run aborts at generate at generateReport step with Error in dev.control()

[JuHey]

After updating ARMOR package, tested new ARMOR install with example dataset on high-performance cluster. slurm-output shows: `

Rout shows:

`
What versions of grSoft and cairo does ARMOR require?

With best wishes and many thanks!

[csoneson]

Hi @JuHey, thanks for your report - could you provide a bit more details? Which version of ARMOR are you using, and have you run a previous version successfully? What settings are you using for the required software (especially R) - it looks like you are using the system installation. Are you able to generate and save plots independently of ARMOR with this R version? It seems to me that there is a missing or incompatible system library (libtiff).

[JuHey]

Hi @csoneson, many thanks for taking this on. Regarding your questions: I installed ARMOR 1.5.10 (2024-09-21) and had used previous version without issues. R is 4.2.2. Yes, I am using the system installation. Packages:
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] rmarkdown_2.29 msigdbr_7.5.1
[3] tximeta_1.24.0 SingleCellExperiment_1.28.1
[5] SummarizedExperiment_1.36.0 Biobase_2.66.0
[7] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
[9] IRanges_2.40.1 MatrixGenerics_1.18.1
[11] matrixStats_1.5.0 DRIMSeq_1.34.0
[13] S4Vectors_0.44.0 BiocGenerics_0.52.0
[15] edgeR_4.4.2 limma_3.62.2
[17] remotes_2.5.0 tidyr_1.3.1
[19] ggplot2_3.5.1 dplyr_1.1.4

loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 httr2_1.1.0
[4] biomaRt_2.62.1 rlang_1.1.5 magrittr_2.0.3
[7] compiler_4.4.2 RSQLite_2.3.9 GenomicFeatures_1.58.0
[10] png_0.1-8 vctrs_0.6.5 reshape2_1.4.4
[13] txdbmaker_1.2.1 stringr_1.5.1 ProtGenerics_1.38.0
[16] pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[19] dbplyr_2.5.0 XVector_0.46.0 Rsamtools_2.22.0
[22] UCSC.utils_1.2.0 purrr_1.0.4 bit_4.5.0.1
[25] xfun_0.51 zlibbioc_1.52.0 cachem_1.1.0
[28] jsonlite_1.9.0 progress_1.2.3 blob_1.2.4
[31] DelayedArray_0.32.0 BiocParallel_1.40.0 parallel_4.4.2
[34] prettyunits_1.2.0 R6_2.6.1 stringi_1.8.4
[37] rtracklayer_1.66.0 knitr_1.49 Rcpp_1.0.14
[40] Matrix_1.5-4.1 tidyselect_1.2.1 abind_1.4-8
[43] yaml_2.3.10 codetools_0.2-20 curl_6.2.1
[46] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9
[49] withr_3.0.2 KEGGREST_1.46.0 evaluate_1.0.3
[52] BiocFileCache_2.14.0 xml2_1.3.6 Biostrings_2.74.1
[55] pillar_1.10.1 BiocManager_1.30.25 filelock_1.0.3
[58] generics_0.1.3 RCurl_1.98-1.16 BiocVersion_3.20.0
[61] ensembldb_2.30.0 hms_1.1.3 munsell_0.5.1
[64] scales_1.3.0 glue_1.8.0 lazyeval_0.2.2
[67] tools_4.4.2 AnnotationHub_3.14.0 BiocIO_1.16.0
[70] locfit_1.5-9.11 GenomicAlignments_1.42.0 babelgene_22.9
[73] XML_3.99-0.18 grid_4.4.2 AnnotationDbi_1.68.0
[76] colorspace_2.1-1 GenomeInfoDbData_1.2.13 restfulr_0.0.15
[79] cli_3.6.4 rappdirs_0.3.3 S4Arrays_1.6.0
[82] AnnotationFilter_1.30.0 gtable_0.3.6 digest_0.6.37
[85] tximport_1.34.0 SparseArray_1.6.1 rjson_0.2.23
[88] htmltools_0.5.8.1 memoise_2.0.1 lifecycle_1.0.4
[91] httr_1.4.7 statmod_1.5.0 bit64_4.6.0-1 pandoc 2.18

From R/4.2.2, I tested:

> data(mtcars)
> pdf("my_plot.pdf")
> plot(mtcars$mpg, mtcars$wt, main = "Miles per Gallon vs. Weight", xlab = "Miles per Gallon", ylab = "Weight") 
> dev.off()
null device 

Plot generated fine.

I will pass the information regarding the system library (libtiff) on to our HPC managers.

Many thanks again!

[csoneson]

Thanks for the update - let me know how it goes (could you also try to generate a png file with your example plot - that's what the report generation above will try to do).

[JuHey]

I could generate the png file just fine. Will explore further. Many thanks.