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.
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.
It seems the GUI functions are not working. Can you please guide me through this.
Below is the sessionInfo
added info of session
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.
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.
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.