Errors running STUtility via linux (imagemagick)

[sunnyzwu]

Hi guys, great work on the package. I am just having issues running STUtility via linux on the cluster/HPC. Its been working nicely on my local Rstudio, but I have needed to move to the cluster for processing larger numbers of dataset. STUtility installed without error (though fell down a large dependency hellhole installing through conda), but i see the following error message when trying to plot the relevant data. These errors do not occur when running on my local desktop Rstudio. I believe its related to imagemagick and image rendering?

Ive attached relevant warning/error messages, and my conda/R environment. Any help would be appreciated !

Cheers, Sunny

This is the main error I see when trying to generate any ggplot object using STUtility, e.g. via FeatureOverlay.

Error in magick_image_annotate(image, text, gravity, location, degrees, : R: non-conforming drawing primitive definition `text' @ error/draw.c/RenderMVGContent/4434

This is the output when loading STutility

library(STutility) Loading required package: Seurat Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

expand.grid

Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

aperm, apply, rowsum

Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:Seurat':

Assays

Loading required package: ggplot2 Registered S3 method overwritten by 'imager': method from plot.imlist Registered S3 method overwritten by 'spdep': method from plot.mst ape Warning messages: 1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display 2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.`

This is the output when loading magick

library(magick) Linking to ImageMagick 7.0.10.10 Enabled features: cairo, fontconfig, freetype, fftw, pango, rsvg, webp, x11 Disabled features: ghostscript, lcms

Rsession info

sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS release 6.10 (Final)

Matrix products: default BLAS/LAPACK: /share/ClusterShare/software/contrib/CTP_single_cell/tools/anaco nda2/envs/r_env/lib/libopenblasp-r0.3.7.so

locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

other attached packages: [1] Matrix_1.2-18 RColorBrewer_1.1-2 [3] magrittr_1.5 zeallot_0.1.0 [5] dplyr_0.8.5 magick_2.3 [7] STutility_0.1.0 ggplot2_3.3.0 [9] SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1 [11] DelayedArray_0.12.3 BiocParallel_1.20.1 [13] matrixStats_0.56.0 Biobase_2.46.0 [15] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 [17] IRanges_2.20.2 S4Vectors_0.24.4 [19] BiocGenerics_0.32.0 Seurat_3.1.4.9904

loaded via a namespace (and not attached): [1] uuid_0.1-2 systemfonts_0.2.1 plyr_1.8.6 [4] igraph_1.2.5 lazyeval_0.2.2 sp_1.4-1 [7] splines_3.6.3 crosstalk_1.1.0.1 listenv_0.8.0 [10] digest_0.6.25 foreach_1.4.4 htmltools_0.4.0 [13] viridis_0.5.1 tiff_0.1-5 gdata_2.18.0 [16] tensor_1.5 cluster_2.1.0 doParallel_1.0.15 [19] ROCR_1.0-11 globals_0.12.5 gmodels_2.18.1 [22] jpeg_0.1-8.1 colorspace_1.4-1 rappdirs_0.3.1 [25] ggrepel_0.8.2 xfun_0.6 crayon_1.3.4 [28] RCurl_1.98-1.2 jsonlite_1.6.1 spatstat_1.63-3 [31] spatstat.data_1.4-3 survival_3.1-12 zoo_1.8-8 [34] iterators_1.0.10 ape_5.3 glue_1.4.0 [37] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.32.0 [40] XVector_0.26.0 webshot_0.5.2 leiden_0.3.3 [43] future.apply_1.5.0 abind_1.4-5 scales_1.1.0 [46] DBI_1.1.0 miniUI_0.1.1.1 Rcpp_1.0.4.6 [49] spData_0.3.5 viridisLite_0.3.0 xtable_1.8-4 [52] units_0.6-6 reticulate_1.15 spdep_1.1-3 [55] rsvd_1.0.3 akima_0.6-2 tsne_0.1-3 [58] htmlwidgets_1.5.1 httr_1.4.1 ellipsis_0.3.0 [61] ica_1.0-2 pkgconfig_2.0.3 uwot_0.1.8 [64] deldir_0.1-25 tidyselect_1.0.0 rlang_0.4.6 [67] manipulateWidget_0.10.1 reshape2_1.4.4 later_1.0.0 [70] munsell_0.5.0 tools_3.6.3 dbscan_1.1-5 [73] ggridges_0.5.2 stringr_1.4.0 fastmap_1.0.1 [76] goftest_1.2-2 npsurv_0.4-0.1 knitr_1.22 [79] fitdistrplus_1.0-14 rgl_0.100.54 purrr_0.3.4 [82] RANN_2.6.1 readbitmap_0.1.5 pbapply_1.4-2 [85] future_1.17.0 nlme_3.1-147 mime_0.9 [88] ggiraph_0.7.0 xml2_1.2.0 compiler_3.6.3 [91] plotly_4.9.2.1 png_0.1-7 e1071_1.7-3 [94] lsei_1.2-0.1 spatstat.utils_1.17-0 Morpho_2.8 [97] tibble_3.0.1 stringi_1.4.6 gdtools_0.2.2 [100] lattice_0.20-41 classInt_0.4-3 shinyjs_1.1 [103] vctrs_0.2.4 LearnBayes_2.15.1 pillar_1.4.4 [106] lifecycle_0.2.0 lmtest_0.9-37 RcppAnnoy_0.0.16 [109] data.table_1.12.8 cowplot_1.0.0 bitops_1.0-6 [112] irlba_2.3.3 Rvcg_0.19.1 raster_3.1-5 [115] httpuv_1.5.2 patchwork_1.0.0 colorRamps_2.3 [118] R6_2.4.1 imager_0.42.1 promises_1.1.0 [121] KernSmooth_2.23-17 gridExtra_2.3 bmp_0.3 [124] codetools_0.2-16 gtools_3.8.2 boot_1.3-20 [127] MASS_7.3-51.6 assertthat_0.2.1 withr_2.2.0 [130] sctransform_0.2.1 GenomeInfoDbData_1.2.2 expm_0.999-4 [133] mgcv_1.8-31 grid_3.6.3 rpart_4.1-15 [136] coda_0.19-3 class_7.3-15 tidyr_1.0.3 [139] Rtsne_0.15 sf_0.9-3 shiny_1.4.0.2

conda environment

(r_env) sunwu@dice01:sunwu$ conda list packages in environment at /share/ClusterShare/software/contrib/CTP_single_cell/tools/anaconda2/envs/r_env:

Name Version Build Channel _libgcc_mutex 0.1 main
_r-mutex 1.0.0 anacondar_1
attrs 19.3.0 py_0
backcall 0.1.0 py36_0
beautifulsoup4 4.9.0 py36h9f0ad1d_0 conda-forge binutils_impl_linux-64 2.33.1 he6710b0_7
binutils_linux-64 2.33.1 h9595d00_15
bleach 3.1.4 py_0
boost-cpp 1.72.0 h8e57a91_0 conda-forge brotlipy 0.7.0 py36h8c4c3a4_1000 conda-forge bwidget 1.9.11 1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge certifi 2020.4.5.1 py36h9f0ad1d_0 conda-forge cffi 1.14.0 py36hd463f26_0 conda-forge cfitsio 3.470 h3eac812_5 conda-forge cgal 5.0.1 py36h830a2c2_0 conda-forge cgal-cpp 5.0.1 h747953b_1 conda-forge chardet 3.0.4 py36h9f0ad1d_1006 conda-forge cmake 3.14.0 h52cb24c_0 anaconda conda 4.8.3 py36h9f0ad1d_1 conda-forge conda-build 3.19.2 py36h9f0ad1d_1 conda-forge conda-package-handling 1.6.1 py36h7b6447c_0
cryptography 2.9.2 py36h45558ae_0 conda-forge curl 7.69.1 h33f0ec9_0 conda-forge decorator 4.4.2 py_0
defusedxml 0.6.0 py_0
eigen 3.3.7 hc9558a2_1001 conda-forge entrypoints 0.3 py36_0
expat 2.2.9 he1b5a44_2 conda-forge ffmpeg 4.2 h167e202_0 conda-forge fftw 3.3.8 nompi_h7f3a6c3_1110 conda-forge filelock 3.0.12 py_0
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 2.001 hab24e00_0 conda-forge font-ttf-source-code-pro 2.030 hab24e00_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge fonts-conda-forge 1 0 conda-forge freeglut 3.0.0 hf484d3e_5 anaconda freetype 2.10.1 he06d7ca_0 conda-forge freexl 1.0.5 h14c3975_1002 conda-forge fribidi 1.0.5 h7b6447c_0
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_15
gdal 3.0.4 py36hd60729c_10 conda-forge gdk-pixbuf 2.38.2 h3f25603_3 conda-forge geos 3.8.1 he1b5a44_0 conda-forge geotiff 1.6.0 h05acad5_0 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge gfortran_impl_linux-64 7.3.0 hdf63c60_1
gfortran_linux-64 7.3.0 h553295d_15
ghostscript 9.22 hf484d3e_1001 conda-forge giflib 5.2.1 h516909a_2 conda-forge glfw 3.3.2 h516909a_1 conda-forge glib 2.63.1 h5a9c865_0
glib-networking-cos6-x86_64 2.28.6.1 0 anaconda glib2-cos6-x86_64 2.28.8 h1a821f5_0 anaconda glib2-devel-cos6-x86_64 2.28.8 hda010f4_0 anaconda glibmm 2.58.1 h2d0d12e_0 conda-forge glob2 0.7 py_0 conda-forge gmp 6.2.0 he1b5a44_2 conda-forge gnutls 3.6.5 hd3a4fd2_1002 conda-forge gobject-introspection 1.58.2 py36h6d43c07_1004 conda-forge graphite2 1.3.13 h23475e2_0
graphviz 2.42.3 h0511662_0 conda-forge gsl 2.6 h294904e_0 conda-forge gtest 1.10.0 hc9558a2_2 conda-forge gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_15
harfbuzz 2.4.0 h9f30f68_3 conda-forge hdf4 4.2.13 hf30be14_1003 conda-forge hdf5 1.10.6 nompi_h3c11f04_100 conda-forge icu 64.2 he1b5a44_1 conda-forge idna 2.9 py_1 conda-forge imagemagick 7.0.10_11 pl526h201ca68_0 conda-forge importlib_metadata 1.5.0 py36_0
ipykernel 5.1.4 py36h39e3cac_0
ipython 7.13.0 py36h5ca1d4c_0
ipython_genutils 0.2.0 py36_0
jbig 2.1 h516909a_2002 conda-forge jedi 0.17.0 py36_0
jinja2 2.11.2 py_0
jpeg 9c h14c3975_1001 conda-forge json-c 0.13.1 h14c3975_1001 conda-forge jsonschema 3.2.0 py36_0
jupyter_client 6.1.3 py_0
jupyter_core 4.6.3 py36_0
kealib 1.4.13 h33137a7_1 conda-forge krb5 1.17.1 h2fd8d38_0 conda-forge lame 3.100 h14c3975_1001 conda-forge lcms2 2.9 hbd6801e_1 conda-forge ld_impl_linux-64 2.33.1 h53a641e_7
libarchive 3.3.3 hc47fbbf_1007 conda-forge libblas 3.8.0 14_openblas conda-forge libcblas 3.8.0 14_openblas conda-forge libcroco 0.6.13 h8d621e5_1 conda-forge libcurl 7.69.1 hf7181ac_0 conda-forge libdap4 3.20.6 h1d1bd15_0 conda-forge libdrm 2.4.100 h516909a_0 conda-forge libdrm-cos6-x86_64 2.4.65 hd39d64f_0 anaconda libdrm-cos7-aarch64 2.4.91 h1341992_0 conda-forge libdrm-cos7-ppc64le 2.4.97 h1341992_0 conda-forge libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgc 7.4.2 1 tsnyder libgcc-ng 9.1.0 hdf63c60_0
libgdal 3.0.4 he6a97d6_10 conda-forge libgfortran-ng 7.3.0 hdf63c60_0
libglu 9.0.0 hf484d3e_1 anaconda libglvnd-glx-cos7-ppc64le 1.0.1 h1341992_0 conda-forge libiconv 1.15 h516909a_1006 conda-forge libkml 1.3.0 hb574062_1011 conda-forge liblapack 3.8.0 14_openblas conda-forge liblief 0.10.1 he6710b0_0
libnetcdf 4.7.4 nompi_h84807e1_104 conda-forge libopenblas 0.3.7 h5ec1e0e_6 conda-forge libpciaccess 0.16 h516909a_0 conda-forge libpng 1.6.37 hed695b0_1 conda-forge libpng-cos6-x86_64 1.2.49 0 anaconda libpng-devel-cos6-x86_64 1.2.49 0 anaconda libpq 12.2 h5513abc_1 conda-forge librsvg 2.48.4 h33a7fed_0 conda-forge libselinux-cos6-x86_64 2.0.94 hc7b3062_0 anaconda libselinux-cos7-aarch64 2.5 h1341992_0 conda-forge libsepol-cos6-x86_64 2.0.41 h6e2433f_0 anaconda libsigcpp 3.0.3 0 conda-forge libsodium 1.0.16 h1bed415_0
libsoup-cos6-x86_64 2.34.3 0 anaconda libsoup-devel-cos6-x86_64 2.34.3 0 anaconda libspatialite 4.3.0a h2482549_1038 conda-forge libssh2 1.8.2 h22169c7_2 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 hc7e4089_6 conda-forge libtool 2.4.6 h14c3975_1002 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libwebp 1.1.0 h56121f0_4 conda-forge libwebp-base 1.1.0 h516909a_3 conda-forge libx11-common-cos6-x86_64 1.6.4 h023ea50_0 anaconda libx11-cos6-x86_64 1.6.4 h64a1553_0 anaconda libx11-devel-cos6-x86_64 1.6.4 hb9851ce_0 anaconda libxcb 1.13 h1bed415_1 anaconda libxdamage-cos6-x86_64 1.1.3 h8e310ee_0 anaconda libxdamage-devel-cos6-x86_64 1.1.3 0 anaconda libxml2 2.9.10 hee79883_0 conda-forge libxxf86vm-cos6-x86_64 1.1.3 h3cd9653_0 anaconda lz4-c 1.8.3 he1b5a44_1001 conda-forge lzo 2.10 h14c3975_1000 conda-forge make 4.2.1 h1bed415_1
markupsafe 1.1.1 py36h7b6447c_0
mesa-dri-drivers-cos6-x86_64 11.0.7 h6ae8bd2_0
mesa-dri1-drivers-cos6-x86_64 7.11 hd08e721_0
mesa-libgbm-cos6-x86_64 11.0.7 0 anaconda mesa-libgl-cos6-x86_64 11.0.7 h045e36e_0 anaconda mesa-libgl-cos7-aarch64 18.0.5 h1341992_0 conda-forge mesa-libgl-cos7-ppc64le 18.3.4 h1341992_0 conda-forge mesa-libgl-devel-cos6-x86_64 11.0.7 h5a2c0ac_0 anaconda mesa-libgl-devel-cos7-aarch64 18.0.5 h1341992_0 conda-forge mesa-libgl-devel-cos7-ppc64le 18.3.4 h1341992_0 conda-forge mesa-libglapi-cos7-aarch64 18.0.5 h1341992_0 conda-forge mesa-libglapi-cos7-ppc64le 18.3.4 h1341992_0 conda-forge mesa-libglw-cos6-x86_64 6.5.1 0 hcc mesalib 18.3.1 h590aaf7_0 conda-forge mistune 0.8.4 py36h7b6447c_0
mpfr 4.0.2 he80fd80_1 conda-forge nbconvert 5.6.1 py36_0
nbformat 5.0.6 py_0
ncurses 6.2 he6710b0_1
nettle 3.4.1 h1bed415_1002 conda-forge notebook 6.0.3 py36_0
numpy 1.18.4 py36h7314795_0 conda-forge openh264 1.8.0 hdbcaa40_1000 conda-forge openjpeg 2.3.1 h981e76c_3 conda-forge openssl 1.1.1g h516909a_0 conda-forge pandoc 2.2.3.2 0
pandocfilters 1.4.2 py36_1
pango 1.42.4 ha030887_1 conda-forge parso 0.7.0 py_0
patchelf 0.10 he1b5a44_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h516909a_1006 conda-forge pexpect 4.8.0 py36_0
pickleshare 0.7.5 py36_0
pip 20.0.2 py36_3
pixman 0.38.0 h7b6447c_0
pixman-cos6-x86_64 0.32.8 h7062e45_0 anaconda pkg-config 0.29.2 h516909a_1006 conda-forge pkgconfig-cos6-x86_64 0.23 h07b4811_0 anaconda pkginfo 1.5.0.1 py_0 conda-forge poppler 0.87.0 h4190859_1 conda-forge poppler-data 0.4.9 1 conda-forge popt 1.16 h299ea2f_2002 conda-forge postgresql 12.2 h8573dbc_1 conda-forge potrace 1.11 ha92aebf_1 bioconda proj 7.0.0 h966b41f_3 conda-forge prometheus_client 0.7.1 py_0
prompt-toolkit 3.0.4 py_0
prompt_toolkit 3.0.4 0
psutil 5.7.0 py36h8c4c3a4_1 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge ptyprocess 0.6.0 py36_0
py-lief 0.10.1 py36h403a769_0
pycairo 1.19.1 py36h4779a57_3 conda-forge pycosat 0.6.3 py36h8c4c3a4_1004 conda-forge pycparser 2.20 py_0 conda-forge pygments 2.6.1 py_0
pyopengl 3.1.5 py_0 conda-forge pyopenssl 19.1.0 py_1 conda-forge pyrsistent 0.16.0 py36h7b6447c_0
pysocks 1.7.1 py36h9f0ad1d_1 conda-forge python 3.6.10 hcf32534_1
python-dateutil 2.8.1 py_0
python-igraph 0.8.2 py36h76676ee_0 conda-forge python-libarchive-c 2.9 py36_0 conda-forge python_abi 3.6 1_cp36m conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge pyyaml 5.3.1 py36h8c4c3a4_0 conda-forge pyzmq 17.1.2 py36h14c3975_0
r-ape 5.3 r36h51c796c_3 conda-forge r-askpass 1.0 r36h14c3975_0
r-assertthat 0.2.1 r36h6115d3f_0
r-backports 1.1.4 r36h96ca727_0
r-base 3.6.3 h316533a_2 conda-forge r-base64enc 0.1_3 r36h96ca727_4
r-bh 1.69.0_1 r36h6115d3f_0
r-boot 1.3_20 r36h6115d3f_0
r-broom 0.5.2 r36h6115d3f_0
r-cairo 1.5_10 r36h96ca727_0 r r-callr 3.2.0 r36h6115d3f_0
r-caret 6.0_83 r36h96ca727_0
r-cellranger 1.1.0 r36h6115d3f_0
r-class 7.3_15 r36h96ca727_0
r-cli 1.1.0 r36h6115d3f_0
r-clipr 0.6.0 r36h6115d3f_0
r-cluster 2.0.8 r36ha65eedd_0
r-codetools 0.2_16 r36h6115d3f_0
r-colorspace 1.4_1 r36h96ca727_0
r-crayon 1.3.4 r36h6115d3f_0
r-crosstalk 1.1.0.1 r36h6115d3f_1 conda-forge r-curl 3.3 r36h96ca727_0
r-data.table 1.12.2 r36h96ca727_0
r-dbi 1.0.0 r36h6115d3f_0
r-dbplyr 1.4.0 r36h6115d3f_0
r-dichromat 2.0_0 r36h6115d3f_4
r-digest 0.6.18 r36h96ca727_0
r-dplyr 0.8.0.1 r36h29659fb_0
r-ellipsis 0.1.0 r36h96ca727_0
r-essentials 3.6.0 r36_0
r-evaluate 0.13 r36h6115d3f_0
r-fansi 0.4.0 r36h96ca727_0
r-forcats 0.4.0 r36h6115d3f_0
r-foreach 1.4.4 r36h6115d3f_0
r-foreign 0.8_71 r36h96ca727_0
r-formatr 1.6 r36h6115d3f_0
r-fs 1.2.7 r36h29659fb_0
r-generics 0.0.2 r36h6115d3f_0
r-ggplot2 3.1.1 r36h6115d3f_0
r-glmnet 2.0_16 r36ha65eedd_0
r-glue 1.3.1 r36h96ca727_0
r-gower 0.2.0 r36h96ca727_0
r-gtable 0.3.0 r36h6115d3f_0
r-haven 2.1.0 r36h29659fb_0
r-hexbin 1.27.2 r36ha65eedd_0
r-highr 0.8 r36h6115d3f_0
r-hms 0.4.2 r36h6115d3f_0
r-htmltools 0.3.6 r36h29659fb_0
r-htmlwidgets 1.3 r36h6115d3f_0
r-httpuv 1.5.1 r36h29659fb_0
r-httr 1.4.0 r36h6115d3f_0
r-igraph 1.2.5 r36hd626d4e_1 conda-forge r-ipred 0.9_8 r36h96ca727_0
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[ludvigla]

Hi Sunny! Half a year too late, but still :-)

As you pointed out, this is probably an issue with imagemagick not working properly in your conda environment. However, the error message that you get comes from FeatureOverlay trying to draw a sample label in the top left corner of the image. You can simply disable this behavior by setting sample.label = FALSE.

[sunnyzwu]

Good tip, thanks Ludwig ! I'm now able to do my plots on the HPC without issues. Cheers, Sunny

[cchd0001]

Hi,

I fixed this non-conforming drawing primitive definition `text' bug by installing the latest version of ImageMagick from github.

Best wishes Lidong Guo