memory not mapped issue specific to a certain file

[danfulop]

[originally posted by Tara]

TODO: fix bug in monkey that seems specific to this example/files
/data/projects/hn-883-hiroko-nobuta-rnaseq-hg19-aug-17/X.logs/hn_883_hiroko_nobuta_rnaseq_hg19_aug_17_second_set__s51b_sum__all.e73447

*** caught segfault ***
address 0x7ff7b10c4028, cause 'memory not mapped'

Traceback:
1: cor(t(mat))
2: as.dist(1 - cor(t(mat)))
3: cluster_mat(mat, distance = clustering_distance_rows, method = clustering_method)
4: pheatmap::pheatmap(mat, width = HEATMAP_WIDTH, height = HEATMAP_HEIGHT, annotation_col = annot.df, scale = "row", clustering_distance_rows = "correlation", clustering_distance_cols = "correlation", clustering_method = "complete", cluster_rows = TRUE, cluster_cols = TRUE, show_colnames = T, show_rownames = T, display_numbers = FALSE, border_color = "#00000000", main = paste("Top ", nrow(mat), " highest-variance genes, row-scaled. Clust dist is pearson corr", sep = ""), fontsize_row = 3.5)
5: agw_do_pca(mmm = expressed.genes.mat, uniquePrefix = paste0("--D-all_genes_with_count_above_", MIN_READS_FOR_EXPR), ntop_most_interesting_genes = 999999, additional_main = paste0(" with at least ", MIN_READS_FOR_EXPR, " reads."))
An irrecoverable exception occurred. R is aborting now ...
-bash: line 1: 38675 Segmentation fault /var/spool/PBS/mom_priv/jobs/73447.rigel-uv2k.SC