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Question: DiffBind installation doesn't work
0
gravatar for Gary
2.5 years ago by
Gary0
Gary0 wrote:

Hi, 

I can run DiffBind well before. However, after I updated R 3.2.0, R RStudio 0.99.441, and DiffBind 1.14.4, the DiffBind cannot be used anymore. It always shows that (fig1 as below):

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 

  there is no package called ‘GO.db’

Error: package or namespace load failed for ‘DiffBind’

I have install GO.db & DiffBind many times, but it doesn't work. Could you give me a help? Many thanks.

Gary

fig1

ADD COMMENTlink modified 2.4 years ago • written 2.5 years ago by Gary0
1
gravatar for Gord Brown
2.5 years ago by
Gord Brown560
United Kingdom
Gord Brown560 wrote:

Hi,

Most likely some other packages need to be re-compiled/installed for the upgraded R.  There is no (fundamental) reason why GO.db should fail to install, so check the installation dates of other packages to see what is out of date.

Note that you should be installing Bioconductor packages via the install method given on the Bioconductor site: http://www.bioconductor.org/install/ , as in:

> source("http://bioconductor.org/biocLite.R")
> biocLite('GO.db')

to ensure that all required packages are installed and/or updated.  Give that a try and see how it goes.

Cheers,

 - Gord

ADD COMMENTlink written 2.5 years ago by Gord Brown560
0
gravatar for Gary
2.5 years ago by
Gary0
Gary0 wrote:

Hi Gord,

Many thanks for your help. In fact, DiffBind is the first R based tool I use. I cannot run it without you & Rory’s continual support. However, I am really not familiar with R.  After updating, I find that edgeR can be run well (DiffBind_fig1). I have installed GO.db based on your suggestion (DiffBind_fig2). But it still shows an error when I run DiffBind (DiffBind_fig3):

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘GO.db’

Error: package or namespace load failed for ‘DiffBind’

I note another different thing. Before updating, the X11 will be automatically started. Now, it doesn’t (DiffBind_fig3). Of course, I can manually open the X11, but it shows an xterm window I never see before (DiffBind_fig4). The X11 was downloaded from XQuartz on R webpage (DiffBind_fig4). I really need to run DiffBind again. Any suggestion is very welcome. Thanks you so much.

Gary

Diffbind_fig1

 

DiffBind_fig2

 

DiffBind_fig3

 

DiffBind_fig4

ADD COMMENTlink modified 2.4 years ago • written 2.5 years ago by Gary0
1

Hi,

Your screenshot 2 (showing installation of GO.db) doesn't show the whole installation, and in particular doesn't show whether it finally succeeded.  What happens if you type
> library(GO.db)
at the command prompt?  If it doesn't load (which I assume it won't) then your problem has nothing to do with DiffBind, but instead, like I said earlier, has to do with other packages that are out of date, preventing GO.db from being installed correctly.  You'll need to update those packages, or delete and re-install them.

Regarding XQuartz, I have the latest version (2.7.7) and it auto-launches fine when using R remotely.  You see the xterm if you launch it manually.  Nothing unusual there.  But whatever problems you are having with it have absolutely nothing to do with DiffBind. 

Cheers,

 - Gord

ADD REPLYlink written 2.5 years ago by Gord Brown560
0
gravatar for Gary
2.4 years ago by
Gary0
Gary0 wrote:

Hi Gord,

Thanks for your help. Now I can run DiffBind again. Below is something what I did that could be useful for other users have the same problem: (1) I re-installed an older version of R, i.e. version 3.1.3 (2) I re-install some packages not in the latest R version 3.2.1 I installed previous with unknown reason, e.g. ggplot2, reshape2, rgl, statmod, org.Hs.eg.db, locfit, and splines. In fact, I still don’t know the reason why DiffBind cannot run on the latest R version on our iMac. However, at least it works well on an older R, it is good enough for me. Thanks again. 

ADD COMMENTlink written 2.4 years ago by Gary0

DiffBind runs fine on R 3.2.x on Mac.  As I said previously, the problem is not mysterious. Some packages that DiffBind depends on were not compatible with R 3.2.x, so needed to be re-installed.  Did you try that?  Alternatively, remove your 3.1.x installation completely (from /Library/Frameworks/R.framework , plus the application, plus any libraries you have installed in your personal directory) and install R 3.2.x and DiffBind from scratch.

ADD REPLYlink written 2.4 years ago by Gord Brown560

hi Gord

I am a new and my DiffBind installation also doesn't work.The problem is as follows:

> library("DiffBind")
Loading required package: GenomicAlignments
Loading required package: Biostrings
Error in unloadNamespace(package) : 
  namespace ?.iostrings?.is imported by ?.enomicAlignments?. ?.samtools?. ?.enomicFeatures?. ?.tracklayer?. ?.EGGREST?.so cannot be unloaded
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,  : 
  Package ?.iostrings?.version 2.36.3 cannot be unloaded

and sessionInfo() is as follows:

> sessionInfo("DiffBind")
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.5 (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:
character(0)

other attached packages:
[1] DiffBind_1.14.5

loaded via a namespace (and not attached):
 [1] KEGGREST_1.8.0                         
 [2] qvalue_2.0.0                           
 [3] clusterProfiler_2.2.4                  
 [4] TxDb.Mmusculus.UCSC.mm9.knownGene_3.1.2
 [5] gtools_3.5.0                           
 [6] reshape2_1.4.1                         
 [7] splines_3.2.1                          
 [8] colorspace_1.2-6                       
 [9] stats4_3.2.1                           
[10] rtracklayer_1.28.9                     
[11] grDevices_3.2.1                        
[12] GenomicFeatures_1.20.3                 
[13] XML_3.98-1.3                           
[14] DBI_0.3.1                              
[15] BiocParallel_1.2.20                    
[16] BiocGenerics_0.14.0                    
[17] RColorBrewer_1.1-2                     
[18] lambda.r_1.1.7                         
[19] plyr_1.8.3                             
[20] stringr_1.0.0                          
[21] zlibbioc_1.14.0                        
[22] Biostrings_2.36.4                      
[23] munsell_0.4.2                          
[24] GOSemSim_1.26.0                        
[25] gtable_0.1.2                           
[26] futile.logger_1.4.1                    
[27] ChIPseeker_1.4.6                       
[28] caTools_1.17.1                         
[29] Biobase_2.28.0                         
[30] IRanges_2.2.7                          
[31] biomaRt_2.24.0                         
[32] GenomeInfoDb_1.4.2                     
[33] parallel_3.2.1                         
[34] AnnotationDbi_1.30.1                   
[35] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2
[36] proto_0.3-10                           
[37] methods_3.2.1                          
[38] Rcpp_0.12.0                            
[39] KernSmooth_2.23-15                     
[40] scales_0.2.5                           
[41] limma_3.24.15                          
[42] gdata_2.17.0                           
[43] plotrix_3.5-12                         
[44] DO.db_2.9                              
[45] S4Vectors_0.6.3                        
[46] XVector_0.8.0                          
[47] Rsamtools_1.20.4                       
[48] gplots_2.17.0                          
[49] ggplot2_1.0.1                          
[50] stats_3.2.1                            
[51] datasets_3.2.1                         
[52] graphics_3.2.1                         
[53] png_0.1-7                              
[54] digest_0.6.8                           
[55] stringi_0.5-5                          
[56] dplyr_0.4.2                            
[57] GenomicRanges_1.20.5                   
[58] grid_3.2.1                             
[59] DOSE_2.6.5                             
[60] tools_3.2.1                            
[61] bitops_1.0-6                           
[62] magrittr_1.5                           
[63] RCurl_1.95-4.7                         
[64] RSQLite_1.0.0                          
[65] futile.options_1.0.0                   
[66] GO.db_3.1.2                            
[67] MASS_7.3-43                            
[68] utils_3.2.1                            
[69] org.Mm.eg.db_3.1.2                     
[70] assertthat_0.1                         
[71] base_3.2.1                             
[72] httr_1.0.0                             
[73] R6_2.1.1                               
[74] boot_1.3-17                            
[75] GenomicAlignments_1.4.1                
[76] igraph_1.0.1 

Is the Biostrings_2.36.4 package that DiffBind depends on is not compatible ? Could you give me a help? Thanks 

- February

 

ADD REPLYlink written 2.3 years ago by February0
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