install latest version issues

[suminwei2772]

Hi, I'm wondering how I can install rhdf5 version 2.30.1. When I try to install this package using BiocManager::install() I always end up installing rhdf5 version 2.26.2. Thank you, Lisa

[PeteHaitch]

Please share the output of running BiocManager::valid(). You will need version 3.10 of Bioconductor to install this version of rhdf5.

[suminwei2772]

Sharing output of running BiocManager::valid():

* sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

Matrix products: default
BLAS: /gsc/software/linux-x86_64-centos6/R-3.5.0_gcc-7.2/lib64/R/lib/libRblas.so
LAPACK: /gsc/software/linux-x86_64-centos6/R-3.5.0_gcc-7.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SnapATAC_1.0.0       rhdf5_2.26.2         Matrix_1.2-18        GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 
[6] IRanges_2.16.0       S4Vectors_0.20.1     BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1         tidyselect_1.0.0       purrr_0.3.3            lattice_0.20-35        colorspace_1.4-1      
 [6] doSNOW_1.0.18          snow_0.4-3             viridisLite_0.3.0      yaml_2.2.1             rlang_0.4.5           
[11] pillar_1.4.3           glue_1.3.1             plot3D_1.3             RColorBrewer_1.1-2     GenomeInfoDbData_1.2.0
[16] foreach_1.4.8          lifecycle_0.1.0        plyr_1.8.4             zlibbioc_1.28.0        munsell_0.5.0         
[21] gtable_0.3.0           codetools_0.2-15       misc3d_0.8-4           doParallel_1.0.15      irlba_2.3.3           
[26] Rcpp_1.0.3             edgeR_3.24.3           BiocManager_1.30.10    scales_1.1.0           limma_3.38.3          
[31] XVector_0.22.0         gridExtra_2.3          RANN_2.6.1             ggplot2_3.2.1          Rtsne_0.15            
[36] dplyr_0.8.4            grid_3.5.0             tools_3.5.0            bitops_1.0-6           magrittr_1.5          
[41] RCurl_1.98-1.1         lazyeval_0.2.2         tibble_2.1.3           crayon_1.3.4           bigmemory.sri_0.1.3   
[46] bigmemory_4.5.36       pkgconfig_2.0.3        assertthat_0.2.1       rstudioapi_0.11        iterators_1.0.12      
[51] viridis_0.5.1          Rhdf5lib_1.4.3         R6_2.4.1               igraph_1.2.4.2         compiler_3.5.0        

Bioconductor version '3.8'

  * 42 packages out-of-date
  * 1 packages too new

create a valid installation with

  BiocManager::install(c(
    "assertthat", "BH", "BiocInstaller", "BiocParallel", "cli", "colorspace", "curl", "devtools", "digest", "edgeR",
    "fansi", "forcats", "formatR", "ggplot2", "git2r", "glue", "gsl", "gtable", "httr", "jsonlite", "lambda.r",
    "lazyeval", "limma", "mime", "openssl", "pillar", "plyr", "R6", "Rcpp", "RcppEigen", "rgl", "rlang", "RSpectra",
    "rstudioapi", "scales", "SCnorm", "Seurat", "snow", "stringi", "stringr", "tibble", "whisker", "XML"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
42 packages out-of-date; 1 packages too new 

[PeteHaitch]

This shows you are using Bioconductor 3.8 on R 3.5. You will need to update to Bioconductor 3.10 on R 3.6 to install rdfh5 2.30.1. You can find instructions for installing/updating to Bioconductor 3.10 at https://www.bioconductor.org/install/