heatmaply
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Published
20 hours ago •
talgalili
talgalili
Warnings when using heatmaply
Describe the bug
Warnings when using heatmaply.
To Reproduce
I ran:
library(heatmaply)
heatmaply(mtcars)
I got:
> heatmaply(mtcars)
Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libfontconfig.1.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
Reason: Incompatible library version: R_X11.so requires version 11.0.0 or later, but libfontconfig.1.dylib provides version 10.0.0
2: 'heatmap' objects don't have these attributes: 'showlegend'
Valid attributes include:
'type', 'visible', 'opacity', 'name', 'uid', 'ids', 'customdata', 'meta', 'hoverinfo', 'hoverlabel', 'stream', 'transforms', 'uirevision', 'z', 'x', 'x0', 'dx', 'y', 'y0', 'dy', 'text', 'hovertext', 'transpose', 'xtype', 'ytype', 'zsmooth', 'connectgaps', 'xgap', 'ygap', 'zhoverformat', 'hovertemplate', 'zauto', 'zmin', 'zmax', 'zmid', 'colorscale', 'autocolorscale', 'reversescale', 'showscale', 'colorbar', 'coloraxis', 'xcalendar', 'ycalendar', 'xaxis', 'yaxis', 'idssrc', 'customdatasrc', 'metasrc', 'hoverinfosrc', 'zsrc', 'xsrc', 'ysrc', 'textsrc', 'hovertextsrc', 'hovertemplatesrc', 'key', 'set', 'frame', 'transforms', '_isNestedKey', '_isSimpleKey', '_isGraticule', '_bbox'
Additional context
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] heatmaply_1.0.0 viridis_0.5.1 viridisLite_0.3.0 plotly_4.9.1 ggplot2_3.2.0
loaded via a namespace (and not attached):
[1] gtools_3.8.1 tidyselect_0.2.5 purrr_0.3.3 reshape2_1.4.3
[5] colorspace_1.4-1 vctrs_0.2.0 htmltools_0.4.0 yaml_2.2.0
[9] rlang_0.4.1 later_1.0.0 pillar_1.4.2 glue_1.3.1
[13] withr_2.1.2 RColorBrewer_1.1-2 registry_0.5-1 foreach_1.4.7
[17] lifecycle_0.1.0 plyr_1.8.4 stringr_1.4.0 munsell_0.5.0
[21] gtable_0.3.0 htmlwidgets_1.5.1 caTools_1.17.1.2 codetools_0.2-16
[25] labeling_0.3 fastmap_1.0.1 httpuv_1.5.2 crosstalk_1.0.0
[29] Cairo_1.5-10 seriation_1.2-8 Rcpp_1.0.2 xtable_1.8-4
[33] KernSmooth_2.23-15 promises_1.1.0 backports_1.1.4 scales_1.0.0
[37] gdata_2.18.0 webshot_0.5.2 jsonlite_1.6 mime_0.7
[41] gplots_3.0.1.1 gridExtra_2.3 digest_0.6.20 stringi_1.4.3
[45] gclus_1.3.2 shiny_1.4.0 dplyr_0.8.3 grid_3.6.1
[49] tools_3.6.1 bitops_1.0-6 magrittr_1.5 lazyeval_0.2.2
[53] tibble_2.1.3 cluster_2.1.0 crayon_1.3.4 tidyr_1.0.0
[57] pkgconfig_2.0.2 zeallot_0.1.0 dendextend_1.13.0 MASS_7.3-51.4
[61] data.table_1.12.6 assertthat_0.2.1 httr_1.4.0 rstudioapi_0.10
[65] iterators_1.0.12 R6_2.4.0 TSP_1.1-7 compiler_3.6.1
Warning 1 I have no idea, I think that's specific to your R installation. Try updating libfontconfig. I've seen lots of colleagues on mac having issues loading shared objs recently. This repo might help https://github.com/rmacoslib/r-macos-rtools
Second issue is from plotly, I've flagged it there https://github.com/ropensci/plotly/issues/1670
I can still reproduce this warning.
library("heatmaply")
heatmaply(mtcars)
Also appears in Linux (mint)
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.2
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_IL.UTF-8 LC_NUMERIC=C LC_TIME=en_IL.UTF-8
[4] LC_COLLATE=en_IL.UTF-8 LC_MONETARY=en_IL.UTF-8 LC_MESSAGES=en_IL.UTF-8
[7] LC_PAPER=en_IL.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IL.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] heatmaply_1.1.2 viridis_0.5.1 viridisLite_0.3.0 plotly_4.9.1 ggplot2_3.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 tidyr_1.0.0 gtools_3.8.1 assertthat_0.2.1 digest_0.6.23
[6] foreach_1.4.7 mime_0.7 R6_2.4.1 plyr_1.8.5 evaluate_0.14
[11] httr_1.4.1 pillar_1.4.2 gplots_3.1.0 rlang_0.4.6 lazyeval_0.2.2
[16] rstudioapi_0.11 data.table_1.12.8 rmarkdown_1.18 labeling_0.3 webshot_0.5.2
[21] stringr_1.4.0 htmlwidgets_1.5.1 munsell_0.5.0 shiny_1.4.0 compiler_3.6.3
[26] httpuv_1.5.2 xfun_0.16 pkgconfig_2.0.3 htmltools_0.4.0 tidyselect_0.2.5
[31] tibble_2.1.3 gridExtra_2.3 seriation_1.2-8 codetools_0.2-16 dendextend_1.14.0
[36] crayon_1.3.4 dplyr_0.8.3 withr_2.1.2 later_1.0.0 MASS_7.3-53
[41] bitops_1.0-6 grid_3.6.3 jsonlite_1.7.0 xtable_1.8-4 gtable_0.3.0
[46] lifecycle_0.1.0 registry_0.5-1 magrittr_1.5 scales_1.1.0 KernSmooth_2.23-17
[51] stringi_1.4.3 farver_2.0.1 reshape2_1.4.3 promises_1.1.0 vctrs_0.3.1
[56] RColorBrewer_1.1-2 iterators_1.0.12 tools_3.6.3 glue_1.3.1 purrr_0.3.3
[61] gclus_1.3.2 crosstalk_1.0.0 fastmap_1.0.1 yaml_2.2.0 colorspace_1.4-1
[66] cluster_2.1.0 caTools_1.18.0 TSP_1.1-8 knitr_1.26
I see you've reported it here: https://github.com/ropensci/plotly/issues/1670
I'll ping there again as well.