I am using homo.sapiens package (1.3.1, hg19 annotation) for my annotation, I have noted that when using

genes(Homo.sapiens, columns = "SYMBOL")

there is no HLA class genes included in mcol(HLA-A, HLA-B, HLA-C ...etc), but when I changed code to

transcripts(Homo.sapiens, columns = "SYMBOL")

I can find HLA class genes included in mcol(with several different transcripts).

I am wondering about what caused this issue because in other situations, "genes" command works fairly fine to extract information. Thanks for answering my question.

The genes function basically takes the furthest extent of all transcripts for a particular gene, and returns that. This works really well for the vast majority of all genes, but fails in two notable instances. First, when the gene is found on more than one chromosome (or unplaced scaffold thereof), and second, when the gene is found in discontiguous regions of a chromosome. You have run into problem #1:

> select(Homo.sapiens,  c("HLA-A","HLA-B","HLA-C"), "TXCHROM","SYMBOL")
'select()' returned 1:many mapping between keys and columns
   SYMBOL        TXCHROM
1   HLA-A           chr6
2   HLA-A  chr6_apd_hap1
3   HLA-A  chr6_cox_hap2
4   HLA-A  chr6_dbb_hap3
5   HLA-A chr6_mann_hap4
6   HLA-A  chr6_mcf_hap5
7   HLA-A  chr6_qbl_hap6
8   HLA-A chr6_ssto_hap7
9   HLA-B           chr6
10  HLA-B  chr6_cox_hap2
11  HLA-B chr6_mann_hap4
12  HLA-B  chr6_mcf_hap5
13  HLA-B  chr6_qbl_hap6
14  HLA-B chr6_ssto_hap7
15  HLA-C           chr6
16  HLA-C  chr6_cox_hap2
17  HLA-C  chr6_dbb_hap3
18  HLA-C chr6_mann_hap4
19  HLA-C  chr6_mcf_hap5
20  HLA-C  chr6_qbl_hap6
21  HLA-C chr6_ssto_hap7

Each of these genes is found on chr6, plus multiple unplaced scaffolds. It's not possible to return a single chromosomal region for these genes, so they get dropped. It is however possible to return multiple transcript locations, so transcripts does work.