Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'L_currentViewport' not found

[kviljoen]

Hi Renaud,

I'm having an issue with the aheatmap() function (same issue both in RStudio or R from terminal) that seems to be linked to the base grid package (running Mac OSX Sierra).

The error is Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'L_currentViewport' not found

traceback() 8. get(name, envir = asNamespace(pkg), inherits = FALSE) 7. grid:::L_currentViewport at grid.R#36 6. grid.Call(grid:::L_currentViewport) at grid.R#43 5. current.viewport() at grid.R#51 4. f_current.vpPath() 3. current.vpPath_patched() 2. heatmap_motor(mat, border_color = border_color, cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, tree_col = tree_col, tree_row = tree_row, filename = filename, width = width, height = height, breaks = breaks, ... 1. aheatmap(otu_table(merged.F), main = main)

sessionInfo

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] gridExtra_2.3 dplyr_0.7.4 metagenomeSeq_1.18.0 RColorBrewer_1.1-2 glmnet_2.0-13 foreach_1.4.3
[7] Matrix_1.2-10 limma_3.32.7 epiR_0.9-87 survival_2.41-3 dunn.test_1.3.4 ROCR_1.0-7
[13] gplots_3.0.1 randomForest_4.6-12 fifer_1.1 MASS_7.3-47 matrixStats_0.52.2 psych_1.7.8
[19] corrplot_0.77 Rmisc_1.5 plyr_1.8.4 ggplot2_2.2.1 vegan_2.4-4 lattice_0.20-35
[25] permute_0.9-4 phyloseq_1.20.0 NMF_0.20.6 Biobase_2.36.2 BiocGenerics_0.22.0 cluster_2.0.6
[31] rngtools_1.2.4 pkgmaker_0.22 registry_0.3

loaded via a namespace (and not attached): [1] nlme_3.1-131 bitops_1.0-6 doParallel_1.0.11 tools_3.4.1 backports_1.1.1 R6_2.2.2
[7] rpart_4.1-11 KernSmooth_2.23-15 Hmisc_4.0-3 lazyeval_0.2.0 mgcv_1.8-17 colorspace_1.3-2
[13] ade4_1.7-8 nnet_7.3-12 mnormt_1.5-5 compiler_3.4.1 htmlTable_1.9 BiasedUrn_1.07
[19] sandwich_2.4-0 caTools_1.17.1 scales_0.5.0 checkmate_1.8.4 mvtnorm_1.0-6 stringr_1.2.0
[25] digest_0.6.12 foreign_0.8-69 XVector_0.16.0 base64enc_0.1-3 pkgconfig_2.0.1 htmltools_0.3.6
[31] plotrix_3.6-6 maps_3.2.0 htmlwidgets_0.9 rlang_0.1.2 bindr_0.1 zoo_1.8-0
[37] jsonlite_1.5 gtools_3.5.0 acepack_1.4.1 magrittr_1.5 modeltools_0.2-21 Formula_1.2-2
[43] dotCall64_0.9-04 biomformat_1.4.0 Rcpp_0.12.13 munsell_0.4.3 S4Vectors_0.14.5 ape_4.1
[49] stringi_1.1.5 multcomp_1.4-7 zlibbioc_1.22.0 rhdf5_2.20.0 grid_3.4.1 strucchange_1.5-1
[55] gdata_2.18.0 Biostrings_2.44.2 splines_3.4.1 multtest_2.32.0 knitr_1.17 igraph_1.1.2
[61] party_1.2-3 reshape2_1.4.2 codetools_0.2-15 stats4_3.4.1 glue_1.1.1 latticeExtra_0.6-28
[67] data.table_1.10.4 spam_2.1-1 gtable_0.2.0 assertthat_0.2.0 gridBase_0.4-7 coin_1.2-1
[73] xtable_1.8-2 randomForestSRC_2.5.0 tibble_1.3.4 iterators_1.0.8 IRanges_2.10.3 bindrcpp_0.2
[79] fields_9.0 TH.data_1.0-8

[renozao]

I believe this has been fixed in the devel branch:

devtools::install_github('renozao/NMF@devel')

Please let me know if you still get the error with this version.

[rkchance]

still getting this error with development version above

[kviljoen]

@renozao @rkchance the devel version works for me on R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

[renozao]

This should indeed be fixed in devel branch.

[Nyangahu]

Hi guys, am using the devel version of NMF but i keep getting this very error. Any thoughts why? R version 3.4.4 (2018-03-15) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

[renozao]

It also works for me on Ubuntu 16.04:

setting  value                       
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.423)

Installed version: renozao/NMF@ea3214d Are you testing within Rstudio, GUI or a terminal session?

[Nyangahu]

Running within R studio, Version 1.1.442