Trying to install bioClite 3.2 onto R 3.2.2 using

biocLite("tgirke/systemPipeR", build_vignettes=TRUE, dependencies=TRUE)

this appears to install all the packages then fails as

* checking for file 'C:...\Temp\Rtmpmm0BY2\devtools278c2297552f\tgirke-systemPipeR-4b48c46/DESCRIPTION' ... OK
* preparing 'systemPipeR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
Warning: running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/Rcmd.exe" INSTALL -l "C:....\Temp\RtmpYF4EL9\Rinst1e543dcb4481" --no-multiarch "C:/..../Temp/RtmpYF4EL9/Rbuild1e544bb64e5d/systemPipeR"' had status 1
      -----------------------------------
ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
* removing 'C:/..../Temp/RtmpYF4EL9/Rinst1e543dcb4481/systemPipeR'

biocValid() finds only the the R-package curl is possibly out of date the curl version is 0.9.7 given as built under R version 3.2.5, I am running R 3.2.2

> traceback()
14: stop("Command failed (", status, ")", call. = FALSE)
13: fun(r, args = args, env_vars = env_vars, path = path, ...)
12: R(cmd, path, quiet = quiet)
11: force(code)
10: withr::with_temp_libpaths(R(cmd, path, quiet = quiet))
9: build(pkg, tempdir(), vignettes = build_vignettes, quiet = quiet)
8: install(source, ..., quiet = quiet, metadata = metadata)
7: FUN(X[[i]], ...)
6: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1))
5: install_remotes(remotes, quiet = quiet, ...)
4: devtools::install_github(doing, ...)
3: .githubInstall(todo, ...)
2: .biocLiteInstall(pkgs, ask = ask, siteRepos = siteRepos, suppressUpdates = suppressUpdates, 
       ...)
1: biocLite("tgirke/systemPipeR", build_vignettes = TRUE, dependencies = TRUE)

Any suggestions would be appreciated.

Thanks for the suggestion, since my entry, I installed R 3.3.1 and updated all the R libraries, now I get

> biocLite("tgirke/systemPipeR", build_vignettes=TRUE, dependencies=TRUE)    
.
.
.
ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
* removing 'C:/.../Local/Temp/RtmpGGgCOK/Rinst2b98b35608/systemPipeR'

I followed with

> biocValid()

* sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] httr_1.2.1           curl_1.0             BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] R6_2.1.2        tools_3.3.1     withr_1.0.2     memoise_1.0.0   knitr_1.13      git2r_0.15.0   
[7] digest_0.6.9    devtools_1.12.0

* Out-of-date packages
                Package           LibPath                                       Installed Built   ReposVer 
GenomicFeatures "GenomicFeatures" "C:/.../R/win-library/3.3" "1.24.4"  "3.3.1" "1.24.5" 
limma           "limma"           "C:/.../R/win-library/3.3" "3.28.14" "3.3.1" "3.28.16"
                Repository                                              
GenomicFeatures "https://bioconductor.org/packages/3.3/bioc/src/contrib"
limma           "https://bioconductor.org/packages/3.3/bioc/src/contrib"

update with biocLite()

Error: 2 package(s) out of date
> biocLite()

.

.

* installing *source* package 'BiocParallel' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (BiocParallel)
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (GenomicFeatures)

The downloaded source packages are in
	‘C:\...\Local\Temp\RtmpYRC5io\downloaded_packages’
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable
Error in install.packages(update[instlib == l, "Package"], l, repos = repos,  : 
  unable to install packages

on your suggestion

> biocLite("GO.db")

.

.

The downloaded binary packages are in
	C:\...\Local\Temp\RtmpYRC5io\downloaded_packages
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable
Error in install.packages(update[instlib == l, "Package"], l, repos = repos,  : 
  unable to install packages

Seems like I cannot write to the directory required....

A few suggestions. First, you want to resolve your permission issue on your system for installing packages (e.g. run with admin permissions). After this please install systemPipeR like any other Bioconductor package with:

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

A few suggestions related to NGS analysis on Windows. While many analysis steps will run fine in systemPipeR on Windows, alignments and other steps depending on external software are unlikely to work. The only R/Bioconductor software I know that supports NGS alignments on Windows is QuasR.

Thomas 

Thank you for the input. I added a pointer to a personnel library in the .Rlogin. I proceeded as

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

> biocLite("systemPipeR")

I allowed to update all and to save in personnel library, this seemed to execute

> biocValid()

I was informed some libraries were out of date

> biocLite()

I allowed to update all to save in personnel library, this seemed to execute

> library(systemPipeR)
Loading required package: ShortRead
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘hwriter’
Error: package ‘ShortRead’ could not be loaded

Any suggestions would be useful. I will try to get admin privileges and try again. I suspect the mixing of personnel and system libraries was a bad idea and is probably messing up the install.

Otherwise, probably have spent enough effort trying to get this to work. I need to move on and try other options. Any information on how to clean off the machine would be useful. Thanks for any help.

I have installed CRAN's hwriter and now get

> library(systemPipeR)
Loading required package: ShortRead
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘Category’
Error: package or namespace load failed for ‘systemPipeR’

> biocLite("Category")

> library(systemPipeR)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘xtable’
Error: package or namespace load failed for ‘systemPipeR’

I have installed CRAN's xtable and now get

> library(systemPipeR)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘AnnotationForge’
Error: package or namespace load failed for ‘systemPipeR’

Does this go on for much longer? Is there a list that I could use to do this in bulk? Will I need to do this all again if I restart R?

You need to fix your R installation or nothing will work. Getting admin permissions for the system you are on may simplify this task.   

Just to continue

> biocLite("AnnotationForge")

> library(systemPipeR)

  there is no package called ‘BBmisc’

> install.packages("BBmisc")

> library(systemPipeR)

  there is no package called ‘fail’

> install.packages("fail")

> library(systemPipeR)

  there is no package called ‘sendmailR’

> install.packages("sendmailR")

> library(systemPipeR)

> library(systemPipeRdata)

  there is no package called ‘systemPipeRdata’

> biocLite("systemPipeRdata")

.

.

The downloaded source packages are in

        ‘C:\Users\paul28\AppData\Local\Temp\Rtmpmw4G7W\downloaded_packages’

Old packages: 'XVector', 'mgcv', 'survival'

Update all/some/none? [a/s/n]:

a

  There is a binary version available but the source version is later:

        binary source needs_compilation

XVector 0.12.0 0.12.1              TRUE

  Binaries will be installed

Warning: package ‘XVector’ is in use and will not be installed

Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :

  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable

The result is that R locks up and will not be restarted from RStudio

Sorry about the frustration, but this will all go away if you can fix your R/Bioc install. In a functional environment, biocLite() will install all dependency package for you automatically and you only need to do this once. On Windows (and OS X) these installs are also very fast since pre-compiled binaries are used. If you have insufficient permissions on your current system then perhaps contact the admin of that computer or try it on another computer. 

I used .Rlogin to add a writeable first entry in .libPaths. After a few more try/add code element/tray again I can actually run the package.

I have been following the text/instructions in VAR-Seq workflow template: Some Descriptive Title of May 15,2016

The first issue was with the command

args<-systemArgs(sysma = "param/trimPE/param", mytargets="targetsPE.txt")[1:4]

The file targetPE.txt point at ./data/... but the files are actually in ./data/fastq/...

The second issue was with the command

args <- systemArgs(sysma="bwa.param", mytargets="targets.txt")

The file bwa.param is not found, so I am tryign to sort that one

Is there a better set of text/instructions that I should be referring to

Thank you.

I fixed the file path issue by editing the target files to the full path.

I did find and switched to working from the Overview Vignette. Very useful.

I did manage to crash Rstudio by resizing the plot window when executing seeFastqPlot(fqlist)but I think that may be a normal response during a large plot.

The note about packages not supported under R-windows is useful.

Thank you for all of your assistance.