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CityUHK-CompBio / HTSanalyzeR2

HTSanalyzeR2: A R package for gene set enrichment and network analysis of various high-throughput data
https://cityuhk-compbio.github.io/HTSanalyzeR2/
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error install #3

Open saisaitian opened 3 years ago

saisaitian commented 3 years ago

image In this question, prada package has been removed. In fact, I have install it by source package, but an error still exist. image My R session is R.4.03

Could you tell me how to fix it?

rgaiacs commented 2 years ago

I was having a similar issue. I update R to 4.1.2 and Bioconductor to 3.14 and I was able to install HTSanalyzeR2.

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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       

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

other attached packages:
[1] HTSanalyzeR2_0.99.19

loaded via a namespace (and not attached):
  [1] fgsea_1.18.0           colorspace_2.0-2       hwriter_1.3.2          ellipsis_0.3.2         rprojroot_2.0.2       
  [6] XVector_0.32.0         fs_1.5.0               rstudioapi_0.13        remotes_2.4.1          affyio_1.62.0         
 [11] DT_0.20                bit64_4.0.5            AnnotationDbi_1.54.1   fansi_0.5.0            splines_4.1.2         
 [16] codetools_0.2-18       doParallel_1.0.16      cachem_1.0.6           knitr_1.36             splots_1.58.0         
 [21] pkgload_1.2.3          annotate_1.70.0        Rmpfr_0.8-7            vsn_3.60.0             GO.db_3.13.0          
 [26] png_0.1-7              shinydashboard_0.7.2   graph_1.70.0           shiny_1.7.1            msigdbr_7.4.1         
 [31] BiocManager_1.30.16    compiler_4.1.2         httr_1.4.2             Matrix_1.3-4           assertthat_0.2.1      
 [36] fastmap_1.1.0          limma_3.48.3           cli_3.1.0              later_1.3.0            htmltools_0.5.2       
 [41] prettyunits_1.1.1      tools_4.1.2            gmp_0.6-2.1            igraph_1.2.8           Category_2.58.0       
 [46] gtable_0.3.0           glue_1.5.0             GenomeInfoDbData_1.2.6 affy_1.70.0            dplyr_1.0.7           
 [51] fastmatch_1.1-3        Rcpp_1.0.7             Biobase_2.52.0         vctrs_0.3.8            Biostrings_2.60.2     
 [56] babelgene_21.4         preprocessCore_1.54.0  iterators_1.0.13       stringr_1.4.0          xfun_0.28             
 [61] ps_1.6.0               testthat_3.1.0         mime_0.12              miniUI_0.1.1.1         lifecycle_1.0.1       
 [66] devtools_2.4.2         XML_3.99-0.8           BioNet_1.52.0          zlibbioc_1.38.0        scales_1.1.1          
 [71] RankProd_3.18.0        colourpicker_1.1.1     promises_1.2.0.1       RBGL_1.68.0            parallel_4.1.2        
 [76] RColorBrewer_1.1-2     yaml_2.2.1             curl_4.3.2             gridExtra_2.3          memoise_2.0.0         
 [81] ggplot2_3.3.5          stringi_1.7.5          RSQLite_2.2.8          genefilter_1.74.1      cellHTS2_2.56.0       
 [86] S4Vectors_0.30.2       desc_1.4.0             foreach_1.5.1          BiocGenerics_0.38.0    pkgbuild_1.2.0        
 [91] BiocParallel_1.26.2    GenomeInfoDb_1.28.4    rlang_0.4.12           pkgconfig_2.0.3        bitops_1.0-7          
 [96] evaluate_0.14          lattice_0.20-45        purrr_0.3.4            htmlwidgets_1.5.4      bit_4.0.4             
[101] processx_3.5.2         tidyselect_1.1.1       GSEABase_1.54.0        magrittr_2.0.1         bookdown_0.24         
[106] R6_2.5.1               IRanges_2.26.0         generics_0.1.1         DBI_1.1.1              pillar_1.6.4          
[111] withr_2.4.2            survival_3.2-13        KEGGREST_1.32.0        RCurl_1.98-1.5         tibble_3.1.6          
[116] crayon_1.4.2           utf8_1.2.2             rmarkdown_2.11         usethis_2.1.3          locfit_1.5-9.4        
[121] grid_4.1.2             data.table_1.14.2      blob_1.2.2             callr_3.7.0            digest_0.6.28         
[126] xtable_1.8-4           httpuv_1.6.3           stats4_4.1.2           munsell_0.5.0          sessioninfo_1.2.1
TJiangBio commented 2 years ago

Well, I had the same issue a few days ago, and I finally solved the problem.

Prada is a dependency of package "cellHTS2". It is not updated until Bioconductor version 2.10. My solution is to install the latest version of cellHTS2 with the source which deleted the dependency of Prada.

Hope my experience can help you.