Error in running the ChAMP test runs from vignette
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vd4mmind • 0
@vd4mmind-11547
Last seen 2.6 years ago
United States

I have just been able to install ChAMP in my local R studio , with the FEM latest package and everything seems to work fine. I already have the shiny and plotly packages installed but however when am trying to launch the GUI it fails. Upon close inspection I see that the version which biocLite installs is 'ChAMP_1.10.0.tgz' and not the latest 2.20 which is mentioned in the vignette. My version of R is 3.3.1 and its running in MAC OS X 12.

for installation I used the below command

biocLite("ChAMP")

Can you please walk me through why is this happening? Is the latest version not synced yet in the Bioconductor as  I see the vignette was updated 2-3 days back. Any guidance is appreciated

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12 (Sierra)

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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rmarkdown_1.1                              plotly_4.5.2                               IlluminaHumanMethylation450kmanifest_0.4.0
 [4] RnBeads_1.4.0                              plyr_1.8.4                                 methylumi_2.18.2                          
 [7] FDb.InfiniumMethylation.hg19_2.2.0         TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2    GenomicFeatures_1.24.5                    
[10] scales_0.4.0                               illuminaio_0.14.0                          gridExtra_2.2.1                           
[13] fields_8.4-1                               maps_3.1.1                                 spam_1.4-0                                
[16] ff_2.2-13                                  bit_1.1-12                                 treemap_2.4-1                             
[19] geneplotter_1.50.0                         annotate_1.50.1                            XML_3.98-1.4                              
[22] shiny_0.14.1                               ChAMP_1.10.0                               Illumina450ProbeVariants.db_1.8.0         
[25] ChAMPdata_1.10.0                           minfi_1.18.6                               bumphunter_1.12.0                         
[28] locfit_1.5-9.1                             iterators_1.0.8                            foreach_1.4.3                             
[31] Biostrings_2.40.2                          XVector_0.12.1                             lattice_0.20-34                           
[34] FEM_3.3.0                                  org.Hs.eg.db_3.3.0                         Matrix_1.2-7.1                            
[37] AnnotationDbi_1.34.4                       impute_1.46.0                              graph_1.50.0                              
[40] marray_1.50.0                              igraph_1.0.1                               corrplot_0.77                             
[43] Cairo_1.5-9                                cluster_2.0.5                              knitr_1.14                                
[46] GTscripts_1.1.2                            biomaRt_2.28.0                             MASS_7.3-45                               
[49] reshape2_1.4.2                             dplyr_0.5.0                                sva_3.20.0                                
[52] genefilter_1.54.2                          mgcv_1.8-15                                nlme_3.1-128                              
[55] golubEsets_1.14.0                          BiocInstaller_1.22.3                       pheatmap_1.0.8                            
[58] RColorBrewer_1.1-2                         ggplot2_2.1.0                              gplots_3.0.1                              
[61] matrixStats_0.51.0                         DESeq2_1.12.4                              SummarizedExperiment_1.2.3                
[64] Biobase_2.32.0                             GenomicRanges_1.24.3                       GenomeInfoDb_1.8.7                        
[67] IRanges_2.6.1                              S4Vectors_0.10.3                           BiocGenerics_0.18.0                       
[70] edgeR_3.14.0                               limma_3.28.21                             

loaded via a namespace (and not attached):
 [1] Hmisc_3.17-4            lazyeval_0.2.0          splines_3.3.1           BiocParallel_1.6.6      fastICA_1.2-0          
 [6] gridBase_0.4-7          digest_0.6.10           htmltools_0.3.5         RPMM_1.20               gdata_2.17.0           
[11] magrittr_1.5            memoise_1.0.0           doParallel_1.0.10       isva_1.8                siggenes_1.46.0        
[16] colorspace_1.2-7        RefFreeEWAS_2.0         RCurl_1.95-4.8          jsonlite_1.1            GEOquery_2.38.4        
[21] survival_2.39-5         registry_0.3            gtable_0.2.0            zlibbioc_1.18.0         DBI_0.5-1              
[26] rngtools_1.2.4          Rcpp_0.12.7             viridisLite_0.1.3       xtable_1.8-2            foreign_0.8-67         
[31] mclust_5.2              preprocessCore_1.34.0   Formula_1.2-1           htmlwidgets_0.7         httr_1.2.1             
[36] acepack_1.4.0           reshape_0.8.6           nnet_7.3-12             DNAcopy_1.46.0          munsell_0.4.3          
[41] tools_3.3.1             RSQLite_1.0.0           devtools_1.12.0         evaluate_0.10           stringr_1.1.0          
[46] beanplot_1.2            caTools_1.17.1          purrr_0.2.2             doRNG_1.6               mime_0.5               
[51] nor1mix_1.2-2           wateRmelon_1.17.0       curl_2.2                tibble_1.2              stringi_1.1.2          
[56] multtest_2.28.0         data.table_1.9.6        bitops_1.0-6            httpuv_1.3.3            rtracklayer_1.32.2     
[61] qvalue_2.4.2            R6_2.2.0                latticeExtra_0.6-28     KernSmooth_2.23-15      codetools_0.2-15       
[66] gtools_3.5.0            assertthat_0.1          chron_2.3-47            openssl_0.9.4           pkgmaker_0.22          
[71] withr_1.0.2             GenomicAlignments_1.8.4 Rsamtools_1.24.0        quadprog_1.5-5          rpart_4.1-10           
[76] tidyr_0.6.0             base64_2.0              git2r_0.15.0            base64enc_0.1-3     

I also tried to download the latest version in the biocondutor separately and now it installs the latest version but still cannot find the GUI functions. Can anyone please give me glossary of what is going wrong at my end? The ChAMP data is still the 1.10.

ChAMP • 1.4k views
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Yuan Tian ▴ 90
@yuan-tian-9598
Last seen 4.2 years ago

Hello:

The latest version of bioconductor might be the reason. I think currently you are still using bioconductor 3.3, on that release, ChAMP is still 1.10.X. So I think you may firstly should upgrade your biocondcutor to 3.4:

 

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")     ## R version 2.15 or later

 

Then you may try to reinstall ChAMP like usual way. If you still can not make it, you may have to download .tar.gz package and use command R CMD INSTALL ChAMP_2.2.0.tar.gz to install.

 

Please try these, if you still can not make it or have other problems please ask me. New version package indeed call for lots of dependence.

Best

Yuan Tian

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I have upgraded the Bioconductor and reinstalled all the packages and even now I see that the ChAMP package is updated with its data but still cannot process a lot of functions. It simply cannot find the functions related to GUI or QC.

myImpute <- champ.impute()
Error: could not find function "champ.impute"

champ.QC()
Error: could not find function "champ.QC"

champ.GUI()
Error: could not find function "champ.GUI"

It seems the GUI functions are not working. Can you please guide me through this.

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Below is the sessionInfo

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12 (Sierra)

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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.24.0                       rmarkdown_1.1                              plotly_4.5.2                              
 [4] IlluminaHumanMethylation450kmanifest_0.4.0 RnBeads_1.6.0                              plyr_1.8.4                                
 [7] methylumi_2.20.0                           FDb.InfiniumMethylation.hg19_2.2.0         TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2   
[10] GenomicFeatures_1.26.0                     scales_0.4.0                               illuminaio_0.16.0                         
[13] gridExtra_2.2.1                            fields_8.4-1                               maps_3.1.1                                
[16] spam_1.4-0                                 ff_2.2-13                                  bit_1.1-12                                
[19] treemap_2.4-1                              geneplotter_1.52.0                         annotate_1.52.0                           
[22] XML_3.98-1.4                               shiny_0.14.1                               ChAMP_2.2.0                               
[25] Illumina450ProbeVariants.db_1.10.0         ChAMPdata_2.2.0                            minfi_1.20.0                              
[28] bumphunter_1.14.0                          locfit_1.5-9.1                             iterators_1.0.8                           
[31] foreach_1.4.3                              Biostrings_2.42.0                          XVector_0.14.0                            
[34] lattice_0.20-34                            FEM_3.3.0                                  org.Hs.eg.db_3.4.0                        
[37] Matrix_1.2-7.1                             AnnotationDbi_1.36.0                       impute_1.48.0                             
[40] graph_1.52.0                               marray_1.52.0                              igraph_1.0.1                              
[43] corrplot_0.77                              Cairo_1.5-9                                cluster_2.0.5                             
[46] knitr_1.14                                 GTscripts_1.1.2                            biomaRt_2.30.0                            
[49] MASS_7.3-45                                reshape2_1.4.2                             dplyr_0.5.0                               
[52] sva_3.22.0                                 genefilter_1.56.0                          mgcv_1.8-15                               
[55] nlme_3.1-128                               golubEsets_1.16.0                          pheatmap_1.0.8                            
[58] RColorBrewer_1.1-2                         ggplot2_2.1.0                              gplots_3.0.1                              
[61] matrixStats_0.51.0                         DESeq2_1.14.0                              SummarizedExperiment_1.4.0                
[64] Biobase_2.34.0                             GenomicRanges_1.26.1                       GenomeInfoDb_1.10.0                       
[67] IRanges_2.8.0                              S4Vectors_0.12.0                           BiocGenerics_0.20.0                       
[70] edgeR_3.16.1                               limma_3.30.0                              

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added info of session

loaded via a namespace (and not attached):
 [1] Hmisc_3.17-4             lazyeval_0.2.0           splines_3.3.1            BiocParallel_1.8.0       fastICA_1.2-0           
 [6] gridBase_0.4-7           digest_0.6.10            htmltools_0.3.5          RPMM_1.20                gdata_2.17.0            
[11] magrittr_1.5             memoise_1.0.0            doParallel_1.0.10        isva_1.8                 siggenes_1.48.0         
[16] colorspace_1.2-7         RefFreeEWAS_2.0          RCurl_1.95-4.8           jsonlite_1.1             GEOquery_2.40.0         
[21] survival_2.39-5          registry_0.3             gtable_0.2.0             zlibbioc_1.20.0          DBI_0.5-1               
[26] rngtools_1.2.4           Rcpp_0.12.7              viridisLite_0.1.3        xtable_1.8-2             foreign_0.8-67          
[31] mclust_5.2               preprocessCore_1.36.0    Formula_1.2-1            htmlwidgets_0.7          httr_1.2.1              
[36] acepack_1.4.0            reshape_0.8.6            nnet_7.3-12              DNAcopy_1.48.0           munsell_0.4.3           
[41] tools_3.3.1              RSQLite_1.0.0            devtools_1.12.0          evaluate_0.10            stringr_1.1.0           
[46] beanplot_1.2             caTools_1.17.1           purrr_0.2.2              doRNG_1.6                mime_0.5                
[51] nor1mix_1.2-2            wateRmelon_1.18.0        curl_2.2                 tibble_1.2               stringi_1.1.2           
[56] multtest_2.30.0          data.table_1.9.6         bitops_1.0-6             httpuv_1.3.3             rtracklayer_1.34.0      
[61] qvalue_2.6.0             R6_2.2.0                 latticeExtra_0.6-28      KernSmooth_2.23-15       codetools_0.2-15        
[66] gtools_3.5.0             assertthat_0.1           chron_2.3-47             openssl_0.9.4            pkgmaker_0.22           
[71] withr_1.0.2              GenomicAlignments_1.10.0 Rsamtools_1.26.1         quadprog_1.5-5           rpart_4.1-10            
[76] tidyr_0.6.0              base64_2.0               git2r_0.15.0             base64enc_0.1-3  
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Hello: I am also confused...based on my experience, your computer should be perfectly fine now... some of your package's version are even newer than mine. I can see no reason why it's not working. champ.impute() does not related to any GUI function, so does champ.QC(). Could you try install it in other computers to see if this error still exist? I developed this package under linux, but it can be published because it can pass Windows and Mac environment as well. Could you check if champ.GSEA(), champ.Block() also accessible? Because they are also new functions along with champ.QC(), QC.GUI() and champ.impute()? If you still can not use them, maybe you failed to load updated package? I admit it's the first time I encounter this problem...Sorry I may need some time to figure it out. Best Yuan Tian On Thu, Oct 27, 2016 at 6:36 PM vd4mmind [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User vd4mmind<https: support.bioconductor.org="" u="" 11547=""/> wrote Comment: Error in running the ChAMP test runs from vignette <https: support.bioconductor.org="" p="" 88769="" #88793=""> : added info of session loaded via a namespace (and not attached): [1] Hmisc_3.17-4 lazyeval_0.2.0 splines_3.3.1 BiocParallel_1.8.0 fastICA_1.2-0 [6] gridBase_0.4-7 digest_0.6.10 htmltools_0.3.5 RPMM_1.20 gdata_2.17.0 [11] magrittr_1.5 memoise_1.0.0 doParallel_1.0.10 isva_1.8 siggenes_1.48.0 [16] colorspace_1.2-7 RefFreeEWAS_2.0 RCurl_1.95-4.8 jsonlite_1.1 GEOquery_2.40.0 [21] survival_2.39-5 registry_0.3 gtable_0.2.0 zlibbioc_1.20.0 DBI_0.5-1 [26] rngtools_1.2.4 Rcpp_0.12.7 viridisLite_0.1.3 xtable_1.8-2 foreign_0.8-67 [31] mclust_5.2 preprocessCore_1.36.0 Formula_1.2-1 htmlwidgets_0.7 httr_1.2.1 [36] acepack_1.4.0 reshape_0.8.6 nnet_7.3-12 DNAcopy_1.48.0 munsell_0.4.3 [41] tools_3.3.1 RSQLite_1.0.0 devtools_1.12.0 evaluate_0.10 stringr_1.1.0 [46] beanplot_1.2 caTools_1.17.1 purrr_0.2.2 doRNG_1.6 mime_0.5 [51] nor1mix_1.2-2 wateRmelon_1.18.0 curl_2.2 tibble_1.2 stringi_1.1.2 [56] multtest_2.30.0 data.table_1.9.6 bitops_1.0-6 httpuv_1.3.3 rtracklayer_1.34.0 [61] qvalue_2.6.0 R6_2.2.0 latticeExtra_0.6-28 KernSmooth_2.23-15 codetools_0.2-15 [66] gtools_3.5.0 assertthat_0.1 chron_2.3-47 openssl_0.9.4 pkgmaker_0.22 [71] withr_1.0.2 GenomicAlignments_1.10.0 Rsamtools_1.26.1 quadprog_1.5-5 rpart_4.1-10 [76] tidyr_0.6.0 base64_2.0 git2r_0.15.0 base64enc_0.1-3 ________________________________ Post tags: ChAMP You may reply via email or visit C: Error in running the ChAMP test runs from vignette
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Yes even they are not loading, I installed the latest version of ChAMP itself as shown in my sessionInfo(). I just  want to know are there any dependancies of ChAMP with any existing tools where it will not function if any other package is installed for masking effect? If so can you please let me know which kind of packages then I can take a look into such packages in my session and remove them.

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ah finally working. I just removed all packages and cancelled the session and restarted and reloaded everything from scratch and seems to work now. I do not even know what the problem was. But thanks for your inputs.

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Finally up and running both locally and also HPC. Cannot work it out in local computer , so installed in HPC, will try to establish everything there. Thanks for the replies. Hope I am able to run it to the best of my usage.

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