no package called ‘reshape’

[knausb]

While attempting to install ggbio I received the following error:

\ preparing package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘reshape’ ERROR: lazy loading failed for package ‘ggbio’

'reshape2' appears on the ggbio list of imports but not 'reshape'. Installing 'reshape' from CRAN resulted in a successful install. I thought I may have discovered some legacy code (perhaps you still call reshape?) so I thought I should post it.

Thank you!

[lawremi]

Please post sessionInfo(), probably caused when a dependency of ggbio is loaded.

[knausb]

I was updating R and Bioconductor today, so good call. Note that I had to upgrade.packages('spatial') because it was part of the build error on earlier attempts.

sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] ggthemes_2.1.2
[2] XVector_0.8.0
[3] Homo.sapiens_1.1.2
[4] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2 [5] org.Hs.eg.db_3.1.2
[6] GO.db_3.1.2
[7] RSQLite_1.0.0
[8] DBI_0.3.1
[9] OrganismDbi_1.10.0
[10] GenomicFeatures_1.20.0
[11] AnnotationDbi_1.30.1
[12] Biobase_2.28.0
[13] BiocInstaller_1.18.1
[14] GenomicRanges_1.20.3
[15] GenomeInfoDb_1.4.0
[16] IRanges_2.2.1
[17] S4Vectors_0.6.0
[18] ggbio_1.16.0
[19] ggplot2_1.0.1
[20] BiocGenerics_0.14.0

loaded via a namespace (and not attached): [1] VariantAnnotation_1.14.0 reshape2_1.4.1 splines_3.2.0
[4] lattice_0.20-31 tcltk_3.2.0 colorspace_1.2-6
[7] rtracklayer_1.28.2 RBGL_1.44.0 survival_2.38-1
[10] XML_3.98-1.1 foreign_0.8-63 BiocParallel_1.2.0
[13] RColorBrewer_1.1-2 lambda.r_1.1.7 plyr_1.8.2
[16] stringr_0.6.2 zlibbioc_1.14.0 Biostrings_2.36.0
[19] munsell_0.4.2 gtable_0.1.2 futile.logger_1.4.1
[22] labeling_0.3 latticeExtra_0.6-26 GGally_0.5.0
[25] biomaRt_2.24.0 proto_0.3-10 Rcpp_0.11.5
[28] acepack_1.3-3.3 scales_0.2.4 BSgenome_1.36.0
[31] graph_1.46.0 Hmisc_3.15-0 Rsamtools_1.20.1
[34] gridExtra_0.9.1 digest_0.6.8 biovizBase_1.16.0
[37] grid_3.2.0 bitops_1.0-6 tools_3.2.0
[40] RCurl_1.95-4.6 dichromat_2.0-0 Formula_1.2-1
[43] cluster_2.0.1 futile.options_1.0.0 MASS_7.3-40
[46] reshape_0.8.5 rpart_4.1-9 GenomicAlignments_1.4.1 [49] nnet_7.3-9

[lawremi]

Perhaps you could delete reshape, and then trying loading likely suspects on which ggbio depends. Like ggplot2, GGally, biovizBase, gtable, scales, ...

Or use pkgDepTools, but that will build a graph based on a repository, not your package library.

[knausb]

I used remove.package() to remove reshape and tried library() to load: ggplot2, GGally, biovizBase, gtable, scales. GGally threw an error that reshape was not installed. But when I used install.packages() to install GGally it does successfully install reshape.

If you're confident that this is a dependency and not ggbio, perhaps it would be best to close this. Thank you!

[lawremi]

Not sure what happened to your R installation, but I don't think this is a general issue, so it's being closed. Thanks!