Question: Error when running getSGFeatureCounts
0
gravatar for jpromero
2.5 years ago by
jpromero0
jpromero0 wrote:

 

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  

 

 

 

 

 

 

software error sgseq • 715 views
ADD COMMENTlink modified 2.5 years ago by Leonard Goldstein80 • written 2.5 years ago by jpromero0
Answer: Error when running getSGFeatureCounts
0
gravatar for Leonard Goldstein
2.5 years ago by
United States
Leonard Goldstein80 wrote:

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

ADD COMMENTlink written 2.5 years ago by Leonard Goldstein80

Hi Leonard,


Thanks for looking at the error. I've already seen the issue in the devel mailing list and I'll be checking to know when it is solved.

Thanks.

- J.P Romero

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by jpromero0

I believe a fix will be for jpromero to re-install several packages, as indicated in https://stat.ethz.ch/pipermail/bioc-devel/2017-February/010463.html

ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 23k

Yes! I did see the e-mail on the BioC level mailing list. This could help to solve the problem locally but, of the build is run in  the BioC servers im guessing that it will still appear until the same roundabout is applied. For the servers, would I just have to wait or another solution is possible?

 

ADD REPLYlink written 2.5 years ago by jpromero0

My guess is that the problem is only for existing installations.

You'd have to 'wait' until the build servers produced packages that triggered an update, i.e., a version bump followed by successful build and propagation. I doubt that bumping the version of 600+ packages is the right thing to do in this case, where the problem is on the 'devel' branch and where 'devel' users are able to take appropriate action locally.

The correct forum to ask about devel packages is on the bioc-devel mailing list.

ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 23k
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