unable to install DESeq2 there is no package called XML
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sarah3 • 0
@sarah3-23916
Last seen 15 months ago

I am unable to install DESeq2. I'm using R version 3.6.3 and the corresponding BiocManager version 3.10.

> BiocManager::install("DESeq2")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/DESeq2_1.26.0.zip'
Content type 'application/zip' length 2552125 bytes (2.4 MB)
downloaded 2.4 MB

package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Matthias\AppData\Local\Temp\Rtmpsr5DxO\downloaded_packages
Old packages: 'data.table', 'backports'
Update all/some/none? [a/s/n]: 
n
> library(DESeq2)
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’

I checked Bioconductor vignette here ( https://tinyurl.com/y4z2aft2 ) and tried uninstalling and updating my version of installations:

> BiocManager::valid()

* sessionInfo()

R version 3.6.3 (2020-02-29)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.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          Biobase_2.46.0             
 [6] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2              S4Vectors_0.24.4            BiocGenerics_0.32.0        
[11] BiocVersion_3.10.1          vegan_2.5-6                 lattice_0.20-41             permute_0.9-5               ggplot2_3.3.2              

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5             Formula_1.2-3          knitr_1.29             XVector_0.26.0         magrittr_1.5           cluster_2.1.0         
 [7] MASS_7.3-51.6          splines_3.6.3          zlibbioc_1.32.0        tidyselect_1.1.0       xtable_1.8-4           colorspace_1.4-1      
[13] R6_2.4.1               rlang_0.4.7            jpeg_0.1-8.1           xfun_0.16              latticeExtra_0.6-29    withr_2.2.0           
[19] ellipsis_0.3.1         htmltools_0.5.0        digest_0.6.25          tibble_3.0.3           lifecycle_0.2.0        Matrix_1.2-18         
[25] acepack_1.4.1          RCurl_1.98-1.2         compiler_3.6.3         pillar_1.4.6           scales_1.1.1           backports_1.1.7       
[31] Hmisc_4.4-0            generics_0.0.2         pkgconfig_2.0.3        rstudioapi_0.11        munsell_0.5.0          dplyr_1.0.0           
[37] stringr_1.4.0          tools_3.6.3            grid_3.6.3             nnet_7.3-14            nlme_3.1-148           htmlTable_2.0.1       
[43] data.table_1.12.8      gtable_0.3.0           checkmate_2.0.0        mgcv_1.8-31            png_0.1-7              survival_3.2-3        
[49] crayon_1.3.4           GenomeInfoDbData_1.2.2 gridExtra_2.3          purrr_0.3.4            BiocManager_1.30.10    RColorBrewer_1.1-2    
[55] bitops_1.0-6           htmlwidgets_1.5.1      base64enc_0.1-3        vctrs_0.3.2            rpart_4.1-15           glue_1.4.1            
[61] stringi_1.4.6          foreign_0.8-75        

Bioconductor version '3.10'

  * 3 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "backports", "data.table"
  ), update = TRUE, ask = FALSE)

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

Warnmeldung:
3 packages out-of-date; 0 packages too new 
> BiocManager::install(c(
+     "backports", "data.table"
+ ), update = TRUE, ask = FALSE)
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'backports', 'data.table'

  There are binary versions available but the source versions are later:
           binary source needs_compilation
backports   1.1.7  1.1.8              TRUE
data.table 1.12.8 1.13.0              TRUE

  Binaries will be installed
versuche URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/backports_1.1.7.zip'
Content type 'application/zip' length 81581 bytes (79 KB)
downloaded 79 KB

versuche URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/data.table_1.12.8.zip'
Content type 'application/zip' length 2276809 bytes (2.2 MB)
downloaded 2.2 MB

package ‘backports’ successfully unpacked and MD5 sums checked
Warnung: cannot remove prior installation of package ‘backports’
Warnung: restored ‘backports’
package ‘data.table’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Matthias\AppData\Local\Temp\RtmpAJDPLK\downloaded_packages
Old packages: 'backports', 'data.table'

  There are binary versions available but the source versions are later:
           binary source needs_compilation
backports   1.1.7  1.1.8              TRUE
data.table 1.12.8 1.13.0              TRUE

  Binaries will be installed
versuche URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/backports_1.1.7.zip'
Content type 'application/zip' length 81581 bytes (79 KB)
downloaded 79 KB

versuche URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/data.table_1.12.8.zip'
Content type 'application/zip' length 2276809 bytes (2.2 MB)
downloaded 2.2 MB

package ‘backports’ successfully unpacked and MD5 sums checked
Warnung: cannot remove prior installation of package ‘backports’
Warnung: restored ‘backports’
package ‘data.table’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Matthias\AppData\Local\Temp\RtmpAJDPLK\downloaded_packages
Warnmeldungen:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
  Problem C:\Users\Matthias\Documents\R\win-library\3.6\00LOCK\backports\libs\i386\backports.dll nach C:\Users\Matthias\Documents\R\win-library\3.6\backports\libs\i386\backports.dll zu kopieren: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  Problem C:\Users\Matthias\Documents\R\win-library\3.6\00LOCK\backports\libs\i386\backports.dll nach C:\Users\Matthias\Documents\R\win-library\3.6\backports\libs\i386\backports.dll zu kopieren: Permission denied

so maybe it is a permission issue? I am working on my own computer and have administrative rights. Could that be the reason why DESeq2 fails to install and if yes, how could I fix it?

Thanks for your help.

Session info:

R version 3.6.3 (2020-02-29)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.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          Biobase_2.46.0             
 [6] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2              S4Vectors_0.24.4            BiocGenerics_0.32.0        
[11] BiocVersion_3.10.1          vegan_2.5-6                 lattice_0.20-41             permute_0.9-5               ggplot2_3.3.2              

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5             Formula_1.2-3          knitr_1.29             XVector_0.26.0         magrittr_1.5           cluster_2.1.0         
 [7] MASS_7.3-51.6          splines_3.6.3          zlibbioc_1.32.0        tidyselect_1.1.0       xtable_1.8-4           colorspace_1.4-1      
[13] R6_2.4.1               rlang_0.4.7            jpeg_0.1-8.1           xfun_0.16              latticeExtra_0.6-29    withr_2.2.0           
[19] ellipsis_0.3.1         htmltools_0.5.0        digest_0.6.25          tibble_3.0.3           lifecycle_0.2.0        Matrix_1.2-18         
[25] acepack_1.4.1          RCurl_1.98-1.2         compiler_3.6.3         pillar_1.4.6           scales_1.1.1           backports_1.1.7       
[31] Hmisc_4.4-0            generics_0.0.2         pkgconfig_2.0.3        rstudioapi_0.11        munsell_0.5.0          dplyr_1.0.0           
[37] stringr_1.4.0          tools_3.6.3            grid_3.6.3             nnet_7.3-14            nlme_3.1-148           htmlTable_2.0.1       
[43] data.table_1.12.8      gtable_0.3.0           checkmate_2.0.0        mgcv_1.8-31            png_0.1-7              survival_3.2-3        
[49] crayon_1.3.4           GenomeInfoDbData_1.2.2 gridExtra_2.3          purrr_0.3.4            BiocManager_1.30.10    RColorBrewer_1.1-2    
[55] bitops_1.0-6           htmlwidgets_1.5.1      base64enc_0.1-3        vctrs_0.3.2            rpart_4.1-15           glue_1.4.1            
[61] stringi_1.4.6          foreign_0.8-75

deseq2 bioconductor windows xml installation • 267 views
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1
Entering edit mode
@mikelove
Last seen 6 hours ago
United States

Can you show what happens when you try to install the XML package? It seems it was once installed but then removed. You can just re-install XML.

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0
Entering edit mode
install.packages("XML")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/Matthias/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘XML’ is not available (for R version 3.6.3)

when I try specifying a source as suggested here (https://tinyurl.com/y4bbfvcs) it says

 Warning in install.packages :
  unable to access index for repository http://www.omegahat.net/R/bin/windows/contrib/3.6:
  kann URL 'http://www.omegahat.net/R/bin/windows/contrib/3.6/PACKAGES' nicht öffnen
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘XML’
  These will not be installed
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0
Entering edit mode

ok, installing the binary version stackoverflow somehow worked. Thanks for your help!

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