Facing problem when trying to install a new packages in R version 3.4.3 (2017-11-30 through latest RStudio.

Question

[Pijush Das]

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' 
>

[turkulerc]

Maybe you can upgrade your Bioconductor first.

Answer 1

[Devon Ryan]

flowCore requires compilation (at least in that release), so you can't select "no" when asked "Do you want to attempt to install these from sources?". You might have luck with the most recent bioconductor version, but I suspect compilation will be required there too.