How could I upgrade 191 old packages in my directory?
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@zhaolin20042008-12777
Last seen 3.7 years ago
U of Michigan

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If I used bioValid(), it showed "Error: 191 package(s) out of date".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

bioclite • 800 views
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@martin-morgan-1513
Last seen 9 weeks ago
United States

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().

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Entering edit mode

Hi, Martin, 

Thank you for suggestions. But it doesn't work in my case. Could you or others suggest more? Many thanks. Zhaolin

> BiocInstaller::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

> 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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.2       BiocInstaller_1.28.0 tools_3.4.2     

> .libPaths()
[1] "~/R/x86_64-pc-linux-gnu-library/3.3"  ## my directory
[2] "/net/mario/cluster/lib/R/site-library"                          
[3] "/usr/local/lib/R/site-library"                                  
[4] "/usr/lib/R/site-library"                                        
[5] "/usr/lib/R/library" 

 

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There is no other suggestion that would help. Either you have to get the sysadmin to update the packages for you  (or if you have sudo access, you can update yourself), or you have to install things in a place where you do have access rights. This doesn't have anything to do with Bioconductor, or R, really, but instead has to do with Linux privileges and How Things Work.

As Martin says, it's inconvenient to install packages in directories that have only root access, as you then need someone with higher privileges than a regular user to install and/or upgrade. But again, this is a Linux user privilege issue.

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Thank you. I will contact the administrator. 

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