I am just starting to use Rbowtie and QuasR, and attempting to do the sample QuasR session. I am able to load the libraries, and the sample data, as shown:

> setwd("C:/Users/fergusonaa2/Desktop/QuasR")
> library(QuasR)
> library(BSgenome)
> library(Rsamtools)
> library(rtracklayer)
> library(GenomicFeatures)
> library(Gviz)
> file.copy(system.file(package="QuasR", "extdata"), ".", recursive=TRUE)
[1] TRUE
> sampleFile <- "extdata/samples_chip_single.txt"
> genomeFile <- "extdata/hg19sub.fa"

However, once I use the qAlign function

proj <- qAlign(sampleFile, genomeFile)

I get the following message:

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Deleting an incomplete index at: C:/Users/fergusonaa2/Desktop/QuasR/extdata/hg19sub.fa.Rbowtie
Creating an Rbowtie index for C:/Users/fergusonaa2/Desktop/QuasR/extdata/hg19sub.fa
Error in system2(file.path(system.file(package = "Rbowtie"), "bowtie-build"),  : 
  'CreateProcess' failed to run 'C:\Users\FERGUS~1\DOCUME~1\R\R-31~1.1\library\Rbowtie\BOWTIE~1.EXE "C:/Users/fergusonaa2/Desktop/QuasR/extdata/hg19sub.fa" "C:/Users/fergusonaa2/Desktop/QuasR/extdata/hg19sub.fa.Rbowtie/bowtieIndex"'

I also get a similar error when I try any of the functions in Rbowtie:

> bowtie_build_usage()
Error in system(call, intern = TRUE) : 
  'CreateProcess' failed to run 'C:\Users\FERGUS~1\DOCUME~1\R\R-31~1.1\library\Rbowtie\BOWTIE~1.EXE --usage "dummy" "dummy/index"'

I am hoping someone can tell me what I am missing. Thanks.

Here is my sessionInfo() output

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: i386-w64-mingw32/i386 (32-bit)

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

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

other attached packages:
 [1] Gviz_1.8.4             GenomicFeatures_1.16.3
 [3] AnnotationDbi_1.26.1   Biobase_2.24.0        
 [5] rtracklayer_1.24.2     Rsamtools_1.16.1      
 [7] BSgenome_1.32.0        Biostrings_2.32.1     
 [9] XVector_0.4.0          QuasR_1.4.2           
[11] Rbowtie_1.4.5          GenomicRanges_1.16.4  
[13] GenomeInfoDb_1.0.2     IRanges_1.22.10       
[15] BiocGenerics_0.10.0    BiocInstaller_1.14.2  

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          base64enc_0.1-2         
 [3] BatchJobs_1.4            BBmisc_1.7              
 [5] BiocParallel_0.6.1       biomaRt_2.20.0          
 [7] biovizBase_1.12.3        bitops_1.0-6            
 [9] brew_1.0-6               checkmate_1.4           
[11] cluster_1.15.3           codetools_0.2-9         
[13] colorspace_1.2-4         DBI_0.3.1               
[15] dichromat_2.0-0          digest_0.6.4            
[17] fail_1.2                 foreach_1.4.2           
[19] foreign_0.8-61           Formula_1.1-2           
[21] GenomicAlignments_1.0.6  Hmisc_3.14-5            
[23] hwriter_1.3.2            iterators_1.0.7         
[25] lattice_0.20-29          latticeExtra_0.6-26     
[27] matrixStats_0.10.0       munsell_0.4.2           
[29] nnet_7.3-8               plyr_1.8.1              
[31] R.methodsS3_1.6.1        RColorBrewer_1.0-5      
[33] Rcpp_0.11.3              RCurl_1.95-4.3          
[35] rpart_4.1-8              RSQLite_0.11.4          
[37] scales_0.2.4             sendmailR_1.2-1         
[39] ShortRead_1.22.0         splines_3.1.1           
[41] stats4_3.1.1             stringr_0.6.2           
[43] survival_2.37-7          tools_3.1.1             
[45] VariantAnnotation_1.10.5 XML_3.98-1.1            
[47] zlibbioc_1.10.0  

Windows is in general a suboptimal OS for aligning and whatnot, so if you have access to a better OS like Linux or MacOS, I would use that instead. Note that there is a Bioconductor AMI and a reasonably sized virtual machine on Amazon tends to be really cheap these days.

http://bioconductor.org/help/bioconductor-cloud-ami/

Anyway, if you have to use your Windows box, it looks like you are having problems with the 8.1 paths (things like C:/PROGRA~1), which some *nix based tools don't understand. You might try something like:

remove.packages(c("QuasR","Rbowtie"))
dir.create("C:/Users/fergusonaa2/R/win-library/3.1", recursive = TRUE)
.libPaths("C:/Users/fergusonaa2/R/win-library/3.1")
library(BiocInstaller)
biocLite(c("QuasR","Rbowtie"))

And see if it works when you have no spaces in your path.

Thanks for the advice.  Seems like trying with a Linux OS will be my best option.  I tried changing the paths with Windows, but have not gotten that to work so far.

For me this is what happens:

> library(QuasR)
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rbowtie
> sampleFile <- system.file("extdata/samples_chip_single.txt", package = "QuasR")
> genomeFile <- system.file("extdata/hg19sub.fa", package = "QuasR")
> sampleFile
[1] "C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/QuasR/extdata/samples_chip_single.txt"
> genomeFile
[1] "C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/QuasR/extdata/hg19sub.fa"
> proj <- qAlign(sampleFile, genomeFile)
Creating .fai file for: C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/QuasR/extdata/hg19sub.fa
alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Creating an Rbowtie index for C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/QuasR/extdata/hg19sub.fa
Error in system2(file.path(system.file(package = "Rbowtie"), "bowtie-build"),  : 
  'CreateProcess' failed to run 'C:\Users\FERGUS~1\DOCUME~1\R\R-31~1.1\library\Rbowtie\BOWTIE~1.EXE "C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/QuasR/extdata/hg19sub.fa" "C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/QuasR/extdata/hg19sub.fa.Rbowtie/bowtieIndex"'
> dir(paste0(path.package("QuasR"), "/extdata"))
 [1] "auxiliaries.txt"         "bis_1_1.fa.bz2"          "chip_1_1.fq.bz2"        
 [4] "chip_2_1.fq.bz2"         "hg19sub.fa"              "hg19sub.fa.fai"         
 [7] "hg19sub.fa.md5"          "hg19sub.fa.Rbowtie"      "hg19sub_annotation.gtf" 
[10] "hg19sub_snp.txt"         "mirbaseXX_qsr.gff3"      "mirna_1.fa"             
[13] "NC_001422.1.fa"          "rna_1_1.fq.bz2"          "rna_1_2.fq.bz2"         
[16] "rna_2_1.fq.bz2"          "rna_2_2.fq.bz2"          "samples_bis_single.txt" 
[19] "samples_chip_single.txt" "samples_mirna.txt"       "samples_rna_paired.txt" 
[22] "samples_rna_single.txt" 

> library(Rbowtie)
> path.package("Rbowtie")
[1] "C:/Users/fergusonaa2/Documents/R/R-3.1.1/library/Rbowtie"