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Question: TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
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gravatar for isultan
4 days ago by
isultan0
isultan0 wrote:

Hello dear, I am really new to all this so forgive me if I am not clear.  I am trying to install TxDb.Hsapiens.UCSC.hg19.knownGene, but keep getting the error below : installation had non-zero exit status and the package is not installed.  My R and Bioconductor installations were all withing the past 2 weeks so I assume everything is updated.  Below is the error and then the session info, 

 

> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1

  (2018-07-02).

Installing package(s) ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

installing the source package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

 

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz'

Content type 'application/x-gzip' length 18669702 bytes (17.8 MB)

downloaded 17.8 MB

 

* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called 'stringi'

Error : package 'GenomicFeatures' could not be loaded

ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'

* removing 'C:/Users/96279/Documents/R/win-library/3.5/TxDb.Hsapiens.UCSC.hg19.knownGene'

In R CMD INSTALL

 

The downloaded source packages are in

‘C:\Users\96279\AppData\Local\Temp\RtmpsVgKeD\downloaded_packages’

installation path not writeable, unable to update packages:

  survival

Warning message:

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

  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status

Sessioninfo

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] GenomicFeatures_1.32.0                 
 [2] AnnotationDbi_1.42.1                   
 [3] Biobase_2.40.0                         
 [4] BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0
 [5] BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0
 [6] BSgenome_1.48.0                        
 [7] rtracklayer_1.40.3                     
 [8] GenomicRanges_1.32.3                   
 [9] GenomeInfoDb_1.16.0                    
[10] Biostrings_2.48.0                      
[11] XVector_0.20.0                         
[12] IRanges_2.14.10                        
[13] S4Vectors_0.18.3                       
[14] BiocGenerics_0.26.0                    
[15] BiocInstaller_1.30.0                   

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 'stringi' is missing or broken

ADD COMMENTlink modified 4 days ago by Martin Morgan ♦♦ 22k • written 4 days ago by isultan0
0
gravatar for Martin Morgan
4 days ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Usually installing a package will install its dependencies. For some reason this is not the case for your installation, leading to the error

Error: package or namespace load failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'stringi'
Error : package 'GenomicFeatures' could not be loaded

So correct that

biocLite("stringi")

and try again

biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
ADD COMMENTlink written 4 days ago by Martin Morgan ♦♦ 22k
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