Question: package gwascat is not available for R version 3.4.4
0
gravatar for daviqd.halvorsen
4 months ago by
daviqd.halvorsen0 wrote:

Hello! I am trying to install the 'gwascat' package, from Bioconductor, for RStudio without success. I'd like to repeat the 23andMe data analysis protocol I found, but I can't even install the first required package. The closest post I could find figuring out my error is a tangential StackOverflow question. My first attempt was a typical install at the R Terminal in Ubuntu 16.04 LTS:

install.packages("gwascat")

Here's the output for that command:
Installing package into ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘gwascat’ is not available (for R version 3.2.3)

Here's the attempt to install the required dependencies along with gwascat at the R Terminal in Ubuntu 16.04 LTS:

install.packages("gwascat", dependencies=TRUE)

^I got the exact same error message as the ">install.packages("gwascat") command, so I didn't bother copying the error output again.

I also tried the same commands in RStudio:

install.packages("gwascat")

The RStudio console prints a much longer series of errors for the same command:

ERROR: dependency ‘XML’ is not available for package ‘biomaRt’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’ Warning in install.packages : installation of package ‘biomaRt’ had non-zero exit status ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/rtracklayer’ Warning in install.packages : installation of package ‘rtracklayer’ had non-zero exit status ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/BSgenome’ Warning in install.packages : installation of package ‘BSgenome’ had non-zero exit status ERROR: dependencies ‘RMySQL’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/GenomicFeatures’ Warning in install.packages : installation of package ‘GenomicFeatures’ had non-zero exit status ERROR: dependency ‘GenomicFeatures’ is not available for package ‘OrganismDbi’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/OrganismDbi’ Warning in install.packages : installation of package ‘OrganismDbi’ had non-zero exit status ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘ensembldb’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/ensembldb’ Warning in install.packages : installation of package ‘ensembldb’ had non-zero exit status ERROR: dependencies ‘BSgenome’, ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/VariantAnnotation’ Warning in install.packages : installation of package ‘VariantAnnotation’ had non-zero exit status ERROR: dependencies ‘rtracklayer’, ‘VariantAnnotation’ are not available for package ‘GenomicFiles’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/GenomicFiles’ Warning in install.packages : installation of package ‘GenomicFiles’ had non-zero exit status ERROR: dependencies ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/biovizBase’ Warning in install.packages : installation of package ‘biovizBase’ had non-zero exit status ERROR: dependencies ‘rtracklayer’, ‘GenomicFiles’ are not available for package ‘gQTLBase’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/gQTLBase’ Warning in install.packages : installation of package ‘gQTLBase’ had non-zero exit status ERROR: dependencies ‘Homo.sapiens’, ‘GenomicFiles’, ‘rtracklayer’ are not available for package ‘erma’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/erma’ Warning in install.packages : installation of package ‘erma’ had non-zero exit status ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’ are not available for package ‘Gviz’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/Gviz’ Warning in install.packages : installation of package ‘Gviz’ had non-zero exit status ERROR: dependencies ‘biovizBase’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’ are not available for package ‘ggbio’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/ggbio’ Warning in install.packages : installation of package ‘ggbio’ had non-zero exit status ERROR: dependencies ‘Homo.sapiens’, ‘erma’, ‘VariantAnnotation’, ‘GenomicFiles’ are not available for package ‘ldblock’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/ldblock’ Warning in install.packages : installation of package ‘ldblock’ had non-zero exit status ERROR: dependencies ‘GenomicFiles’, ‘VariantAnnotation’, ‘gQTLBase’, ‘GenomicFeatures’, ‘ldblock’, ‘erma’ are not available for package ‘gQTLstats’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/gQTLstats’ Warning in install.packages : installation of package ‘gQTLstats’ had non-zero exit status ERROR: dependencies ‘Homo.sapiens’, ‘rtracklayer’, ‘gQTLstats’, ‘Gviz’, ‘VariantAnnotation’, ‘GenomicFeatures’, ‘ggbio’ are not available for package ‘gwascat’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/gwascat’ Warning in install.packages : installation of package ‘gwascat’ had non-zero exit status

The downloaded source packages are in ‘/tmp/RtmptM3bzC/downloaded_packages’

I also tried updating my version of R to the latest version. When I first encountered the failure to install 'gwascat' my version of R was 3.2.3. I updated my version of R to 3.4.4 with the help of this StackOverflow question. BUT, I still got the same error as before "package 'gwascat' is not available (for R version 3.4.4)".

Then I tried to follow the official Bioconductor 'gwascat' installation instructions.

source("https://bioconductor.org/biocLite.R")

Bioconductor seems to be installed fine:
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see   http://bioconductor.org/install

biocLite("gwascat")

The error messages for biocLite("gwascat") are long:
ERROR: configuration failed for package ‘RMySQL’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/RMySQL’ ERROR: dependency ‘XML’ is not available for package ‘biomaRt’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’ ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/rtracklayer’ ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/BSgenome’ ERROR: dependencies ‘RMySQL’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/GenomicFeatures’ ERROR: dependency ‘GenomicFeatures’ is not available for package ‘OrganismDbi’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/OrganismDbi’ ERROR: dependency ‘GenomicFeatures’ is not available for package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/TxDb.Hsapiens.UCSC.hg19.knownGene’ ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘ensembldb’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/ensembldb’ ERROR: dependencies ‘BSgenome’, ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/VariantAnnotation’ ERROR: dependencies ‘rtracklayer’, ‘VariantAnnotation’ are not available for package ‘GenomicFiles’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/GenomicFiles’ ERROR: dependencies ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/biovizBase’ ERROR: dependencies ‘OrganismDbi’, ‘GenomicFeatures’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ are not available for package ‘Homo.sapiens’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/Homo.sapiens’ ERROR: dependencies ‘rtracklayer’, ‘GenomicFiles’ are not available for package ‘gQTLBase’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/gQTLBase’ ERROR: dependencies ‘Homo.sapiens’, ‘GenomicFiles’, ‘rtracklayer’ are not available for package ‘erma’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/erma’ ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’ are not available for package ‘Gviz’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/Gviz’ ERROR: dependencies ‘biovizBase’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’ are not available for package ‘ggbio’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/ggbio’ ERROR: dependencies ‘Homo.sapiens’, ‘erma’, ‘VariantAnnotation’, ‘GenomicFiles’ are not available for package ‘ldblock’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/ldblock’ ERROR: dependencies ‘GenomicFiles’, ‘VariantAnnotation’, ‘gQTLBase’, ‘GenomicFeatures’, ‘ldblock’, ‘erma’ are not available for package ‘gQTLstats’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/gQTLstats’ ERROR: dependencies ‘Homo.sapiens’, ‘rtracklayer’, ‘gQTLstats’, ‘Gviz’, ‘VariantAnnotation’, ‘GenomicFeatures’, ‘ggbio’ are not available for package ‘gwascat’ * removing ‘/home/david/R/x86_64-pc-linux-gnu-library/3.4/gwascat’

The downloaded source packages are in ‘/tmp/RtmptM3bzC/downloaded_packages’ installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival There were 20 warnings (use warnings() to see them)

I also entered 'warnings()' to see the other warnings:

warnings()

Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RMySQL’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘biomaRt’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘rtracklayer’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘BSgenome’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GenomicFeatures’ had non-zero exit status 7: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘OrganismDbi’ had non-zero exit status 8: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status 9: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘ensembldb’ had non-zero exit status 10: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘VariantAnnotation’ had non-zero exit status 11: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GenomicFiles’ had non-zero exit status 12: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘biovizBase’ had non-zero exit status 13: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘Homo.sapiens’ had non-zero exit status 14: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘gQTLBase’ had non-zero exit status 15: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘erma’ had non-zero exit status 16: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘Gviz’ had non-zero exit status 17: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘ggbio’ had non-zero exit status 18: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘ldblock’ had non-zero exit status 19: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘gQTLstats’ had non-zero exit status 20: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘gwascat’ had non-zero exit status

Any ideas on how I can install gwascat? I've got my raw 23andMe data and I'm excited to get to analyze it!

Best, David

snp sequence R gene • 929 views
ADD COMMENTlink modified 4 months ago by Vimalkumar Velayudhan190 • written 4 months ago by daviqd.halvorsen0
1
gravatar for Vimalkumar Velayudhan
4 months ago by
Ireland
Vimalkumar Velayudhan190 wrote:

For the XML package to compile, you will need the xml libraries and header files (sudo apt install libxml2-dev) installed. The error message doesn't say that! Other packages might require additional libraries. You could try installing one failing package at a time and once they are installed successfully, you can try installing gwascat again.

ADD COMMENTlink written 4 months ago by Vimalkumar Velayudhan190
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