I am using the miR2Pathway package and have encountered an error message and warning messages that I need help troubleshooting. The finite observations warning is interesting to me, since it alludes to there being too few mirna listed. The input file contains 1,046 miRNAs that are being analyzed and are potentially being reduced to a list of less than 3 miRNAs.

Please visit the following github for the main functions, example input and example usage code:

miR2Pathway: https://github.com/GenomicsPrograms/miR2Pathway

Error and Warning Messages:

[1] 1044

[1] 1045

[1] 1046

[1] "miRtarnetwork step is done!!!"

Error in { : task 7 failed - "not enough finite observations"

In addition: There were 48 warnings (use warnings() to see them)

warnings()

Warning messages:

1: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

2: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

3: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

4: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

5: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

6: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1245

7: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1260

8: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1268

9: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1269

10: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1273

11: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1274a

12: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1274b

13: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

14: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-1295

15: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

16: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

17: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

18: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

19: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

20: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

21: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

22: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

23: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

24: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-3135

25: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-3150

26: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-3155

27: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

28: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-3647

29: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

30: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

31: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

32: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

33: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

34: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

35: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

36: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

37: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

38: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

39: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

40: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

41: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

42: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

43: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-550b

44: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

no targets found for mirna mir-550b

45: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

46: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

47: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

48: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom", ... :

sources which returned a target list<min_src, min_src="" reduced="" to="" 1<="" p="">

sessionInfo()

sessionInfo()
R Under development (unstable) (2018-03-10 r74380)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages: [1] stats4 parallel compiler stats graphics grDevices utils datasets methods base

other attached packages: [1] igraph_1.2.1 graph_1.57.1 graphite_1.25.1 miRNAtap.db_0.99.10 miRNAtap_1.13.0 AnnotationDbi_1.41.4 IRanges_2.13.28
[8] S4Vectors_0.17.35 Biobase_2.39.2 BiocGenerics_0.25.3 doParallel_1.0.11 iterators_1.0.9 foreach_1.4.4

loaded via a namespace (and not attached): [1] Rcpp_0.12.16 pillar_1.2.1 plyr_1.8.4 tools_3.5.0 digest_0.6.15 bit_1.1-12 RSQLite_2.0 memoise_1.1.0
[9] tibble_1.4.2 checkmate_1.8.5 pkgconfig_2.0.1 rlang_0.2.0 DBI_0.8 proto_1.0.0 stringr_1.3.0 httr_1.3.1
[17] rappdirs_0.3.1 bit64_0.9-7 sqldf_0.4-11 R6_2.2.2 gsubfn_0.7 blob_1.1.0 magrittr_1.5 backports_1.1.2 [25] codetools_0.2-15 stringi_1.1.7 chron_2.3-52

Object list: ls()

[1] "genelist" "miR2Pathway" "miRlist" "miRlist.full" "mydata.gene" "mydata.miR" "N.gene" "N.miR" "N.path"
[10] "name.genelist" "name.miRlist"