Hi there,
First post so please have patience and many thanks to anyone looking at this.
I need to look at a cancer patient cohort study for gene expression analysis and so have copied the method proposed in https://bioconductor.riken.jp/packages/devel/data/experiment/html/mcsurvdata.html
The post will only allow me add two links so i've removed 'https from any links hereafter
The session goes as follows:
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
install.packages("BiocManager")
Installing package into ‘C:/Users/PathologyUser/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL ://cran.rstudio.com/bin/windows/contrib/4.0/BiocManager_1.30.10.zip'
Content type 'application/zip' length 99889 bytes (97 KB)
downloaded 97 KB
package ‘BiocManager’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\PathologyUser\AppData\Local\Temp\Rtmp4WVGB0\downloaded_packages
BiocManager::valid("mcsurvdata")
[1] TRUE
BiocManager::install("mcsurvdata")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'BiocVersion', 'mcsurvdata'
also installing the dependencies ‘BiocGenerics’, ‘Biobase’
trying URL ://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/BiocGenerics_0.34.0.zip'
Content type 'application/zip' length 746705 bytes (729 KB)
downloaded 729 KB
trying URL ://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/Biobase_2.48.0.zip'
Content type 'application/zip' length 2418713 bytes (2.3 MB)
downloaded 2.3 MB
trying URL ://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/BiocVersion_3.11.1.zip'
Content type 'application/zip' length 8904 bytes
downloaded 8904 bytes
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘BiocVersion’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\PathologyUser\AppData\Local\Temp\Rtmp4WVGB0\downloaded_packages
installing the source package ‘mcsurvdata’
trying URL ://bioconductor.org/packages/3.11/data/experiment/src/contrib/mcsurvdata_1.6.0.tar.gz'
Content type 'application/x-gzip' length 236460 bytes (230 KB)
downloaded 230 KB
The downloaded source packages are in
‘C:\Users\PathologyUser\AppData\Local\Temp\Rtmp4WVGB0\downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘mcsurvdata’ had non-zero exit status
Any help would be great thanks