Issue with devtools::document() after updating to R 4.4.3 on macOS (M1/16GB)

[liubingdong]

Hi all,

After upgrading to R 4.4.3, I encountered an issue when running devtools::document() during package development.

devtools::document()
ℹ Updating EasyMultiProfiler documentation
Error: vector memory limit of 16.0 Gb reached, see mem.maxVSize()

sessionInfo()
R version 4.4.3 (2025-02-28)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.3.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] EasyMultiProfiler_0.2.8

loaded via a namespace (and not attached):
[1] fs_1.6.5 matrixStats_1.5.0 enrichplot_1.26.6
[4] devtools_2.4.5 httr_1.4.7 RColorBrewer_1.1-3
[7] doParallel_1.0.17 dynamicTreeCut_1.63-1 profvis_0.4.0
[10] tools_4.4.3 backports_1.5.0 utf8_1.2.4
[13] vegan_2.6-10 R6_2.5.1 mgcv_1.9-1
[16] lazyeval_0.2.2 permute_0.9-7 jomo_2.7-6
[19] rhdf5filters_1.18.0 urlchecker_1.0.1 withr_3.0.2
[22] gridExtra_2.3 preprocessCore_1.68.0 fdrtool_1.2.18
[25] qgraph_1.9.8 WGCNA_1.73 cli_3.6.3
[28] Biobase_2.66.0 labeling_0.4.3 nnls_1.6
[31] mvtnorm_1.3-3 readr_2.1.5 randomForest_4.7-1.2
[34] proxy_0.4-27 pbapply_1.7-2 pbivnorm_0.6.0
[37] systemfonts_1.2.1 yulab.utils_0.2.0 gson_0.1.0
[40] foreign_0.8-88 DOSE_4.0.0 R.utils_2.12.3
[43] sessioninfo_1.2.2 plotrix_3.8-4 rstudioapi_0.17.1
[46] impute_1.80.0 RSQLite_2.3.9 generics_0.1.3
[49] gridGraphics_0.5-1 shape_1.4.6.1 gtools_3.9.5
[52] dplyr_1.1.4 GO.db_3.20.0 Matrix_1.7-2
[55] biomformat_1.34.0 S4Vectors_0.44.0 abind_1.4-8
[58] R.methodsS3_1.8.2 weights_1.0.4 infotheo_1.2.0.1
[61] lifecycle_1.0.4 SummarizedExperiment_1.36.0 rhdf5_2.50.2
[64] qvalue_2.38.0 SparseArray_1.6.1 grid_4.4.3
[67] lavaan_0.6-19 blob_1.2.4 promises_1.3.2
[70] gdata_3.0.1 crayon_1.5.3 mitml_0.4-5
[73] miniUI_0.1.1.1 ggtangle_0.0.6 lattice_0.22-6
[76] IsingSampler_0.2.3 cowplot_1.1.3 KEGGREST_1.46.0
[79] pillar_1.10.1 knitr_1.49 fgsea_1.32.0
[82] GenomicRanges_1.58.0 boot_1.3-31 pak_0.8.0.1
[85] xgboost_1.7.8.1 corpcor_1.6.10 bigstatsr_1.6.1
[88] codetools_0.2-20 fastmatch_1.1-6 pan_1.9
[91] bigassertr_0.1.6 glue_1.8.0 ggiraph_0.8.12
[94] ggfun_0.1.8 remotes_2.5.0 data.table_1.16.4
[97] MultiAssayExperiment_1.32.0 vctrs_0.6.5 png_0.1-8
[100] treeio_1.30.0 Rdpack_2.6.3 gtable_0.3.6
[103] cachem_1.1.0 xfun_0.50 mime_0.12
[106] rbibutils_2.3 S4Arrays_1.6.0 reformulas_0.4.0
[109] survival_3.8-3 iterators_1.0.14 ellipsis_0.3.2
[112] nlme_3.1-167 usethis_3.1.0 ggtree_3.14.0
[115] flock_0.7 bit64_4.6.0-1 GenomeInfoDb_1.42.3
[118] rpart_4.1.24 colorspace_2.1-1 BiocGenerics_0.52.0
[121] DBI_1.2.3 Hmisc_5.2-2 nnet_7.3-20
[124] mnormt_2.1.1 tidyselect_1.2.1 bit_4.5.0.1
[127] compiler_4.4.3 bigparallelr_0.3.2 glmnet_4.1-8
[130] htmlTable_2.4.3 NetworkToolbox_1.4.2 mice_3.17.0
[133] xml2_1.3.6 desc_1.4.3 plotly_4.10.4
[136] DelayedArray_0.32.0 checkmate_2.3.2 scales_1.3.0
[139] psych_2.5.3 quadprog_1.5-8 smacof_2.1-7
[142] stringr_1.5.1 digest_0.6.37 snowfall_1.84-6.3
[145] minqa_1.2.8 rmarkdown_2.29 XVector_0.46.0
[148] IsingFit_0.4 htmltools_0.5.8.1 pkgconfig_2.0.3
[151] jpeg_0.1-11 base64enc_0.1-3 missRanger_2.6.1
[154] lme4_1.1-37 MatrixGenerics_1.18.1 fastmap_1.2.0
[157] rlang_1.1.5 htmlwidgets_1.6.4 ggthemes_5.1.0
[160] UCSC.utils_1.2.0 shiny_1.10.0 farver_2.1.2
[163] jsonlite_1.8.9 BiocParallel_1.40.0 eigenmodel_1.11
[166] GOSemSim_2.32.0 R.oo_1.27.0 magrittr_2.0.3
[169] polynom_1.4-1 Formula_1.2-5 GenomeInfoDbData_1.2.13
[172] ggplotify_0.1.2 wordcloud_2.6 patchwork_1.3.0
[175] Rhdf5lib_1.28.0 munsell_0.5.1 Rcpp_1.0.14
[178] ape_5.8-1 networktools_1.6.0 stringi_1.8.4
[181] zlibbioc_1.52.0 MASS_7.3-64 pkgbuild_1.4.6
[184] plyr_1.8.9 parallel_4.4.3 ggrepel_0.9.6
[187] forcats_1.0.0 Biostrings_2.74.1 splines_4.4.3
[190] hms_1.1.3 Boruta_8.0.0 igraph_2.1.4
[193] uuid_1.2-1 fastcluster_1.2.6 ggsignif_0.6.4
[196] pkgload_1.4.0 reshape2_1.4.4 stats4_4.4.3
[199] ttservice_0.4.1 tidybulk_1.18.0 evaluate_1.0.3
[202] BiocManager_1.30.25 mgm_1.2-15 httpuv_1.6.15
[205] tzdb_0.4.0 bootnet_1.6 nloptr_2.2.1
[208] foreach_1.5.2 networkD3_0.4 tidyr_1.3.1
[211] purrr_1.0.2 ggplot2_3.5.1 xtable_1.8-4
[214] broom_1.0.7 e1071_1.7-16 tidytree_0.4.6
[217] roxygen2_7.3.2 later_1.4.1 viridisLite_0.4.2
[220] glasso_1.11 class_7.3-23 spsUtil_0.2.2
[223] snow_0.4-4 tibble_3.2.1 clusterProfiler_4.14.4
[226] aplot_0.2.4 memoise_2.0.1 AnnotationDbi_1.68.0
[229] ellipse_0.5.0 IRanges_2.40.1 cluster_2.1.8
[232] rmio_0.4.0

[r2evans]

Not a dev, but some thoughts:

• check any/all @examples blocks in case some are running when they shouldn't, consider \dontrun{..}
• is there a .RData file in the package?
• any code in ./R/*.R that is an immediate-run, i.e., not within function(..) {...}? I have some patches in function files wrapped in if (FALSE) { ... } as useful scratch-code specific to that one file, so that building the package doesn't evaluate it

[liubingdong]

Thank you for your suggestion. After updating RStudio, the issue has been significantly mitigated, though it still occurs occasionally. I'm not entirely clear about the underlying resolution mechanism.

Not a dev, but some thoughts:

• check any/all @examples blocks in case some are running when they shouldn't, consider \dontrun{..}
• is there a .RData file in the package?
• any code in ./R/*.R that is an immediate-run, i.e., not within function(..) {...}? I have some patches in function files wrapped in if (FALSE) { ... } as useful scratch-code specific to that one file, so that building the package doesn't evaluate it
  Thank you for your suggestion. After updating RStudio, the issue has been significantly mitigated, though it still occurs occasionally. I'm not entirely clear about the underlying resolution mechanism.