Entering edit mode
6.3 years ago
Pijush Das
▴
10
I have recently update the R version 3.4.3 (2017-11-30 and the latest RStudio in my windows 64 bit PC. After updating those software whenever I am going to install any package facing lots of error. I unable to find out any way to solve the problem. The warnings and the errors are given below. Please help
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
>biocLite("flowStats")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.3), R version 3.4.3.
Temporarily using Bioconductor version 2.14
Installing package(s) 'flowStats'
also installing the dependencies ‘ncdfFlow’, ‘RBGL’, ‘flowCore’, ‘flowWorkspace’, ‘flowViz’
Warning: unable to access index for repository http://bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.4:
cannot open URL 'http://bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/2.14/data/annotation/bin/windows/contrib/3.4:
cannot open URL 'http://bioconductor.org/packages/2.14/data/annotation/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/2.14/data/experiment/bin/windows/contrib/3.4:
cannot open URL 'http://bioconductor.org/packages/2.14/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/2.14/extra/bin/windows/contrib/3.4:
cannot open URL 'http://bioconductor.org/packages/2.14/extra/bin/windows/contrib/3.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘ncdfFlow’ ‘RBGL’ ‘flowCore’
‘flowWorkspace’
Do you want to attempt to install these from sources?
y/n: n
installing the source packages ‘flowViz’, ‘flowStats’
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/flowViz_1.28.22.tar.gz'
Content type 'application/x-gzip' length 810843 bytes (791 KB)
downloaded 791 KB
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/flowStats_3.22.6.tar.gz'
Content type 'application/x-gzip' length 4157046 bytes (4.0 MB)
downloaded 4.0 MB
ERROR: dependency 'flowCore' is not available for package 'flowViz'
* removing 'C:/Users/SANJIB/Documents/R/win-library/3.4/flowViz'
In R CMD INSTALL
ERROR: dependencies 'flowCore', 'flowWorkspace', 'flowViz' are not available for package 'flowStats'
* removing 'C:/Users/SANJIB/Documents/R/win-library/3.4/flowStats'
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\SANJIB\AppData\Local\Temp\Rtmpc7Obyw\downloaded_packages’
Old packages: 'spatial', 'spdep', 'statmod', 'stringdist', 'survminer', 'svmpath', 'testthat', 'tgp', 'tibble', 'tidyr', 'tinytex', 'tm',
'VennDiagram', 'viridis', 'WriteXLS', 'XLConnect', 'XLConnectJars', 'XML'
Update all/some/none? [a/s/n]:
n
Warning messages:
1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\SANJIB\Documents\R\win-library\3.4" C:\Users\SANJIB\AppData\Local\Temp\Rtmpc7Obyw/downloaded_packages/flowViz_1.28.22.tar.gz' had status 1
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘flowViz’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\SANJIB\Documents\R\win-library\3.4" C:\Users\SANJIB\AppData\Local\Temp\Rtmpc7Obyw/downloaded_packages/flowStats_3.22.6.tar.gz' had status 1
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘flowStats’ had non-zero exit status
5: installed directory not writable, cannot update packages 'MASS'
>
Maybe you can upgrade your Bioconductor first.