H     6 not allel
354     A1   34_I     5 not allel
355     A1   35_C     5 not allel
356     A1   36_G     5 not allel
357     A1   37_E     5 not allel
358     A1   38_C     5 not allel
359     A1   39_N     6 not allel
360     A1   40_W     6 not allel
361     A2    1_I    10 not allel
362     A2    2_P     6 not allel
363     A2    3_D     7 not allel
364     A2    4_T     3 not allel
365     A2    5_N     9 not allel
366     A2    6_G     8 not allel
367     A2    7_C     9 not allel
368     A2    8_T     8 not allel
369     A2    9_C     8 not allel
370     A2   10_G     9 not allel
371     A2   11_I     9 not allel
372     A2   12_Q     8 not allel
373     A2   13_Q     9 not allel
374     A2   14_A     9 not allel
375     A2   15_L     8 not allel
376     A2   16_I     8 not allel
377     A2   17_W     8 not allel
378     A2   18_W     9 not allel
379     A2   19_G     8 not allel
380     A2   20_G    10 not allel
381     A2   21_H     9 not allel
382     A2   22_E     9 not allel
383     A2   23_H     9 not allel
384     A2   24_M     9 not allel
385     A2   25_I     8 not allel
386     A2   26_K     8 not allel
387     A2   27_Q     7 not allel
388     A2   28_L     9 not allel
389     A2   29_L     8 not allel
390     A2   30_C     9 not allel
391     A2   31_I     9 not allel
392     A2   32_V     9 not allel
393     A2   33_H     8 not allel
394     A2   34_I     8 not allel
395     A2   35_C     8 not allel
396     A2   36_G     9 not allel
397     A2   37_E     9 not allel
398     A2   38_C     9 not allel
399     A2   39_N     8 not allel
400     A2   40_W     9 not allel
401     A3    1_I     6 not allel
402     A3    2_P     1 not allel
403     A3    3_D     0 not allel
404     A3    4_T     6 not allel
405     A3    5_N     6 not allel
406     A3    6_G     4 not allel
407     A3    7_C     7 not allel
408     A3    8_T     6 not allel
409     A3    9_C     5 not allel
410     A3   10_G     7 not allel
411     A3   11_I     6 not allel
412     A3   12_Q     7 not allel
413     A3   13_Q     5 not allel
414     A3   14_A     5 not allel
415     A3   15_L     5 not allel
416     A3   16_I     5 not allel
417     A3   17_W     7 not allel
418     A3   18_W     7 not allel
419     A3   19_G     6 not allel
420     A3   20_G     5 not allel
421     A3   21_H     6 not allel
422     A3   22_E     6 not allel
423     A3   23_H     5 not allel
424     A3   24_M     7 not allel
425     A3   25_I     6 not allel
426     A3   26_K     7 not allel
427     A3   27_Q     0 not allel
428     A3   28_L     5 not allel
429     A3   29_L     5 not allel
430     A3   30_C     6 not allel
431     A3   31_I     6 not allel
432     A3   32_V     5 not allel
433     A3   33_H     5 not allel
434     A3   34_I     6 not allel
435     A3   35_C     6 not allel
436     A3   36_G     6 not allel
437     A3   37_E     7 not allel
438     A3   38_C     7 not allel
439     A3   39_N     5 not allel
440     A3   40_W     5 not allel
441     A4    1_I     6 not allel
442     A4    2_P     1 not allel
443     A4    3_D     0 not allel
444     A4    4_T     6 not allel
445     A4    5_N     6 not allel
446     A4    6_G     4 not allel
447     A4    7_C     7 not allel
448     A4    8_T     6 not allel
449     A4    9_C     5 not allel
450     A4   10_G     7 not allel
451     A4   11_I     6 not allel
452     A4   12_Q     7 not allel
453     A4   13_Q     5 not allel
454     A4   14_A     5 not allel
455     A4   15_L     5 not allel
456     A4   16_I     5 not allel
457     A4   17_W     7 not allel
458     A4   18_W     7 not allel
459     A4   19_G     6 not allel
460     A4   20_G     5 not allel
461     A4   21_H     6 not allel
462     A4   22_E     6 not allel
463     A4   23_H     5 not allel
464     A4   24_M     7 not allel
465     A4   25_I     6 not allel
466     A4   26_K     7 not allel
467     A4   27_Q     0 not allel
468     A4   28_L     5 not allel
469     A4   29_L     5 not allel
470     A4   30_C     6 not allel
471     A4   31_I     6 not allel
472     A4   32_V     5 not allel
473     A4   33_H     5 not allel
474     A4   34_I     6 not allel
475     A4   35_C     6 not allel
476     A4   36_G     6 not allel
477     A4   37_E     7 not allel
478     A4   38_C     7 not allel
479     A4   39_N     5 not allel
480     A4   40_W     5 not allel
481     B1    1_I     6 not allel
482     B1    2_P     6 not allel
483     B1    3_D     7 not allel
484     B1    4_T     0 not allel
485     B1    5_N     6 not allel
486     B1    6_G     6 not allel
487     B1    7_C     5 not allel
488     B1    8_T     5 not allel
489     B1    9_C     5 not allel
490     B1   10_G     5 not allel
491     B1   11_I     5 not allel
492     B1   12_Q     4 not allel
493     B1   13_Q     6 not allel
494     B1   14_A     7 not allel
495     B1   15_L     5 not allel
496     B1   16_I     6 not allel
497     B1   17_W     4 not allel
498     B1   18_W     5 not allel
499     B1   19_G     5 not allel
500     B1   20_G     7 not allel
501     B1   21_H     6 not allel
502     B1   22_E     6 not allel
503     B1   23_H     5 not allel
504     B1   24_M     5 not allel
505     B1   25_I     5 not allel
506     B1   26_K     4 not allel
507     B1   27_Q     7 not allel
508     B1   28_L     5 not allel
509     B1   29_L     6 not allel
510     B1   30_C     6 not allel
511     B1   31_I     5 not allel
512     B1   32_V     7 not allel
513     B1   33_H     6 not allel
514     B1   34_I     5 not allel
515     B1   35_C     5 not allel
516     B1   36_G     5 not allel
517     B1   37_E     5 not allel
518     B1   38_C     5 not allel
519     B1   39_N     6 not allel
520     B1   40_W     6 not allel
521     B2    1_I     6 not allel
522     B2    2_P     6 not allel
523     B2    3_D     7 not allel
524     B2    4_T     0 not allel
525     B2    5_N     6 not allel
526     B2    6_G     6 not allel
527     B2    7_C     5 not allel
528     B2    8_T     5 not allel
529     B2    9_C     5 not allel
530     B2   10_G     5 not allel
531     B2   11_I     5 not allel
532     B2   12_Q     4 not allel
533     B2   13_Q     6 not allel
534     B2   14_A     7 not allel
535     B2   15_L     5 not allel
536     B2   16_I     6 not allel
537     B2   17_W     4 not allel
538     B2   18_W     5 not allel
539     B2   19_G     5 not allel
540     B2   20_G     7 not allel
541     B2   21_H     6 not allel
542     B2   22_E     6 not allel
543     B2   23_H     5 not allel
544     B2   24_M     5 not allel
545     B2   25_I     5 not allel
546     B2   26_K     4 not allel
547     B2   27_Q     7 not allel
548     B2   28_L     5 not allel
549     B2   29_L     6 not allel
550     B2   30_C     6 not allel
551     B2   31_I     5 not allel
552     B2   32_V     7 not allel
553     B2   33_H     6 not allel
554     B2   34_I     5 not allel
555     B2   35_C     5 not allel
556     B2   36_G     5 not allel
557     B2   37_E     5 not allel
558     B2   38_C     5 not allel
559     B2   39_N     6 not allel
560     B2   40_W     6 not allel
561     B3    1_I     7 not allel
562     B3    2_P     3 not allel
563     B3    3_D     2 not allel
564     B3    4_T     6 not allel
565     B3    5_N     8 not allel
566     B3    6_G     6 not allel
567     B3    7_C     8 not allel
568     B3    8_T     8 not allel
569     B3    9_C     5 not allel
570     B3   10_G     9 not allel
571     B3   11_I     7 not allel
572     B3   12_Q     9 not allel
573     B3   13_Q     6 not allel
574     B3   14_A     7 not allel
575     B3   15_L     7 not allel
576     B3   16_I     6 not allel
577     B3   17_W     8 not allel
578     B3   18_W     7 not allel
579     B3   19_G     8 not allel
580     B3   20_G     7 not allel
581     B3   21_H     7 not allel
582     B3   22_E     8 not allel
583     B3   23_H     6 not allel
584     B3   24_M     8 not allel
585     B3   25_I     7 not allel
586     B3   26_K     9 not allel
587     B3   27_Q     2 not allel
588     B3   28_L     7 not allel
589     B3   29_L     7 not allel
590     B3   30_C     8 not allel
591     B3   31_I     8 not allel
592     B3   32_V     7 not allel
593     B3   33_H     7 not allel
594     B3   34_I     8 not allel
595     B3   35_C     7 not allel
596     B3   36_G     8 not allel
597     B3   37_E     9 not allel
598     B3   38_C     9 not allel
599     B3   39_N     7 not allel
600     B3   40_W     7 not allel
601     B4    1_I     6 not allel
602     B4    2_P     1 not allel
603     B4    3_D     0 not allel
604     B4    4_T     6 not allel
605     B4    5_N     6 not allel
606     B4    6_G     4 not allel
607     B4    7_C     7 not allel
608     B4    8_T     6 not allel
609     B4    9_C     5 not allel
610     B4   10_G     7 not allel
611     B4   11_I     6 not allel
612     B4   12_Q     7 not allel
613     B4   13_Q     5 not allel
614     B4   14_A     5 not allel
615     B4   15_L     5 not allel
616     B4   16_I     5 not allel
617     B4   17_W     7 not allel
618     B4   18_W     7 not allel
619     B4   19_G     6 not allel
620     B4   20_G     5 not allel
621     B4   21_H     6 not allel
622     B4   22_E     6 not allel
623     B4   23_H     5 not allel
624     B4   24_M     7 not allel
625     B4   25_I     6 not allel
626     B4   26_K     7 not allel
627     B4   27_Q     0 not allel
628     B4   28_L     5 not allel
629     B4   29_L     5 not allel
630     B4   30_C     6 not allel
631     B4   31_I     6 not allel
632     B4   32_V     5 not allel
633     B4   33_H     5 not allel
634     B4   34_I     6 not allel
635     B4   35_C     6 not allel
636     B4   36_G     6 not allel
637     B4   37_E     7 not allel
638     B4   38_C     7 not allel
639     B4   39_N     5 not allel
640     B4   40_W     5 not allel
Saving 7 x 7 in image
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: getfreqs ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted