LTLA
commented
1 month ago Oops, missed this message; sorry for the late reply.
Anyway, it looks like your Linux installation doesn't have the -ldeflate system library. I'm not sure where this flag is coming from, I don't have it in alabaster.base's linker flags, nor is it added by Rhdf5lib. I'd guess that it's added by your R installation's top-level Makevars.site or your per-user Makevars.
You may have to talk to whoever maintains that R instance on your machine.
Hi, I am facing a problem trying to install celldex; especially in the installation of alabaster and its dependencies.
I have used code: BiocManager::install("celldex")
I get the following in my console:
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Installing package(s) 'celldex' also installing the dependencies 'alabaster.ranges', 'alabaster.base', 'alabaster.matrix', 'alabaster.se'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.ranges_1.4.2.tar.gz' Content type 'application/x-gzip' length 231086 bytes (225 KB)
downloaded 225 KB
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.base_1.4.2.tar.gz' Content type 'application/x-gzip' length 404596 bytes (395 KB)
downloaded 395 KB
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.matrix_1.4.2.tar.gz' Content type 'application/x-gzip' length 271995 bytes (265 KB)
downloaded 265 KB
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.se_1.4.1.tar.gz' Content type 'application/x-gzip' length 229971 bytes (224 KB)
downloaded 224 KB
trying URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/celldex_1.14.0.tar.gz' Content type 'application/x-gzip' length 412271 bytes (402 KB)
downloaded 402 KB
The downloaded source packages are in '/tmp/Rtmpitctbz/downloaded_packages' Installation paths not writeable, unable to update packages path: /rds/bear-apps/2023a/EL8-ice/software/arrow-R/14.0.1-foss-2023a-R-4.4.1 packages: arrow path: /rds/bear-apps/2023a/EL8-ice/software/R-bundle-Bioconductor/3.19-foss-2023a-R-4.4.1 packages: biomaRt, bookdown, ChIPpeakAnno, clusterProfiler, DOSE, edgeR, enrichplot, fresh, GEOmap, ggnewscale, IRanges, limma, metap, MSstats, MultiAssayExperiment, QFeatures, ResidualMatrix, S4Vectors, scater, txdbmaker, zellkonverter path: /rds/bear-apps/2023a/EL8-ice/software/R-bundle-CRAN/2024.06-foss-2023a packages: betareg, BIGL, bitops, bnlearn, checkmate, chk, clock, cNORM, collapse, colorspace, crul, cubature, CVXR, dbscan, DescTools, emmeans, Exact, fields, filehash, finalfit, fitdistrplus, fmri, foreign, future, gam, gbm, ggdag, grImport2, gt, gtsummary, hdf5r, htmlTable, ipred, jstable, lhs, lme4, longmemo, loo, lpSolveAPI, magick, matlab, mirt, mpath, mstate, multcomp, nloptr, openxlsx, pamr, parallelly, party, partykit, pbkrtest, pls, polyclip, posterior, prodlim, psych, QuickJSR, randomForestSRC, RcppArmadillo, RcppParallel, RcppRoll, RCurl, reactR, recipes, reprex, rgexf, rio, robustbase, RSpectra, s2, segmented, sensemakr, shadowtext, shinycssloaders, signal, slam, SparseM, spatstat, spatstat.explore, spatstat.geom, spatstat.linnet, spatstat.model, spatstat.random, StanHeaders, stars, subplex, swagger, TMB, TruncatedNormal, twang, ucminf, uuid, vioplot, wk, WriteXLS, xgboost, XML, yulab.utils path: /rds/bear-apps/2023a/EL8-ice/software/R/4.4.1-gfbf-2023a/lib64/R/library packages: bslib, gert, httr2, knitr, pkgdown, pkgload, ps, Rcpp, roxygen2, shiny, tinytex, usethis, withr, xfun, yaml Warning messages: 1: In install.packages(...) : installation of package 'alabaster.base' had non-zero exit status 2: In install.packages(...) : installation of package 'alabaster.ranges' had non-zero exit status 3: In install.packages(...) : installation of package 'alabaster.matrix' had non-zero exit status 4: In install.packages(...) : installation of package 'alabaster.se' had non-zero exit status 5: In install.packages(...) : installation of package 'celldex' had non-zero exit status
Matrix products: default BLAS/LAPACK: FlexiBLAS OPENBLAS; LAPACK version 3.11.0
locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London tzcode source: system (glibc)
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] ensembldb_2.28.0 ROCR_1.0-11 KernSmooth_2.23-24 fields_16.2
[5] viridisLite_0.4.2 spam_2.10-0 DoubletFinder_2.0.4 scDblFinder_1.18.0
[9] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 MatrixGenerics_1.16.0 matrixStats_1.3.0
[13] glmGamPoi_1.16.0 data.table_1.15.4 sctransform_0.4.1 AnnotationFilter_1.28.0
[17] GenomicFeatures_1.56.0 AnnotationDbi_1.66.0 Biobase_2.64.0 GenomicRanges_1.56.1
[21] GenomeInfoDb_1.40.1 IRanges_2.38.0 S4Vectors_0.42.0 AnnotationHub_3.12.0
[25] BiocFileCache_2.12.0 dbplyr_2.5.0 BiocGenerics_0.50.0 lubridate_1.9.3
[29] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.5
[33] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 patchwork_1.2.0
[37] tidyr_1.3.1 dplyr_1.1.4 Seurat_5.1.0 SeuratObject_5.0.2
[41] sp_2.1-4
loaded via a namespace (and not attached): [1] fs_1.6.4 ProtGenerics_1.36.0 spatstat.sparse_3.1-0 bitops_1.0-7
[5] devtools_2.4.5 httr_1.4.7 RColorBrewer_1.1-3 profvis_0.3.8
[9] tools_4.4.1 utf8_1.2.4 R6_2.5.1 lazyeval_0.2.2
[13] uwot_0.2.2 urlchecker_1.0.1 withr_3.0.0 gridExtra_2.3
[17] progressr_0.14.0 cli_3.6.3 spatstat.explore_3.2-7 fastDummies_1.7.3
[21] spatstat.data_3.1-2 ggridges_0.5.6 pbapply_1.7-2 Rsamtools_2.20.0
[25] scater_1.32.0 sessioninfo_1.2.2 parallelly_1.37.1 maps_3.4.2
[29] limma_3.60.3 rstudioapi_0.16.0 RSQLite_2.3.7 generics_0.1.3
[33] BiocIO_1.14.0 ica_1.0-3 spatstat.random_3.2-3 Matrix_1.7-0
[37] ggbeeswarm_0.7.2 fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4
[41] yaml_2.3.8 edgeR_4.2.0 SparseArray_1.4.8 Rtsne_0.17
[45] grid_4.4.1 blob_1.2.4 promises_1.3.0 dqrng_0.4.1
[49] crayon_1.5.3 miniUI_0.1.1.1 lattice_0.22-6 beachmat_2.20.0
[53] cowplot_1.1.3 KEGGREST_1.44.1 pillar_1.9.0 metapod_1.12.0
[57] rjson_0.2.21 xgboost_1.7.7.1 future.apply_1.11.2 codetools_0.2-20
[61] leiden_0.4.3.1 glue_1.7.0 remotes_2.5.0 vctrs_0.6.5
[65] png_0.1-8 gtable_0.3.5 cachem_1.1.0 S4Arrays_1.4.1
[69] mime_0.12 rsconnect_1.3.1 survival_3.7-0 statmod_1.5.0
[73] bluster_1.14.0 ellipsis_0.3.2 fitdistrplus_1.1-11 nlme_3.1-165
[77] usethis_2.2.3 bit64_4.0.5 filelock_1.0.3 RcppAnnoy_0.0.22
[81] irlba_2.3.5.1 vipor_0.4.7 colorspace_2.1-0 DBI_1.2.3
[85] processx_3.8.4 tidyselect_1.2.1 bit_4.0.5 compiler_4.4.1
[89] curl_5.2.1 BiocNeighbors_1.22.0 desc_1.4.3 DelayedArray_0.30.1
[93] plotly_4.10.4 rtracklayer_1.64.0 scales_1.3.0 lmtest_0.9-40
[97] callr_3.7.6 rappdirs_0.3.3 digest_0.6.36 goftest_1.2-3
[101] spatstat.utils_3.0-5 XVector_0.44.0 htmltools_0.5.8.1 pkgconfig_2.0.3
[105] sparseMatrixStats_1.16.0 fastmap_1.2.0 rlang_1.1.4 htmlwidgets_1.6.4
[109] UCSC.utils_1.0.0 shiny_1.8.1.1 DelayedMatrixStats_1.26.0 zoo_1.8-12
[113] jsonlite_1.8.8 BiocParallel_1.38.0 BiocSingular_1.20.0 RCurl_1.98-1.14
[117] magrittr_2.0.3 scuttle_1.14.0 GenomeInfoDbData_1.2.12 dotCall64_1.1-1
[121] munsell_0.5.1 Rcpp_1.0.13 viridis_0.6.5 reticulate_1.38.0
[125] stringi_1.8.4 zlibbioc_1.50.0 MASS_7.3-61 pkgbuild_1.4.4
[129] plyr_1.8.9 listenv_0.9.1 ggrepel_0.9.5 deldir_2.0-4
[133] Biostrings_2.72.1 splines_4.4.1 tensor_1.5 hms_1.1.3
[137] locfit_1.5-9.10 ps_1.7.6 igraph_2.0.3 spatstat.geom_3.2-9
[141] RcppHNSW_0.6.0 pkgload_1.3.4 reshape2_1.4.4 ScaledMatrix_1.12.0
[145] BiocVersion_3.19.1 XML_3.99-0.16.1 scran_1.32.0 BiocManager_1.30.23
[149] tzdb_0.4.0 httpuv_1.6.15 RANN_2.6.1 polyclip_1.10-6
[153] future_1.33.2 scattermore_1.2 rsvd_1.0.5 xtable_1.8-4
[157] restfulr_0.0.15 RSpectra_0.16-1 later_1.3.2 memoise_2.0.1
[161] beeswarm_0.4.0 GenomicAlignments_1.40.0 cluster_2.1.6 timechange_0.3.0
[165] globals_0.16.3