DESeq2 installation in R
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Entering edit mode
wes • 0
@wes-24179
Last seen 6 months ago

Dear All

I would like to install DESeq2 for DE analysis.

After I type the following script

if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager") BiocManager::install("DESeq2")

The following comes out:

package ‘backports’ successfully unpacked and MD5 sums checked
package ‘bit64’ successfully unpacked and MD5 sums checked
package ‘callr’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘Hmisc’ successfully unpacked and MD5 sums checked
package ‘jsonlite’ successfully unpacked and MD5 sums checked
package ‘MASS’ successfully unpacked and MD5 sums checked
package ‘mgcv’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘processx’ successfully unpacked and MD5 sums checked
package ‘ps’ successfully unpacked and MD5 sums checked
package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘xfun’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages
installing the source package ‘htmlTable’

trying URL 'https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz'
Content type 'application/x-gzip' length 421796 bytes (411 KB)
downloaded 411 KB

* installing *source* package 'htmlTable' ...
** package 'htmlTable' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'htmlTable'
    finding HTML links ... done
    SCB                                     html  
    addStyles                               html  
    concatHtmlTables                        html  
    getHtmlTableStyle                       html  
    getHtmlTableTheme                       html  
    hasHtmlTableStyle                       html  
    htmlTable                               html  
    htmlTableWidget-shiny                   html  
    htmlTableWidget                         html  
    innerJoinByCommonCols                   html  
    interactiveTable                        html  
    outputInt                               html  
    prAddCells                              html  
    prAddEmptySpacerCell                    html  
    prAddSemicolon2StrEnd                   html  
    prAttr4RgroupAdd                        html  
    prBindDataListIntoColumns               html  
    prConvertDfFactors                      html  
    prEscapeHtml                            html  
    prExtractElementsAndConvertToTbl        html  
    prGetAlign                              html  
    prGetCgroupHeader                       html  
    prGetRgroupLine                         html  
    prGetRowlabelPos                        html  
    prGetScriptString                       html  
    prGetStyle                              html  
    prGetThead                              html  
    prIsNotebook                            html  
    prMergeClr                              html  
    prPrepInputMatrixDimensions             html  
    prPrepareAlign                          html  
    prPrepareCgroup                         html  
    prPrepareColors                         html  
    prPrepareCss                            html  
    prSkipRownames                          html  
    prTblNo                                 html  
    prepGroupCounts                         html  
    pvalueFormatter                         html  
    setHtmlTableTheme                       html  
    splitLines4Table                        html  
    tblNoLast                               html  
    tblNoNext                               html  
    tidyHtmlTable                           html  
    txtInt                                  html  
    txtMergeLines                           html  
    txtPval                                 html  
    txtRound                                html  
    vector2string                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (htmlTable)

The downloaded source packages are in
        ‘C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages’
However, the function cannot be found when the following augment was typed:

DESeq.ds <- DESeqDataSetFromMatrix(countData=Fruit_ripening_TPM)
Error in DESeqDataSetFromMatrix(countData = Fruit_ripening_TPM) : 
  could not find function "DESeqDataSetFromMatrix"
Then, I tried to load the package but following comes out.

library("DESeq2")

Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

    Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
     there is no package called ‘XML’
    In addition: Warning messages:
    1: package ‘S4Vectors’ was built under R version 3.6.3 
    2: package ‘IRanges’ was built under R version 3.6.2 
    3: package ‘GenomeInfoDb’ was built under R version 3.6.3 
    4: package ‘SummarizedExperiment’ was built under R version 3.6.2 
    5: package ‘DelayedArray’ was built under R version 3.6.3 
    6: package ‘matrixStats’ was built under R version 3.6.3 
    7: package ‘BiocParallel’ was built under R version 3.6.2

FYI, my R version is 3.6.1. Someone from other post recommend me to install XML. 

> install.packages("XML")
Installing package into ‘C:/Users/ASUS/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://wbc.upm.edu.my/cran/src/contrib:
  cannot open URL 'https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'
Warning: unable to access index for repository https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6:
  cannot open URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES'
Warning message:
package ‘XML’ is not available (for R version 3.6.1)

However, still not successful.

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_Malaysia.1252  LC_CTYPE=English_Malaysia.1252    LC_MONETARY=English_Malaysia.1252
[4] LC_NUMERIC=C                      LC_TIME=English_Malaysia.1252    

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

other attached packages:
 [1] SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.1         matrixStats_0.56.0         
 [5] Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
 [9] S4Vectors_0.24.4            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] xfun_0.17              splines_3.6.1          lattice_0.20-41        colorspace_1.4-1       vctrs_0.3.4           
 [6] htmltools_0.5.0        base64enc_0.1-3        survival_3.2-3         rlang_0.4.7            pillar_1.4.6          
[11] foreign_0.8-71         glue_1.4.2             RColorBrewer_1.1-2     jpeg_0.1-8.1           GenomeInfoDbData_1.2.2
[16] lifecycle_0.2.0        stringr_1.4.0          zlibbioc_1.32.0        munsell_0.5.0          gtable_0.3.0          
[21] htmlwidgets_1.5.1      latticeExtra_0.6-29    knitr_1.29             htmlTable_2.1.0        Rcpp_1.0.5            
[26] xtable_1.8-4           scales_1.1.1           backports_1.1.9        checkmate_2.0.0        BiocManager_1.30.10   
[31] Hmisc_4.4-1            XVector_0.26.0         gridExtra_2.3          ggplot2_3.3.2          png_0.1-7             
[36] digest_0.6.25          stringi_1.4.6          grid_3.6.1             tools_3.6.1            bitops_1.0-6          
[41] magrittr_1.5           RCurl_1.98-1.2         tibble_3.0.3           Formula_1.2-3          cluster_2.1.0         
[46] crayon_1.3.4           pkgconfig_2.0.3        ellipsis_0.3.1         Matrix_1.2-18          data.table_1.13.0     
[51] rstudioapi_0.11        R6_2.4.1               rpart_4.1-15           nnet_7.3-14            compiler_3.6.1

May I know is there any other approach I can try?

software error • 467 views
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0
Entering edit mode

I see

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘XML’

so I would try to use BiocManager::install("XML"). But I guess you have many problems with your installation, and I'd suggest

BiocManager::valid()

and then updating the packages that command indicates.

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Entering edit mode

Dear Martin

Thanks for your suggestion. I have tried your suggestion and also updating the packages that command indicates. I even tried BiocManager::install("XML") but all failed as shown below. Any other suggestion? Should I update the Bioconductor to latest version instead?

BiocManager::valid()

  • sessionInfo()

R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252

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

other attached packages: [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0
[5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2
[9] S4Vectors0.24.4 BiocGenerics0.32.0

loaded via a namespace (and not attached): [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4
[6] htmltools
0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6
[11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0
[21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5
[26] xtable
1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10
[31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7
[36] digest
0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6
[41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0
[46] crayon
1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0
[51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1

Bioconductor version '3.10'

  • 0 packages out-of-date
  • 2 packages too new

create a valid installation with

BiocManager::install(c( "htmlTable", "xfun" ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date

Warning message: 0 packages out-of-date; 2 packages too new

BiocManager::install(c( + "htmlTable", "xfun" + ), update = TRUE, ask = FALSE) Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Installing package(s) 'htmlTable', 'xfun' trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Content type 'application/zip' length 386703 bytes (377 KB) downloaded 377 KB

trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Content type 'application/zip' length 233860 bytes (228 KB) downloaded 228 KB

package ‘htmlTable’ successfully unpacked and MD5 sums checked package ‘xfun’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘xfun’ Warning: restored ‘xfun’

The downloaded binary packages are in C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival Warning message: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied

BiocManager::install("XML") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Installing package(s) 'XML' trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Content type 'application/zip' length 4255589 bytes (4.1 MB) downloaded 4.1 MB

package ‘XML’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival

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Entering edit mode

Hmm, but it says package ‘XML’ successfully unpacked and MD5 sums checked it looks mostly like these have been successful?

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Entering edit mode

Dear Martin

Sorry, I'm newbie. Just realize that I need to write the script "library("DESeq2")" before I proceed. It is working now.

Really thanks so much for your help.

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