I have deployed an application. I use many bioconductor R packages. Locally the application works fine but not fine when deployed online (I guess affy and simpleaffy R packages are not working properly). I get a warning message on using
ReadAffy(filename)
Warning in install.packages(cdfname, lib = lib, repos = biocinstallRepos()
followed by an error message
Error in install.packages: unable to install packages
Session information:
* sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 [6] LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2cdf_2.18.0 RMySQL_0.9-3 DBI_0.5-1 hwgcod.db_3.4.0 h10kcod.db_3.4.0 h20kcod.db_3.4.0 org.Hs.eg.db_3.4.0 [8] AnnotationDbi_1.36.0 lumi_2.26.3 simpleaffy_2.50.0 gcrma_2.46.0 codelink_1.42.0 limma_3.30.3 dplyr_0.5.0 [15] affy_1.52.0 data.table_1.9.6 plyr_1.8.4 markdown_0.7.7 hgu133plus2cdf_2.18.0 genefilter_1.56.0 zlibbioc_1.20.0 [22] affyio_1.44.0 preprocessCore_1.36.0 Biostrings_2.42.0 XVector_0.14.0 IRanges_2.8.1 S4Vectors_0.12.0 biomaRt_2.30.0 [29] BiocParallel_1.8.1 Biobase_2.34.0 BiocGenerics_0.20.0 shiny_0.14.2 BiocInstaller_1.24.0 devtools_1.12.0 rsconnect_0.5 loaded via a namespace (and not attached): [1] nlme_3.1-128 bitops_1.0-6 matrixStats_0.51.0 RColorBrewer_1.1-2 httr_1.2.1 [6] GenomeInfoDb_1.10.1 tools_3.3.2 doRNG_1.6 nor1mix_1.2-2 R6_2.2.0 [11] KernSmooth_2.23-15 mgcv_1.8-16 colorspace_1.3-0 methylumi_2.20.0 withr_1.0.2 [16] base64_2.0 curl_2.2 git2r_0.15.0 chron_2.3-47 pkgmaker_0.22 [21] rtracklayer_1.34.1 quadprog_1.5-5 stringr_1.1.0 digest_0.6.10 Rsamtools_1.26.1 [26] illuminaio_0.16.0 siggenes_1.48.0 GEOquery_2.40.0 htmltools_0.3.5 RSQLite_1.0.0 [31] jsonlite_1.1 mclust_5.2 RCurl_1.95-4.8 magrittr_1.5 Matrix_1.2-7.1 [36] Rcpp_0.12.7 stringi_1.1.2 nleqslv_3.0.3 MASS_7.3-45 RJSONIO_1.3-0 [41] SummarizedExperiment_1.4.0 bumphunter_1.14.0 grid_3.3.2 minfi_1.20.0 lattice_0.20-34 [46] splines_3.3.2 multtest_2.30.0 GenomicFeatures_1.26.0 annotate_1.52.0 locfit_1.5-9.1 [51] knitr_1.15 beanplot_1.2 GenomicRanges_1.26.1 rngtools_1.2.4 codetools_0.2-15 [56] XML_3.98-1.5 packrat_0.4.8-1 httpuv_1.3.3 foreach_1.4.3 openssl_0.9.5 [61] reshape_0.8.6 assertthat_0.1 mime_0.5 xtable_1.8-2 survival_2.40-1 [66] tibble_1.2 iterators_1.0.8 GenomicAlignments_1.10.0 registry_0.3 memoise_1.0.0 * Out-of-date packages Package LibPath Installed Built ReposVer Repository DBI "DBI" "/usr/lib/R/site-library" "0.2-7" "3.0.0" "0.5-1" "https://cran.rstudio.com/src/contrib" RMySQL "RMySQL" "/usr/lib/R/site-library" "0.9-3" "3.0.0" "0.10.9" "https://cran.rstudio.com/src/contrib" update with biocLite() Error: 2 package(s) out of date
Following are session logs while running application
2016-11-17T06:05:35.808039+00:00 shinyapps[137665]: Attaching package: ‘limma’
2016-11-17T06:05:35.808039+00:00 shinyapps[137665]:
2016-11-17T06:05:35.808774+00:00 shinyapps[137665]: The following object is masked from ‘package:BiocGenerics’:
2016-11-17T06:05:35.808776+00:00 shinyapps[137665]:
2016-11-17T06:05:35.808777+00:00 shinyapps[137665]: plotMA
2016-11-17T06:05:35.933352+00:00 shinyapps[137665]: Attaching package: ‘codelink’
2016-11-17T06:05:35.933353+00:00 shinyapps[137665]:
2016-11-17T06:05:35.934025+00:00 shinyapps[137665]: The following objects are masked from ‘package:limma’:
2016-11-17T06:05:35.934027+00:00 shinyapps[137665]: plotDensities, plotMA
2016-11-17T06:05:35.934028+00:00 shinyapps[137665]:
2016-11-17T06:05:35.934784+00:00 shinyapps[137665]: The following object is masked from ‘package:affy’:
2016-11-17T06:05:35.934786+00:00 shinyapps[137665]:
2016-11-17T06:05:35.934786+00:00 shinyapps[137665]: probeNames
2016-11-17T06:05:35.808777+00:00 shinyapps[137665]:
2016-11-17T06:05:35.936117+00:00 shinyapps[137665]: plotMA
2016-11-17T06:05:35.933347+00:00 shinyapps[137665]:
2016-11-17T06:05:35.952677+00:00 shinyapps[137665]: Loading required package: gcrma
2016-11-17T06:05:35.934026+00:00 shinyapps[137665]:
2016-11-17T06:05:35.934787+00:00 shinyapps[137665]:
2016-11-17T06:05:35.936115+00:00 shinyapps[137665]: The following object is masked from ‘package:BiocGenerics’:
2016-11-17T06:05:35.936117+00:00 shinyapps[137665]:
2016-11-17T06:05:35.936118+00:00 shinyapps[137665]:
2016-11-17T06:05:36.073857+00:00 shinyapps[137665]:
2016-11-17T06:05:36.073860+00:00 shinyapps[137665]: Attaching package: ‘simpleaffy’
2016-11-17T06:05:36.073861+00:00 shinyapps[137665]:
2016-11-17T06:05:36.074501+00:00 shinyapps[137665]: The following object is masked from ‘package:IRanges’:
2016-11-17T06:05:36.074502+00:00 shinyapps[137665]:
2016-11-17T06:05:36.074503+00:00 shinyapps[137665]: members
2016-11-17T06:05:36.074504+00:00 shinyapps[137665]:
2016-11-17T06:05:40.002294+00:00 shinyapps[137665]: Setting options('download.file.method.GEOquery'='auto')
2016-11-17T06:05:40.002783+00:00 shinyapps[137665]: Setting options('GEOquery.inmemory.gpl'=FALSE)
2016-11-17T06:05:40.531722+00:00 shinyapps[137665]:
2016-11-17T06:05:40.563135+00:00 shinyapps[137665]: Attaching package: ‘AnnotationDbi’
2016-11-17T06:05:40.531725+00:00 shinyapps[137665]: Attaching package: ‘lumi’
2016-11-17T06:05:40.544974+00:00 shinyapps[137665]: Loading required package: AnnotationDbi
2016-11-17T06:05:40.706571+00:00 shinyapps[137665]:
2016-11-17T06:05:40.531726+00:00 shinyapps[137665]:
2016-11-17T06:05:40.563799+00:00 shinyapps[137665]: select
2016-11-17T06:05:40.532342+00:00 shinyapps[137665]: The following objects are masked from ‘package:affy’:
2016-11-17T06:05:40.563136+00:00 shinyapps[137665]:
2016-11-17T06:05:40.532344+00:00 shinyapps[137665]:
2016-11-17T06:05:40.563134+00:00 shinyapps[137665]:
2016-11-17T06:05:40.532345+00:00 shinyapps[137665]: MAplot, plotDensity
2016-11-17T06:05:40.532345+00:00 shinyapps[137665]:
2016-11-17T06:05:40.563797+00:00 shinyapps[137665]: The following object is masked from ‘package:dplyr’:
2016-11-17T06:05:40.563798+00:00 shinyapps[137665]:
2016-11-17T06:05:40.563799+00:00 shinyapps[137665]:
2016-11-17T06:05:40.573071+00:00 shinyapps[137665]: Loading required package: org.Hs.eg.db
2016-11-17T06:05:40.837922+00:00 shinyapps[137665]:
2016-11-17T06:05:40.925381+00:00 shinyapps[137665]:
2016-11-17T06:05:41.040576+00:00 shinyapps[137665]:
Session logs with warning and error message:
2016-11-17T06:22:01.329816+00:00 shinyapps[137665]: background correction: mas 2016-11-17T06:22:01.329851+00:00 shinyapps[137665]: PM/MM correction : mas 2016-11-17T06:22:01.329853+00:00 shinyapps[137665]: expression values: mas 2016-11-17T06:22:03.710864+00:00 shinyapps[137665]: background correcting...Warning in install.packages(cdfname, lib = lib, repos = biocinstallRepos(), : 2016-11-17T06:22:03.710868+00:00 shinyapps[137665]: 'lib = "/usr/local/lib/R/site-library"' is not writable 2016-11-17T06:22:03.714225+00:00 shinyapps[137665]: Warning: Error in install.packages: unable to install packages 2016-11-17T06:22:03.723377+00:00 shinyapps[137665]: Stack trace (innermost first): 2016-11-17T06:22:03.723378+00:00 shinyapps[137665]: 133: install.packages 2016-11-17T06:22:03.723379+00:00 shinyapps[137665]: 132: cdfFromBioC 2016-11-17T06:22:03.723379+00:00 shinyapps[137665]: 131: getCdfInfo 2016-11-17T06:22:03.723380+00:00 shinyapps[137665]: 130: .local 2016-11-17T06:22:03.723380+00:00 shinyapps[137665]: 129: indexProbes 2016-11-17T06:22:03.723380+00:00 shinyapps[137665]: 128: indexProbes 2016-11-17T06:22:03.723381+00:00 shinyapps[137665]: 127: unlist 2016-11-17T06:22:03.723381+00:00 shinyapps[137665]: 126: unique 2016-11-17T06:22:03.723382+00:00 shinyapps[137665]: 125: bg.correct.mas 2016-11-17T06:22:03.723382+00:00 shinyapps[137665]: 124: do.call 2016-11-17T06:22:03.723382+00:00 shinyapps[137665]: 123: <Anonymous> 2016-11-17T06:22:03.723383+00:00 shinyapps[137665]: 122: <Anonymous> 2016-11-17T06:22:03.723383+00:00 shinyapps[137665]: 121: do.call 2016-11-17T06:22:03.723383+00:00 shinyapps[137665]: 120: expresso 2016-11-17T06:22:03.723384+00:00 shinyapps[137665]: 119: mas5 2016-11-17T06:22:03.723384+00:00 shinyapps[137665]: 118: processed_data [/srv/connect/apps/mamged/server.r#114] 2016-11-17T06:22:03.723385+00:00 shinyapps[137665]: 117: eval [/srv/connect/apps/mamged/server.r#1259] 2016-11-17T06:22:03.723385+00:00 shinyapps[137665]: 116: eval 2016-11-17T06:22:03.723385+00:00 shinyapps[137665]: 115: withProgress 2016-11-17T06:22:03.723407+00:00 shinyapps[137665]: 114: eventReactiveHandler [/srv/connect/apps/mamged/server.r#1246] 2016-11-17T06:22:03.723408+00:00 shinyapps[137665]: 94: list_files 2016-11-17T06:22:03.723408+00:00 shinyapps[137665]: 93: renderDataTable [/srv/connect/apps/mamged/server.r#1564] 2016-11-17T06:22:03.723409+00:00 shinyapps[137665]: 92: func 2016-11-17T06:22:03.723409+00:00 shinyapps[137665]: 91: origRenderFunc 2016-11-17T06:22:03.723409+00:00 shinyapps[137665]: 90: output$sourced 2016-11-17T06:22:03.723410+00:00 shinyapps[137665]: 13: runApp 2016-11-17T06:22:03.723410+00:00 shinyapps[137665]: 12: fn 2016-11-17T06:22:03.723411+00:00 shinyapps[137665]: 11: doTryCatch 2016-11-17T06:22:03.723411+00:00 shinyapps[137665]: 10: tryCatchOne 2016-11-17T06:22:03.723412+00:00 shinyapps[137665]: 9: tryCatchList 2016-11-17T06:22:03.723455+00:00 shinyapps[137665]: 8: tryCatch 2016-11-17T06:22:03.723455+00:00 shinyapps[137665]: 7: connect$retry 2016-11-17T06:22:03.723456+00:00 shinyapps[137665]: 6: eval 2016-11-17T06:22:03.723456+00:00 shinyapps[137665]: 5: eval 2016-11-17T06:22:03.723457+00:00 shinyapps[137665]: 4: eval 2016-11-17T06:22:03.723462+00:00 shinyapps[137665]: 3: eval 2016-11-17T06:22:03.723462+00:00 shinyapps[137665]: 2: eval.parent 2016-11-17T06:22:03.723463+00:00 shinyapps[137665]: 1: local
Thanks Martin Morgan. Somehow I managed to get rid of the error by installing some other bioconductor packages, but the application gets blur (does not proceed) after processing the first file. As you can see in the below session logs that one file with 54675 ids is processed.
the log is not sufficient for me to help.
Again coming back to you. I have many functionalities in my application including processing raw data of different platforms such as Affymetrix, Codelink, Illumina. I can successfully process raw data of Codelink and Illumina. But going through a hard time to make functionality of processing Affymetrix to work. The processing stops before doing anything.
When I run the application locally, it works smooth. But after deployment on shiny server, the processing of Affymetrix does not work. I wounder If it is a bug or something seriously is going wrong.
In addition I get warning :
To be honest, I feel there is no issue with your code (if you do not get any error message). The issue is on the server side i.e shinyapps server.