Question: TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
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gravatar for 1225384383
29 days ago by
12253843830
12253843830 wrote:
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
Bioconductor version 3.10 (BiocManager 1.30.8), R 3.6.1 (2019-07-05)
Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
installing the source package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

trying URL 'https://bioconductor.org/packages/3.10/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


The downloaded source packages are in
        ‘C:\Users\立夏\AppData\Local\Temp\RtmpyiJEO5\downloaded_packages’
Update old packages: 'data.table', 'KernSmooth'
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is later:
           binary source needs_compilation
data.table 1.12.4 1.12.6              TRUE

  Binaries will be installed
trying URL 'https://mirror-hk.koddos.net/CRAN/bin/windows/contrib/3.6/data.table_1.12.4.zip'
Content type 'application/zip' length 2303665 bytes (2.2 MB)
downloaded 2.2 MB

trying URL 'https://mirror-hk.koddos.net/CRAN/bin/windows/contrib/3.6/KernSmooth_2.23-16.zip'
Content type 'application/zip' length 115164 bytes (112 KB)
downloaded 112 KB

package ‘data.table’ successfully unpacked and MD5 sums checked
package ‘KernSmooth’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\立夏\AppData\Local\Temp\RtmpyiJEO5\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
> BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.10 (BiocManager 1.30.8), R 3.6.1 (2019-07-05)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz'
Content type 'application/x-gzip' length 9792100 bytes (9.3 MB)
downloaded 9.3 MB


The downloaded source packages are in
        ‘C:\Users\立夏\AppData\Local\Temp\RtmpyiJEO5\downloaded_packages’
Update old packages: 'data.table'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
> library(methylationArrayAnalysis)
Error in library(methylationArrayAnalysis) : 
  there is no package called ‘methylationArrayAnalysis’
> library(methylationArrayAnalysis)
Error in library(methylationArrayAnalysis) : 
  there is no package called ‘methylationArrayAnalysis’
> BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
Bioconductor version 3.10 (BiocManager 1.30.8), R 3.6.1 (2019-07-05)
Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
installing the source package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

trying URL 'https://bioconductor.org/packages/3.10/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


The downloaded source packages are in
        ‘C:\Users\立夏\AppData\Local\Temp\RtmpyiJEO5\downloaded_packages’
Update old packages: 'data.table', 'HDF5Array'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
annotation software error • 85 views
ADD COMMENTlink written 29 days ago by 12253843830

Set environment variable TEMPDIR to a path that does NOT contain '立夏' ?

ADD REPLYlink written 29 days ago by Martin Morgan ♦♦ 24k
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