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can not install the SpatialExperiment in R 4.1.3 #162

@honghh2018

Description

@honghh2018

Hi developer,

In my centos7.9 platform
the package SpatialExperiment can not be install with below error:
the libxml2 and the ImageMagick-7.1.1-29 was build myself and set the env in shell
but still getting below error

Content type 'application/octet-stream' length 2395926 bytes (2.3 MB)

downloaded 2.3 MB

  • installing source package ‘SpatialExperiment’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in dyn.load(file, DLLpath = DLLpath, ...) :
    unable to load shared object '/share/apps/R/R-4.1.2-4/lib64/R/library/magick/libs/magick.so':
    /share/apps/syssoft/ImageMagick-7.1.1-29_update/lib/libMagickCore-7.Q16HDRI.so.10: symbol xmlNanoFTPInit, version LIBXML2_2.4.30 not defined in file libxml2.so.2 with link time reference
    Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
    Execution halted

    the R session

    sessionInfo()
    R version 4.1.2 (2021-11-01)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /share/apps/R/R-4.1.2-4/lib64/R/lib/libRblas.so
LAPACK: /share/apps/R/R-4.1.2-4/lib64/R/lib/libRlapack.so

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

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

other attached packages:
[1] miloR_1.2.0 edgeR_3.36.0 limma_3.50.3
[4] BiocParallel_1.28.3

loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.62.0
[3] fs_1.5.2 usethis_2.1.6
[5] devtools_2.4.3 RColorBrewer_1.1-3
[7] rprojroot_2.0.3 GenomeInfoDb_1.30.1
[9] tools_4.1.2 irlba_2.3.5
[11] utf8_1.2.2 R6_2.5.1
[13] vipor_0.4.5 BiocGenerics_0.40.0
[15] colorspace_2.0-3 withr_2.5.0
[17] tidyselect_1.2.1 gridExtra_2.3
[19] prettyunits_1.1.1 processx_3.8.0
[21] curl_5.2.1 compiler_4.1.2
[23] cli_3.6.1 Biobase_2.54.0
[25] BiocNeighbors_1.12.0 desc_1.4.1
[27] DelayedArray_0.20.0 scales_1.3.0
[29] callr_3.7.3 stringr_1.5.1
[31] digest_0.6.29 XVector_0.34.0
[33] pkgconfig_2.0.3 sessioninfo_1.2.2
[35] MatrixGenerics_1.6.0 fastmap_1.1.1
[37] rlang_1.1.4 generics_0.1.3
[39] farver_2.1.0 gtools_3.9.2.2
[41] dplyr_1.1.4 BiocSingular_1.10.0
[43] RCurl_1.98-1.14 magrittr_2.0.3
[45] GenomeInfoDbData_1.2.7 patchwork_1.2.0
[47] Matrix_1.5-3 ggbeeswarm_0.6.0
[49] Rcpp_1.0.12 munsell_0.5.0
[51] S4Vectors_0.32.4 fansi_1.0.3
[53] viridis_0.6.2 lifecycle_1.0.4
[55] stringi_1.7.6 ggraph_2.1.0
[57] MASS_7.3-57 SummarizedExperiment_1.24.0
[59] zlibbioc_1.40.0 brio_1.1.3
[61] pkgbuild_1.3.1 grid_4.1.2
[63] parallel_4.1.2 ggrepel_0.9.1
[65] crayon_1.5.1 lattice_0.20-45
[67] cowplot_1.1.1 beachmat_2.10.0
[69] graphlayouts_0.8.0 locfit_1.5-9.5
[71] ps_1.7.0 pillar_1.9.0
[73] igraph_2.0.3 GenomicRanges_1.46.1
[75] ScaledMatrix_1.2.0 stats4_4.1.2
[77] pkgload_1.2.4 glue_1.6.2
[79] remotes_2.4.2 BiocManager_1.30.20
[81] vctrs_0.6.4 tweenr_1.0.2
[83] testthat_3.1.4 gtable_0.3.0
[85] purrr_1.0.2 polyclip_1.10-0
[87] tidyr_1.2.0 cachem_1.0.6
[89] ggplot2_3.5.0 ggforce_0.3.3
[91] rsvd_1.0.5 tidygraph_1.2.1
[93] viridisLite_0.4.0 SingleCellExperiment_1.16.0
[95] tibble_3.2.1 beeswarm_0.4.0
[97] memoise_2.0.1 IRanges_2.28.0
[99] ellipsis_0.3.2

how to fix this error?
any advice would be appreciated
Best
hanhuihong

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