Hello!

Im currently developing an R package which depends on SGSeq. 

In the current devel version for SGSeq, there seems to be a bug or error in the function getSGFeatureCounts. Here is the error that appears when running the example for this function:

> path <- system.file("extdata", package = "SGSeq")
>  si$file_bam <- file.path(path, "bams", si$file_bam)
>  sgfc <- getSGFeatureCounts(si, sgf_pred)
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “NULL” is not valid for slot ‘NAMES’ in an object of class “SGFeatureCounts”; is(value, "characterORNULL") is not TRUE
>

Which is the same error that appears int the BioC build.

Thanks in Advance.

- J.P Romero
 

> sessionInfo()
R Under development (unstable) (2017-02-05 r72121)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
 [1] GenomicFeatures_1.27.6     AnnotationDbi_1.37.2       EventPointer_0.99.15      
 [4] Matrix_1.2-8               SGSeq_1.9.1                SummarizedExperiment_1.5.4
 [7] Biobase_2.35.0             Rsamtools_1.27.12          Biostrings_2.43.4         
[10] XVector_0.15.2             GenomicRanges_1.27.22      GenomeInfoDb_1.11.6       
[13] IRanges_2.9.18             S4Vectors_0.13.13          graph_1.53.0              
[16] BiocGenerics_0.21.3        BiocInstaller_1.25.3      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9              compiler_3.4.0           iterators_1.0.8         
 [4] bitops_1.0-6             tools_3.4.0              zlibbioc_1.21.0         
 [7] biomaRt_2.31.4           digest_0.6.12            RSQLite_1.1-2           
[10] memoise_1.0.0            lattice_0.20-34          foreach_1.4.3           
[13] igraph_1.0.1             DBI_0.5-1                prodlim_1.5.9           
[16] stringr_1.1.0            rtracklayer_1.35.5       affxparser_1.47.0       
[19] grid_3.4.0               survival_2.40-1          XML_3.98-1.5            
[22] RBGL_1.51.0              BiocParallel_1.9.5       lava_1.4.7              
[25] limma_3.31.11            magrittr_1.5             splines_3.4.0           
[28] nnls_1.4                 matrixStats_0.51.0       codetools_0.2-15        
[31] GenomicAlignments_1.11.9 MASS_7.3-45              RUnit_0.4.31            
[34] stringi_1.1.2            RCurl_1.95-4.8           doParallel_1.0.10  

Hi, 

Thanks for reporting this. I can reproduce the error for the development version. It must be due to a recent change in a package that SGSeq depends on. I'll try to address this shortly. 

Thanks, 
Leonard