When I run the example script from here
http://bioconductor.org/packages/release/bioc/vignettes/flowClean/inst/doc/flowClean.R
I get the following error.
It produces some synPerturbed data, then processes it. 
I have looked around, but have been unable to find out how to fix this.


jamfer@PsyFer-Work:~/Dropbox/Bioinformatics/tools/flowclean$ Rscript flowClean_example.R 
Loading required package: flowCore
Loading required package: lattice
flowFrame object '9301d9e4-a160-477f-a5fb-ee7d785d5655'
with 76466 cells and 17 observables:
         name          desc  range   minRange maxRange
$P1     FSC-A          <NA> 262144    0.00000   262144
$P2     FSC-H          <NA> 262144    0.00000   262144
$P3     SSC-A          <NA> 261589    0.00000   261589
$P4      Time          <NA>   2048    0.00000     2048
$P5  <B515-A>     CD27 FITC 260954  -26.88460   260954
$P6  <V705-A>    CD57 QD705 261947 -111.00000   261947
$P7  <G560-A>       CD95 PE 261196 -111.00000   261196
$P8  <G660-A>   CD28 Cy5 PE 261507 -111.00000   261507
$P9  <G710-A> CD244 Cy55 PE 261763 -111.00000   261763
$P10 <G780-A>   CD31 Cy7 PE 261402 -111.00000   261402
$P11 <R710-A>    CCR7 Ax680 261602 -111.00000   261602
$P12 <R780-A>    CD3 H7 APC 261301 -111.00000   261301
$P13 <V450-A>   CD127 BV421 260964  -35.98385   260964
$P14 <V545-A>        Aq Blu 260949  -22.20724   260949
$P15 <V585-A>     CD8 QD585 261965 -111.00000   261965
$P16 <R660-A>    CD45RA APC 261023  -96.50925   261023
$P17 <V605-A>     CD4 BV605 261131 -111.00000   261131
212 keywords are stored in the 'description' slot
Error in new("flowFrame", exprs = ex, parameters = new("AnnotatedDataFrame",  : 
  could not find function "new"
Calls: clean -> makeFCS
Execution halted

session info is

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] gridExtra_2.2.1  flowViz_1.40.0   lattice_0.20-35 
[4] flowClean_1.14.0 flowCore_1.42.2 

loaded via a namespace (and not attached):
 [1] graph_1.54.0        Rcpp_0.12.12        cluster_2.0.6      
 [4] BiocGenerics_0.22.0 sfsmisc_1.1-1       MASS_7.3-47        
 [7] bit_1.1-12          rrcov_1.4-3         pcaPP_1.9-72       
[10] tools_3.4.0         parallel_3.4.0      gtable_0.2.0       
[13] Biobase_2.36.2      KernSmooth_2.23-15  latticeExtra_0.6-28
[16] corpcor_1.6.9       IDPmisc_1.1.17      matrixStats_0.52.2 
[19] RColorBrewer_1.1-2  changepoint_2.2.2   robustbase_0.92-7  
[22] compiler_3.4.0      DEoptimR_1.0-8      methods_3.4.0      
[25] stats4_3.4.0        mvtnorm_1.0-6       hexbin_1.27.1      
[28] zoo_1.8-0  

Thanks

I got it to work by pasting the library into the top of my script.

Then modifying line 312 to be

k <- new("AnnotatedDataFrame",o)
outFCS <- new("flowFrame", exprs=ex, parameters=k, description=description(fF))

Then loaded in the synPerturbed.rda file manually 

Then to get the plots to work I installed 

KernSmooth

 biocLite("KernSmooth")

Now I have some pretty plots that match the example. awesome :D