Loading required package: usethis
Loading required package: devtools
Error: package or namespace load failed for ‘devtools’:
 .onLoad failed in loadNamespace() for 'processx', details:
  call: loadNamespace(name)
  error: there is no package called ‘ps’
Loading required package: BiocManager
Warning messages:
1: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'Couldn't connect to server'
2: In file(con, "r") :
  URL 'http://bioconductor.org/config.yaml': status was 'Couldn't connect to server'
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘bitops’
Loading required package: methylKit
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘bitops’
Failed with error:  ‘package ‘GenomeInfoDb’ could not be loaded’
Loading required package: R6
Loading required package: dplyr
Error: package or namespace load failed for ‘dplyr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘utf8’
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /gscratch/srlab/programs/R-3.6.2/lib/libRblas.so
LAPACK: /gscratch/srlab/programs/R-3.6.2/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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] R6_2.5.0            IRanges_2.20.2      S4Vectors_0.24.4   
[4] BiocGenerics_0.32.0 BiocManager_1.30.12 usethis_2.0.1      

loaded via a namespace (and not attached):
 [1] magrittr_2.0.1  rlang_0.4.10    fastmap_1.1.0   fansi_0.4.2    
 [5] tools_3.6.2     cli_2.4.0       ellipsis_0.3.1  lifecycle_1.0.0
 [9] purrr_0.3.4     vctrs_0.3.7     fs_1.5.0        memoise_2.0.0  
[13] glue_1.4.2      cachem_1.0.4    compiler_3.6.2  generics_0.1.0 
  sampleID slide.label pHTreatment
1        1       02-T1           1
2        2       04-T3           1
3        3       06-T1           1
4        4       08-T2           1
5        5       11-T4           0
6        6       UK-02           0
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘bitops’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted