Import Error of clusterProfiler 4.6.2 on R 4.2.3 #811
Description
Dear authors,
I have installed the version 4.6.2 in a R 4.2.3 environment. There was no warning or error reported in installation. But after installation, when I try to use the package, I met the error that ggplot2 version was not compatible.
> library(clusterProfiler)
Registered S3 methods overwritten by 'treeio':
method from
MRCA.phylo tidytree
MRCA.treedata tidytree
Nnode.treedata tidytree
Ntip.treedata tidytree
ancestor.phylo tidytree
ancestor.treedata tidytree
child.phylo tidytree
child.treedata tidytree
full_join.phylo tidytree
full_join.treedata tidytree
groupClade.phylo tidytree
groupClade.treedata tidytree
groupOTU.phylo tidytree
groupOTU.treedata tidytree
is.rooted.treedata tidytree
nodeid.phylo tidytree
nodeid.treedata tidytree
nodelab.phylo tidytree
nodelab.treedata tidytree
offspring.phylo tidytree
offspring.treedata tidytree
parent.phylo tidytree
parent.treedata tidytree
root.treedata tidytree
rootnode.phylo tidytree
sibling.phylo tidytree
Error: package or namespace load failed for ‘clusterProfiler’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘ggplot2’ 3.5.2 is already loaded, but >= 4.0.0 is required
Other package version are like below:
> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.5 LTS
Matrix products: default
BLAS/LAPACK: /opt/conda/envs/r42/lib/libopenblasp-r0.3.30.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] nlme_3.1-165 bitops_1.0-7 fs_1.6.4
[4] ggtree_3.6.0 bit64_4.0.5 HDO.db_0.99.1
[7] RColorBrewer_1.1-3 httr_1.4.7 GenomeInfoDb_1.34.9
[10] tools_4.2.3 utf8_1.2.4 R6_2.5.1
[13] lazyeval_0.2.2 DBI_1.2.3 BiocGenerics_0.44.0
[16] withr_3.0.0 tidyselect_1.2.1 gridExtra_2.3
[19] bit_4.0.5 compiler_4.2.3 cli_3.6.3
[22] Biobase_2.58.0 scatterpie_0.2.6 scales_1.4.0
[25] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.36
[28] yulab.utils_0.2.4 DOSE_3.24.2 XVector_0.38.0
[31] pkgconfig_2.0.3 fastmap_1.2.0 rlang_1.1.7
[34] RSQLite_2.4.6 gridGraphics_0.5-1 farver_2.1.2
[37] generics_0.1.3 jsonlite_1.8.8 BiocParallel_1.32.6
[40] GOSemSim_2.24.0 dplyr_1.2.0 RCurl_1.98-1.17
[43] magrittr_2.0.3 ggplotify_0.1.2 GO.db_3.16.0
[46] GenomeInfoDbData_1.2.9 patchwork_1.2.0 Matrix_1.6-1.1
[49] Rcpp_1.1.1 S4Vectors_0.36.2 fansi_1.0.6
[52] ape_5.8 viridis_0.6.5 lifecycle_1.0.5
[55] stringi_1.8.7 ggraph_2.2.2 MASS_7.3-60.0.1
[58] zlibbioc_1.44.0 plyr_1.8.9 qvalue_2.30.0
[61] grid_4.2.3 blob_1.2.4 parallel_4.2.3
[64] ggrepel_0.9.5 crayon_1.5.3 lattice_0.22-6
[67] graphlayouts_1.2.3 Biostrings_2.66.0 cowplot_1.1.3
[70] splines_4.2.3 KEGGREST_1.38.0 pillar_1.9.0
[73] fgsea_1.24.0 igraph_2.0.3 reshape2_1.4.4
[76] codetools_0.2-20 stats4_4.2.3 fastmatch_1.1-8
[79] glue_1.7.0 ggfun_0.1.5 downloader_0.4.1
[82] data.table_1.15.4 treeio_1.22.0 png_0.1-8
[85] vctrs_0.7.1 tweenr_2.0.3 gtable_0.3.6
[88] purrr_1.0.2 polyclip_1.10-6 tidyr_1.3.1
[91] cachem_1.1.0 ggplot2_3.5.2 ggforce_0.5.0
[94] tidygraph_1.3.1 tidytree_0.4.6 viridisLite_0.4.2
[97] tibble_3.2.1 aplot_0.2.3 AnnotationDbi_1.60.2
[100] memoise_2.0.1 IRanges_2.32.0
My question is, how can I fix this problem? Or is there any other version that can replace? I cann't find any path to download previous releases.
Bests.