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 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
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
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?
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.