its pity that your recent version does not work properly due to you have updated some functions and their arguments.
## changes in some functions that you made:
In bitr function:
previous it was "annoDb="org.Dr.eg.db"" and now it become "OrgDb".
In enrichGO function:
previous it was organism="zebrafish" " and now you changed into "OrgDb".
Note: Anyway i made changes into my script but i found its not working at all. PLEASE HELP AND FIX IT ASAP.
Even though, your example data seems does not executed:
data(gcSample) yy <- enrichGO(gcSample[], 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01) head(summary(yy))  ID Description GeneRatio BgRatio pvalue p.adjust qvalue  geneID Count <0 rows> (or 0-length row.names)
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252  LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  grid parallel stats4 stats graphics grDevices utils datasets methods  base other attached packages:  org.Dr.eg.db_3.3.0 gridExtra_2.2.1 plyr_1.8.4 pathview_1.12.0  org.Hs.eg.db_3.3.0 KEGGprofile_1.14.0 stringi_1.1.2 magrittr_1.5  igraph_1.0.1 networkD3_0.2.13 biomaRt_2.28.0 GO.db_3.3.0  AnnotationDbi_1.34.4 IRanges_2.6.1 Biobase_2.32.0 ReactomePA_1.16.2  clusterProfiler_3.0.5 DOSE_2.10.7 S4Vectors_0.10.3 BiocGenerics_0.18.0  BiocInstaller_1.22.3 loaded via a namespace (and not attached):  KEGGREST_1.12.3 qvalue_2.4.2 reshape2_1.4.2 splines_3.3.1  lattice_0.20-34 colorspace_1.2-7 graphite_1.18.1 htmltools_0.3.5  yaml_2.1.13 XML_3.98-1.4 DBI_0.5-1 Rgraphviz_2.16.0  rappdirs_0.3.1 topGO_2.24.0 matrixStats_0.51.0 KEGG.db_3.2.3  stringr_1.1.0 zlibbioc_1.18.0 Biostrings_2.40.2 munsell_0.4.3  GOSemSim_1.30.3 gtable_0.2.0 htmlwidgets_0.7 SparseM_1.74  curl_2.2 GSEABase_1.34.1 Rcpp_0.12.7 xtable_1.8-2  reactome.db_1.55.0 scales_0.4.0 DO.db_2.9 jsonlite_1.1  graph_1.50.0 annotate_1.50.1 XVector_0.12.1 TeachingDemos_2.10  ggplot2_2.1.0 png_0.1-7 digest_0.6.10 tools_3.3.1  bitops_1.0-6 RCurl_1.95-4.8 tibble_1.2 RSQLite_1.0.0  tidyr_0.6.0 KEGGgraph_1.30.0 assertthat_0.1 httr_1.2.1  R6_2.2.0