############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ELMER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ELMER_2.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ELMER/DESCRIPTION' ... OK * this is package 'ELMER' version '2.19.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'ELMER' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Stat.nonpara: no visible global function definition for 'head' Stat.nonpara: no visible global function definition for 'tail' Stat.nonpara.permu: no visible global function definition for 'head' Stat.nonpara.permu: no visible global function definition for 'tail' TFsurvival.plot: no visible global function definition for 'head' TFsurvival.plot: no visible global function definition for 'tail' addMutCol: no visible binding for global variable 'Hugo_Symbol' calcDistNearestTSS: no visible binding for global variable 'DistanceTSS' get.enriched.motif: no visible global function definition for 'ranges' get.top.tf.by.pval: no visible global function definition for 'head' getRegionNearGenes : f: no visible binding for global variable 'Side' getRegionNearGenes: no visible binding for global variable 'ID' getTFtargets: no visible binding for global variable 'TF' Undefined global functions or variables: DistanceTSS Hugo_Symbol ID Side TF head ranges tail Consider adding importFrom("utils", "head", "tail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'ELMER-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: TCGA.pipe > ### Title: ELMER analysis pipeline for TCGA data. > ### Aliases: TCGA.pipe > > ### ** Examples > > data <- ELMER:::getdata("elmer.data.example") > TCGA.pipe(disease = "LUSC", + data = data, + analysis = c("diffMeth","pair", "motif","TF.search"), + mode = "supervised", + group.col = "definition", + group1 = "Primary solid Tumor", + group2 = "Solid Tissue Normal", + diff.dir = c("hypo"), + dir.out = "pipe", + sig.dif = 0.0001, + pvalue = 1.0, + min.incidence = 0, + lower.OR = 0.0) => supervised was selected: using all samples => Analysis results wil be save in: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo Recording analysis information into: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo/TCGA.pipe_records.txt ---------------------------------------- * Get differential DNA methylation loci ---------------------------------------- ELMER will search for probes hypomethylated in group Primary solid Tumor (n:226) compared to Solid Tissue Normal (n:8) ooo Arguments ooo o Number of probes: 101 o Beta value difference cut-off: 1e-04 o FDR cut-off: 1 o Mode: unsupervised o % of samples per group in each comparison: 1 o Min number of samples per group in each comparison: 5 o Nb of samples group1 in each comparison: 226 o Nb of samples group2 in each comparison: 8 Output direction: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo ooooooooooooooooo | | 0% | |0.990099% ~0 s remaining |= |1.980198% ~0 s remaining |= |2.970297% ~0 s remaining |== |3.960396% ~0 s remaining |== |4.950495% ~0 s remaining |=== |5.940594% ~0 s remaining |=== |6.930693% ~0 s remaining |==== |7.920792% ~0 s remaining |==== 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|================================================== |98.0198% ~0 s remaining |=================================================== |99.0099% ~0 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s Saving results Number of relevant probes found: 76 ---------------- * Predict pairs ---------------- Rows: 76 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," chr (1): probe dbl (3): pvalue, Primary.solid.Tumor_Minus_Solid.Tissue.Normal, adjust.p i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Get nearby genes Searching for the 20 near genes Identifying gene position for each probe File saved: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo/hypo.probes_nearGenes.rda Identify putative probe-gene pair for hypomethylated probes Using pre-defined groups. U (unmethylated): Primary solid Tumor, M (methylated): Solid Tissue Normal ------------------- * Filtering probes ------------------- For more information see function preAssociationProbeFiltering Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3. 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|=================================================== |99.8703% ~0 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 1 s Retrieving TFClass family classification from ELMER.data. Retrieving TFClass subfamily classification from ELMER.data. ------------------------------------ ** Filtering motifs based on quality ------------------------------------ Number of enriched motifs with quality: ----------- => A: 220 => B: 98 => C: 141 => D: 269 => S: 0 ----------- Considering only motifs with quality from A up to DS: 728 motifs are enriched. --------------------------------------------------- * Adding enriched motifs to significant pairs file --------------------------------------------------- Adding coordinates for probes and genes from the provided data Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': could not find function "ranges" Calls: TCGA.pipe ... -> as.data.frame -> .handleSimpleError -> h Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: == Failed tests ================================================================ -- Error (test-pipe.R:5:3): TCGA.pipe is working ------------------------------- Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': could not find function "ranges" Backtrace: x 1. +-ELMER::TCGA.pipe(...) at test-pipe.R:5:2 2. | +-base::do.call(...) 3. | \-ELMER ``(...) 4. | \-BiocGenerics::as.data.frame(ranges(getMet(data))) 5. \-base::.handleSimpleError(...) 6. \-base h(simpleError(msg, call)) [ FAIL 1 | WARN 5 | SKIP 0 | PASS 112 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/00check.log' for details.