namespace issues re: `tibble`?
andrewejaffe opened this issue · comments
It looks like the tibble package dependency is off somewhere - this was a fresh derfinder install where maybe 10 other packages were installed. manually installing the tibble package resolves the issues.
-a
> library(derfinder)
Error: package or namespace load failed for ‘derfinder’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘tibble’
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] derfinder_1.10.4 BiocInstaller_1.26.0 SummarizedExperiment_1.6.1
[4] DelayedArray_0.2.2 matrixStats_0.52.2 Biobase_2.36.2
[7] GenomicRanges_1.28.1 GenomeInfoDb_1.12.0 IRanges_2.10.1
[10] S4Vectors_0.14.1 BiocGenerics_0.22.0 edgeR_3.18.1
[13] limma_3.32.2 jaffelab_0.99.10 rafalib_1.0.0
loaded via a namespace (and not attached):
[1] splines_3.4.0 foreach_1.4.3 GenomicFiles_1.12.0 Formula_1.2-1
[5] bumphunter_1.16.0 latticeExtra_0.6-28 doRNG_1.6.6 BSgenome_1.44.0
[9] GenomeInfoDbData_0.99.0 Rsamtools_1.28.0 RSQLite_1.1-2 backports_1.0.5
[13] lattice_0.20-35 digest_0.6.12 RColorBrewer_1.1-2 XVector_0.16.0
[17] checkmate_1.8.2 qvalue_2.8.0 colorspace_1.3-2 htmltools_0.3.6
[21] Matrix_1.2-10 plyr_1.8.4 XML_3.98-1.7 biomaRt_2.32.0
[25] zlibbioc_1.22.0 xtable_1.8-2 scales_0.4.1 BiocParallel_1.10.1
[29] htmlTable_1.9 tibble_1.3.0 pkgmaker_0.22 ggplot2_2.2.1
[33] GenomicFeatures_1.28.0 nnet_7.3-12 lazyeval_0.2.0 survival_2.41-3
[37] magrittr_1.5 memoise_1.1.0 foreign_0.8-68 tools_3.4.0
[41] registry_0.3 data.table_1.10.4 stringr_1.2.0 munsell_0.4.3
[45] locfit_1.5-9.1 rngtools_1.2.4 cluster_2.0.6 AnnotationDbi_1.38.0
[49] Biostrings_2.44.0 compiler_3.4.0 grid_3.4.0 RCurl_1.95-4.8
[53] iterators_1.0.8 VariantAnnotation_1.22.0 htmlwidgets_0.8 bitops_1.0-6
[57] base64enc_0.1-3 derfinderHelper_1.10.0 gtable_0.2.0 codetools_0.2-15
[61] DBI_0.6-1 reshape2_1.4.2 GenomicAlignments_1.12.1 gridExtra_2.2.1
[65] knitr_1.15.1 rtracklayer_1.36.0 Hmisc_4.0-3 stringi_1.1.5
[69] Rcpp_0.12.10 rpart_4.1-11 acepack_1.4.1
Hm... this is not a derfinder issue. The package doesn't depend/import/suggest tibble directly https://github.com/lcolladotor/derfinder/blob/master/DESCRIPTION. Some other package must be. Anyhow, looks like using the latest tibble makes it work and there's not much I can do from derfinder directly.