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Question: Installation of package DelayedArray had non-zero exit status
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gravatar for cristoforo-grasso
3 months ago by
cristoforo-grasso0 wrote:

I am a beginner user of R and the Biocunductor packages. I am analysing RNA seq data, amang many pakages that I have installed thare is the Delayedarray package, of which I am having trouble to install. The output is a warning message. I wonder if you coud help me. Thank you in advance

 There is a binary version available but the source version is later:

            binary source needs_compilation

matrixStats 0.53.1 0.54.0              TRUE

  Binaries will be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/matrixStats_0.53.1.zip'

Content type 'application/zip' length 1632527 bytes (1.6 MB)

downloaded 1.6 MB

package ‘matrixStats’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\cgrasso\AppData\Local\Temp\RtmpkfIVn0\downloaded_packages

Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘DelayedArray’ had non-zero exit status

> BiocInstaller::biocValid()

* sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252  
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                     
[5] LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
[1] BiocInstaller_1.30.0 Biobase_2.40.0       Rsamtools_1.32.2   
[4] GenomicRanges_1.32.6 GenomeInfoDb_1.16.0  Biostrings_2.48.0  
[7] XVector_0.20.0       IRanges_2.14.10      S4Vectors_0.18.3   
[10] BiocParallel_1.14.2  BiocGenerics_0.26.0 

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'yaml' is missing or broken

 > traceback()
10: FUN(X[[i]], ...)
9: lapply(X = X, FUN = FUN, ...)
8: sapply(L[[n]], function(x) x[["Version"]])
7: mkLabel(x, "loadedOnly")
6: print(mkLabel(x, "loadedOnly"), quote = FALSE, ...)
5: print.sessionInfo(sessionInfo())
4: print(sessionInfo())
3: print.biocValid(result)
2: print(result)
1: BiocInstaller::biocValid()

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
 [1] BiocInstaller_1.30.0 Biobase_2.40.0       Rsamtools_1.32.2    
 [4] GenomicRanges_1.32.6 GenomeInfoDb_1.16.0  Biostrings_2.48.0   
 [7] XVector_0.20.0       IRanges_2.14.10      S4Vectors_0.18.3    
[10] BiocParallel_1.14.2  BiocGenerics_0.26.0 

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'yaml' is missing or broken
ADD COMMENTlink written 3 months ago by cristoforo-grasso0

To clarify, was this using BiocInstaller::biocLite("DelayedArray")?

ADD REPLYlink modified 3 months ago • written 3 months ago by Peter Hickey440
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