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
