namespace locked

[jamesdalg]

CNVScope::runCNVScopeShiny(baseurl = "~", basefn = "") Error in registerNames(names, package, ".global", add) : The namespace for package "CNVScope" is locked; no changes in the global variables list may be made.

[jamesdalg]

https://stat.ethz.ch/pipermail/r-package-devel/2018q3/003046.html suggests putting the globalVariables() call outside the function, but this is the case for both server and UI functions.

[jamesdalg]

traceback and sessionInfo() on this issue.

traceback() 4: stop(gettextf("The namespace for package \"%s\" is locked; no changes in the global variables list may be made.", package)) 3: registerNames(names, package, ".global", add) 2: utils::globalVariables(c(".")) 1: CNVScope::runCNVScopeShiny(baseurl = "~", basefn = "~") sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages: [1] CNVScope_2.1.9 ggplot2_3.1.0

loaded via a namespace (and not attached): [1] backports_1.1.3 spam_2.2-1 circlize_0.4.5 Hmisc_4.1-1
[5] plyr_1.8.4 igraph_1.2.2 lazyeval_0.2.1 splines_3.5.1
[9] BiocParallel_1.16.2 GenomeInfoDb_1.18.1 digest_0.6.18 foreach_1.4.4
[13] ensembldb_2.6.3 htmltools_0.3.6 viridis_0.5.1 tiff_0.1-5
[17] gdata_2.18.0 magrittr_1.5 checkmate_1.9.0 memoise_1.1.0
[21] BSgenome_1.50.0 cluster_2.0.7-1 doParallel_1.0.14 gclus_1.3.2
[25] InteractionSet_1.10.0 Biostrings_2.50.1 acnr_1.0.0 matrixStats_0.54.0
[29] spatialfil_0.15 prettyunits_1.0.2 jpeg_0.1-8 colorspace_1.4-0
[33] blob_1.1.1 xfun_0.4 dplyr_0.7.8 crayon_1.3.4
[37] RCurl_1.95-4.11 jsonlite_1.6 bindr_0.1.1 survival_2.43-3
[41] VariantAnnotation_1.28.3 iterators_1.0.10 glue_1.3.0 registry_0.5
[45] gtable_0.2.0 zlibbioc_1.28.0 XVector_0.22.0 webshot_0.5.1
[49] DelayedArray_0.8.0 kernlab_0.9-27 shape_1.4.4 DEoptimR_1.0-8
[53] prabclus_2.2-6 BiocGenerics_0.28.0 maps_3.3.0 abind_1.4-5
[57] scales_1.0.0 mvtnorm_1.0-8 DBI_1.0.0 Rcpp_1.0.0
[61] HiCseg_1.1 viridisLite_0.3.0 xtable_1.8-3 progress_1.2.0
[65] htmlTable_1.13.1 mclust_5.4.2 foreign_0.8-71 bit_1.1-14
[69] dotCall64_1.0-0 Formula_1.2-3 stats4_3.5.1 htmlwidgets_1.3
[73] httr_1.4.0 gplots_3.0.1 fpc_2.1-11.1 RColorBrewer_1.1-2
[77] modeltools_0.2-22 acepack_1.4.1 flexmix_2.3-14 pkgconfig_2.0.2
[81] XML_3.98-1.16 Gviz_1.26.4 nnet_7.3-12 tidyselect_0.2.5
[85] rlang_0.3.1 reshape2_1.4.3 later_0.7.5 AnnotationDbi_1.44.0
[89] munsell_0.5.0 OpenImageR_1.1.4 tools_3.5.1 visNetwork_2.0.5
[93] rslurm_0.4.0 RSQLite_2.1.1 stringr_1.3.1 heatmaply_0.15.2
[97] yaml_2.2.0 knitr_1.21 bit64_0.9-7 shinycssloaders_0.2.0
[101] robustbase_0.93-3 caTools_1.17.1.1 purrr_0.2.5 dendextend_1.9.0
[105] AnnotationFilter_1.6.0 bindrcpp_0.2.2 whisker_0.3-2 mime_0.6
[109] biomaRt_2.38.0 compiler_3.5.1 shinythemes_1.1.2 rstudioapi_0.9.0
[113] plotly_4.8.0 curl_3.3 png_0.1-7 tibble_2.0.1
[117] stringi_1.2.4 GenomicFeatures_1.34.1 fields_9.6 trimcluster_0.1-2.1
[121] lattice_0.20-38 ProtGenerics_1.14.0 Matrix_1.2-15 shinyjs_1.0
[125] pillar_1.3.1 GenomicInteractions_1.16.0 BiocManager_1.30.4 GlobalOptions_0.1.0
[129] data.table_1.12.0 bitops_1.0-6 seriation_1.2-3 httpuv_1.4.5.1
[133] rtracklayer_1.42.1 GenomicRanges_1.34.0 R6_2.3.0 latticeExtra_0.6-28
[137] TSP_1.1-6 promises_1.0.1 KernSmooth_2.23-15 gridExtra_2.3
[141] IRanges_2.16.0 codetools_0.2-16 dichromat_2.0-0 gtools_3.8.1
[145] MASS_7.3-51.1 assertthat_0.2.0 SummarizedExperiment_1.12.0 withr_2.1.2
[149] GenomicAlignments_1.18.0 Rsamtools_1.34.0 S4Vectors_0.20.1 GenomeInfoDbData_1.2.0
[153] diptest_0.75-7 jointseg_1.0.2 parallel_3.5.1 hms_0.4.2
[157] grid_3.5.1 rpart_4.1-13 class_7.3-15 tidyr_0.8.2
[161] logging_0.7-103 biovizBase_1.30.1 Biobase_2.42.0 shiny_1.2.0
[165] base64enc_0.1-3

[jamesdalg]

Fixed as of v.2.2.6 by disabling globalVariables() calls and rewriting the namespace. There still remains the issue of getting this to pass CRAN, but the package version of the app works!

[jamesdalg]

Closing this issue as the app works within the package using an install from devtools::install("jamesdalg/CNVScope"). It may take some additional work to modify scoping to be CRAN friendly.

[jamesdalg]

As of 2.5.9, this is completely fixed.