Question: openCyto fails to load
0
gravatar for pavitrarc
4.1 years ago by
pavitrarc20
United States/Seattle/Fred Hutch
pavitrarc20 wrote:

Hi, 

I'm getting an error when trying to load openCyto. It was working fine before but now I'm getting the following error message:

> library(openCyto);
Error : objects ‘dfltCounts’, ‘drvkde’ are not exported by 'namespace:ks'
Error: package or namespace load failed for ‘openCyto’

 

I tried an update using biocLite but I still get the same message:

> biocLite('openCyto')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.0), R
  3.2.2 (2015-08-14).
Installing package(s) ‘openCyto’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/macosx/mavericks/contrib/3.2/openCyto_1.8.0.tgz'
Content type 'application/x-gzip' length 1242716 bytes (1.2 MB)
==================================================
downloaded 1.2 MB


The downloaded binary packages are in
    /var/folders/k2/wvj3nfcn021_lyfx04sqyxcm0000gn/T//RtmpR3CxcF/downloaded_packages
> library('openCyto');
Error : objects ‘dfltCounts’, ‘drvkde’ are not exported by 'namespace:ks'
Error: package or namespace load failed for ‘openCyto’

 

My R session info:

> sessionInfo();
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] flowWorkspace_3.16.0     
[2] gridExtra_2.0.0          
[3] ncdfFlow_2.16.0          
[4] BH_1.58.0-1              
[5] RcppArmadillo_0.6.100.0.0
[6] flowViz_1.34.0           
[7] lattice_0.20-33          
[8] flowCore_1.36.0          
[9] BiocInstaller_1.20.0     

loaded via a namespace (and not attached):
 [1] multicool_0.1-8     ks_1.10.0          
 [3] pcaPP_1.9-60        stats4_3.2.2       
 [5] chron_2.3-47        MCMCpack_1.3-3     
 [7] XML_3.98-1.3        RBGL_1.46.0        
 [9] R.oo_1.19.0         hexbin_1.27.1      
[11] DBI_0.3.1           R.utils_2.1.0      
[13] Rgraphviz_2.14.0    BiocGenerics_0.16.0
[15] RColorBrewer_1.1-2  robustbase_0.92-5  
[17] stringr_1.0.0       zlibbioc_1.16.0    
[19] gtable_0.1.2        R.methodsS3_1.7.0  
[21] mvtnorm_1.0-3       coda_0.18-1        
[23] misc3d_0.8-4        latticeExtra_0.6-26
[25] Biobase_2.30.0      knitr_1.11         
[27] flowClust_3.8.0     parallel_3.2.2     
[29] DEoptimR_1.0-4      Rcpp_0.12.1        
[31] KernSmooth_2.23-15  corpcor_1.6.8      
[33] graph_1.48.0        IDPmisc_1.1.17     
[35] stringi_1.0-1       dplyr_0.4.3        
[37] grid_3.2.2          clue_0.3-50        
[39] tools_3.2.2         rgl_0.95.1367      
[41] magrittr_1.5        cluster_2.0.3      
[43] rrcov_1.3-8         MASS_7.3-44        
[45] data.table_1.9.6    assertthat_0.1     
[47] R6_2.1.1  

Appreciate any help. 

Thanks!

 

opencyto bioclite • 1.1k views
ADD COMMENTlink modified 4.1 years ago by yang.chen0 • written 4.1 years ago by pavitrarc20
Answer: openCyto fails to load
0
gravatar for Jiang, Mike
4.1 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

It is because one of its dependency package 'ks' changes its APIs. I will fix it.

ADD COMMENTlink written 4.1 years ago by Jiang, Mike1.2k

Thanks Mike!

ADD REPLYlink written 4.1 years ago by pavitrarc20

I've push the fix.  See https://github.com/RGLab/flowStats/issues/16

ADD REPLYlink written 4.1 years ago by Jiang, Mike1.2k
Answer: openCyto fails to load
0
gravatar for yang.chen
4.1 years ago by
yang.chen0
European Union
yang.chen0 wrote:

Hello, 

I still meet the error even after updating flowStats to 3.28.1. Any suggestions?

** R
** inst
** preparing package for lazy loading
Error : object ‘drvkde’ is not exported by 'namespace:ks'
ERROR: lazy loading failed for package ‘openCyto’
sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

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

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

other attached packages:
 [1] flowStats_3.28.1          flowWorkspace_3.16.0     
 [3] gridExtra_2.0.0           ncdfFlow_2.16.0          
 [5] BH_1.58.0-1               RcppArmadillo_0.6.100.0.0
 [7] flowViz_1.34.0            lattice_0.20-33          
 [9] cluster_2.0.3             mvoutlier_2.0.6          
[11] sgeostat_1.0-26           fda_2.4.4                
[13] Matrix_1.2-2              flowCore_1.36.0          
[15] BiocInstaller_1.20.0      R.utils_2.1.0            
[17] R.oo_1.19.0               R.methodsS3_1.7.0        

loaded via a namespace (and not attached):
 [1] multicool_0.1-9       ks_1.10.0             reshape2_1.4.1       
 [4] pcaPP_1.9-60          colorspace_1.2-6      stats4_3.2.2         
 [7] chron_2.3-47          XML_3.98-1.3          hexbin_1.27.1        
[10] DBI_0.3.1             Rgraphviz_2.14.0      BiocGenerics_0.16.0  
[13] RColorBrewer_1.1-2    plyr_1.8.3            robustbase_0.92-5    
[16] stringr_1.0.0         zlibbioc_1.16.0       munsell_0.4.2        
[19] robCompositions_1.9.1 pls_2.5-0             gtable_0.1.2         
[22] mvtnorm_1.0-3         codetools_0.2-14      misc3d_0.8-4         
[25] latticeExtra_0.6-26   Biobase_2.30.0        GGally_0.5.0         
[28] parallel_3.2.2        sROC_0.1-2            DEoptimR_1.0-4       
[31] proto_0.3-10          Rcpp_0.12.1           KernSmooth_2.23-15   
[34] corpcor_1.6.8         scales_0.3.0          graph_1.48.0         
[37] IDPmisc_1.1.17        ggplot2_1.0.1         digest_0.6.8         
[40] stringi_1.0-1         dplyr_0.4.3           grid_3.2.2           
[43] tools_3.2.2           rgl_0.95.1367         magrittr_1.5         
[46] rrcov_1.3-8           MASS_7.3-44           data.table_1.9.6     
[49] assertthat_0.1        reshape_0.8.5         R6_2.1.1  

 

Thank you in advance! 
 

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by yang.chen0

You also need to update openCyto to 1.8.2

ADD REPLYlink written 4.1 years ago by Jiang, Mike1.2k
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