Hello, I just upgraded diffbind to 2.6.1 using bioconductor 3.6 in my directory under SSH secure shell. I got 12 warnings. Here is information : A: Warnings when update DiffBind and running errors

To solve the warnings, I think I should upgrade all the packages using biocLite (), but error showed:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
installation path not writeable, unable to update packages: 

If I used bioValid(), it showed "Error: 191 package(s) out of date". I could use install.packages (pkg)  if I  update one by one.But  could anyone suggest me a commander that will update all the packages together under my directory?

Thank you. 

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] BiocInstaller_1.28.0       DiffBind_2.6.1            
 [3] SummarizedExperiment_1.6.5 DelayedArray_0.2.7        
 [5] matrixStats_0.52.2         Biobase_2.36.2            
 [7] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0       
 [9] IRanges_2.12.0             S4Vectors_0.16.0          
[11] BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
 [1] edgeR_3.18.1             RMySQL_0.10.13           bit64_0.9-7             
 [4] splines_3.4.2            gtools_3.5.0             assertthat_0.2.0        
 [7] latticeExtra_0.6-28      amap_0.8-14              RBGL_1.52.0             
[10] blob_1.1.0               GenomeInfoDbData_0.99.0  Rsamtools_1.30.0        
[13] ggrepel_0.7.0            Category_2.42.1          RSQLite_2.0             
[16] backports_1.1.1          lattice_0.20-35          glue_1.2.0              
[19] limma_3.32.7             digest_0.6.12            RColorBrewer_1.1-2      
[22] XVector_0.16.0           checkmate_1.8.5          colorspace_1.3-2        
[25] Matrix_1.2-12            plyr_1.8.4               GSEABase_1.38.2         
[28] XML_3.98-1.9             pkgconfig_2.0.1          pheatmap_1.0.8          
[31] ShortRead_1.34.1         biomaRt_2.32.1           genefilter_1.58.1       
[34] zlibbioc_1.22.0          xtable_1.8-2             GO.db_3.4.1             
[37] scales_0.5.0             brew_1.0-6               gdata_2.18.0            
[40] BiocParallel_1.10.1      tibble_1.3.4             annotate_1.54.0         
[43] ggplot2_2.2.1            GenomicFeatures_1.30.0   lazyeval_0.2.0          
[46] magrittr_1.5             survival_2.41-3          memoise_1.1.0           
[49] systemPipeR_1.10.2       fail_1.3                 gplots_3.0.1            
[52] hwriter_1.3.2            GOstats_2.42.0           graph_1.54.0            
[55] tools_3.4.2              BBmisc_1.11              stringr_1.2.0           
[58] sendmailR_1.2-1          munsell_0.4.3            locfit_1.5-9.1          
[61] bindrcpp_0.2             AnnotationDbi_1.38.2     Biostrings_2.44.2       
[64] compiler_3.4.2           caTools_1.17.1           rlang_0.1.4             
[67] grid_3.4.2               RCurl_1.95-4.8           rjson_0.2.15            
[70] AnnotationForge_1.18.2   bitops_1.0-6             base64enc_0.1-3         
[73] gtable_0.2.0             DBI_0.7                  R6_2.2.2                
[76] GenomicAlignments_1.12.2 dplyr_0.7.4              rtracklayer_1.30.4      
[79] bit_1.1-12               bindr_0.1                KernSmooth_2.23-15      
[82] stringi_1.1.5            BatchJobs_1.6            Rcpp_0.12.14            
> biocLite ()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
installation path not writeable, unable to update packages: adegenet, affy,
  affydata, affyio, annotate, AnnotationDbi, AnnotationForge, ape, AssocTests,
  bbmle, beadarray, BeadDataPackR, bigmemory, Biobase, BiocGenerics,
  BiocInstaller, BiocParallel, biomaRt, Biostrings, BSgenome, bumphunter,
  cairoDevice, car, Category, checkmate, chron, covr, crlmm, curl, data.table,
  DelayedArray, dendextend, DESeq2, devtools, DiffBind, DNAcopy, edgeR,
  epitools, fBasics, fExtremes, fGarch, fImport, fTrading, future, gamlss,
  gamlss.dist, gdsfmt, genefilter, geneplotter, GenomeInfoDb, GenomeInfoDbData,
  GenomicAlignments, GenomicFeatures, GenomicRanges, genoset, GEOquery,
  geoRglm, globals, glue, GO.db, GOstats, graph, gridSVG, GSEABase, GWASTools,
  gWidgetsRGtk2, hms, httpuv, illuminaio, impute, IRanges, irlba, lazyeval,
  limma, lubridate, lumi, lumiBarnes, Matrix, MBESS, mclust, memuse, methylumi,
  mice, minet, minfi, mixOmics, MotIV, multcomp, multtest, nanotime,
  oligoClasses, OpenMx, openssl, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db,
  org.Mm.eg.db, org.Rn.eg.db, PBSmapping, penalized, phangorn, plm, pracma,
  preprocessCore, proxy, pscl, purrr, quantmod, quantreg, quantsmooth, raster,
  RBGL, Rcmdr, Rcpp, RcppArmadillo, RcppCCTZ, RcppEigen, rex, rGADEM, rgenoud,
  rgeos, Rgraphviz, rJava, rlang, rmarkdown, robustbase, rockchalk, rpf,
  Rsamtools, rtracklayer, rugarch, R.utils, S4Vectors, seqLogo, shapes, shiny,
  ShortRead, siggenes, SNPchip, SNPRelate, spatstat, spatstat.utils, spdep,
  stringi, SummarizedExperiment, systemPipeR, tables, tidyr, tidyselect,
  timeDate, timeSeries, tweedie, VariantAnnotation, vcfR, vsn, withr, XVector,
  Zelig, zlibbioc, abind, bitops, caTools, coda, colorspace, DBI, DEoptimR,
  Formula, gdata, gtools, latticeExtra, littler, lmtest, minqa, mvtnorm,
  RColorBrewer, rgl, RMySQL, RUnit, sandwich, sm, stabledist, strucchange,
  tcltk2, TH.data, VGAM, zoo, codetools, lattice, spatial

It looks like these packages were installed under a different account. If you installed them, then I would suggest that you do NOT install packages as root. Instead, see ?R_LIBS_USER and configure an R / Bioconductor version specific library where all non-base R packages are installed.

To update packages when they are installed in a directory where you have write access, simply use BiocInstaller::biocLite().