When I was trying to save volcano plot in pdf format, error popped up: "Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
Metric information not available for this family/device".
I checked fonts that I intalled on my Centos 7 HPC with other server that can generate volcano plot in pdf normally, did not find fonts that missed in my server.
Below is my sessionInfo:
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0
When I was trying to save volcano plot in pdf format, error popped up: "Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : Metric information not available for this family/device". I checked fonts that I intalled on my Centos 7 HPC with other server that can generate volcano plot in pdf normally, did not find fonts that missed in my server.
Below is my sessionInfo: R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /usr/lib64/R/lib/libRblas.so LAPACK: /usr/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0
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
time zone: Asia/Shanghai tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] extrafont_0.19 EnhancedVolcano_1.18.0 ggrepel_0.9.3
[4] ggplot2_3.4.3
loaded via a namespace (and not attached): [1] vctrs_0.6.3 cli_3.6.1 rlang_1.1.1 Rttf2pt1_1.3.12
[5] generics_0.1.3 textshaping_0.3.6 glue_1.6.2 labeling_0.4.3
[9] colorspace_2.1-0 extrafontdb_1.0 ragg_1.2.5 scales_1.2.1
[13] fansi_1.0.4 grid_4.3.1 munsell_0.5.0 tibble_3.2.1
[17] lifecycle_1.0.3 compiler_4.3.1 dplyr_1.1.3 Rcpp_1.0.11
[21] pkgconfig_2.0.3 systemfonts_1.0.4 farver_2.1.1 R6_2.5.1
[25] tidyselect_1.2.0 utf8_1.2.3 pillar_1.9.0 magrittr_2.0.3
[29] tools_4.3.1 withr_2.5.0 gtable_0.3.4
And below are the fonts that I loaded from system: [1] "Abyssinica SIL" "AR PL SungtiL GB" "Caladea"
[4] "Carlito" "David CLM" "DejaVu Sans"
[7] "DejaVu Sans Light" "DejaVu Sans Condensed" "DejaVu Sans Mono"
[10] "DejaVu Serif" "DejaVu Serif Condensed" "FontAwesome"
[13] "Frank Ruehl CLM" "FreeMono" "FreeSans"
[16] "FreeSerif" "AR PL KaitiM GB" "Hadasim CLM"
[19] "Jomolhari" "Khmer OS" "Khmer OS Content"
[22] "Khmer OS System" "Liberation Mono" "Liberation Sans"
[25] "Liberation Serif" "LKLUG" "Lohit Assamese"
[28] "Lohit Bengali" "Lohit Devanagari" "Lohit Gujarati"
[31] "Lohit Kannada" "Lohit Malayalam" "Lohit Marathi"
[34] "Lohit Nepali" "Lohit Oriya" "Lohit Punjabi"
[37] "Lohit Tamil" "Lohit Telugu" "Madan2"
[40] "Meera" "Miriam CLM" "Miriam Mono CLM"
[43] "NanumGothic" "NanumGothicExtraBold" "Noto Emoji"
[46] "Nuosu SIL" "Open Sans" "Open Sans Extrabold"
[49] "Open Sans Light" "Open Sans Semibold" "OpenSymbol"
[52] "Overpass" "Padauk" "PT Sans"
[55] "PT Sans Narrow" "Simple CLM" "Stam Ashkenaz CLM"
[58] "Stam Sefarad CLM" "VL Gothic" "Waree"
[61] "ZYSong18030" "Andale Mono" "Arial Black"
[64] "Arial" "Comic Sans MS" "Courier New"
[67] "Georgia" "Impact" "Tahoma"
[70] "Times New Roman" "Trebuchet MS" "Verdana"
[73] "Webdings"
Have no clue on this one. Any help would be appreciated.