############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'TCGAbiolinks/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TCGAbiolinks' version '2.27.0' * 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 'TCGAbiolinks' can be installed ... OK * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: R 1.6Mb data 4.5Mb * 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 ... WARNING 'library' or 'require' call not declared from: 'dplyr' 'library' or 'require' calls in package code: 'dplyr' 'maftools' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCprepare_clinic: no visible binding for global variable 'bcr_patient_barcode' GDCprepare_clinic: no visible binding for global variable 'days_to_last_followup' GDCprepare_clinic: no visible binding for global variable 'vital_status' GDCquery : : no visible binding for global variable 'submitter_id' GDCquery : : no visible binding for global variable 'is_ffpe' GDCquery_clinic : : no visible binding for global variable 'submitter_id' TCGAanalyze_DEA: no visible binding for global variable 'barcode' TCGAanalyze_DEA: no visible binding for global variable 'clinical' TCGAquery_recount2: no visible binding for global variable 'rse_gene' TCGAtumor_purity: no visible binding for global variable 'Tumor.purity' TCGAvisualize_oncoprint: no visible binding for global variable 'value' TCGAvisualize_starburst: no visible binding for global variable 'gene_name' TCGAvisualize_starburst: no visible binding for global variable 'geFDR2' TCGAvisualize_starburst: no visible binding for global variable 'logFC' TCGAvisualize_starburst: no visible binding for global variable 'meFDR2' TCGAvisualize_starburst: no visible binding for global variable 'threshold.starburst' TCGAvisualize_starburst: no visible binding for global variable 'starburst.status' colDataPrepare: no visible binding for global variable 'sample_submitter_id' colDataPrepare: no visible binding for global variable 'submitter_id' colDataPrepare: no visible binding for global variable 'sample_type' readExonQuantification: no visible binding for global variable 'exon' readExonQuantification: no visible binding for global variable 'coordinates' readGeneExpressionQuantification : : no visible binding for '<<-' assignment to 'assay.list' readGeneExpressionQuantification: no visible binding for global variable 'assay.list' readSingleCellAnalysis : : no visible global function definition for 'Read10X' Undefined global functions or variables: Read10X Tumor.purity assay.list barcode bcr_patient_barcode clinical coordinates days_to_last_followup exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id sample_type starburst.status submitter_id threshold.starburst value vital_status * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'TCGAbiolinks-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: TCGAvisualize_meanMethylation > ### Title: Mean methylation boxplot > ### Aliases: TCGAvisualize_meanMethylation > > ### ** Examples > > nrows <- 200; ncols <- 21 > counts <- matrix(runif(nrows * ncols, 0, 1), nrows) > rowRanges <- GenomicRanges::GRanges(rep(c("chr1", "chr2"), c(50, 150)), + IRanges::IRanges(floor(runif(200, 1e5, 1e6)), width=100), + strand=sample(c("+", "-"), 200, TRUE), + feature_id=sprintf("ID%03d", 1:200)) > colData <- S4Vectors::DataFrame(Treatment=rep(c("ChIP", "Input","Other"), 7), + row.names=LETTERS[1:21], + group=rep(c("group1","group2","group3"),c(7,7,7)), + subgroup=rep(c("subgroup1","subgroup2","subgroup3"),7)) > data <- SummarizedExperiment::SummarizedExperiment( + assays=S4Vectors::SimpleList(counts=counts), + rowRanges=rowRanges, + colData=colData) > TCGAvisualize_meanMethylation(data,groupCol = "group") ==================== DATA Summary ==================== groups Mean Median Max Min 1 group1 0.4935503 0.4844465 0.5193171 0.4690160 2 group2 0.4913444 0.4878388 0.5334364 0.4502542 3 group3 0.4970774 0.5012800 0.5218784 0.4649520 ==================== END DATA Summary ==================== ==================== T test results ==================== group1 group2 group3 group1 NA 0.8649153 0.7425559 group2 0.8649153 NA 0.6447791 group3 0.7425559 0.6447791 NA ==================== END T test results ==================== [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "#FF0000" "#00FF00" "#0000FF" Plot saved in: F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf > # change lower/upper y-axis limit > TCGAvisualize_meanMethylation(data,groupCol = "group", y.limits = c(0,1)) ==================== DATA Summary ==================== groups Mean Median Max Min 1 group1 0.4935503 0.4844465 0.5193171 0.4690160 2 group2 0.4913444 0.4878388 0.5334364 0.4502542 3 group3 0.4970774 0.5012800 0.5218784 0.4649520 ==================== END DATA Summary ==================== ==================== T test results ==================== group1 group2 group3 group1 NA 0.8649153 0.7425559 group2 0.8649153 NA 0.6447791 group3 0.7425559 0.6447791 NA ==================== END T test results ==================== [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "#FF0000" "#00FF00" "#0000FF" Plot saved in: F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf > # change lower y-axis limit > TCGAvisualize_meanMethylation(data,groupCol = "group", y.limits = 0) ==================== DATA Summary ==================== groups Mean Median Max Min 1 group1 0.4935503 0.4844465 0.5193171 0.4690160 2 group2 0.4913444 0.4878388 0.5334364 0.4502542 3 group3 0.4970774 0.5012800 0.5218784 0.4649520 ==================== END DATA Summary ==================== ==================== T test results ==================== group1 group2 group3 group1 NA 0.8649153 0.7425559 group2 0.8649153 NA 0.6447791 group3 0.7425559 0.6447791 NA ==================== END T test results ==================== [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "#FF0000" "#00FF00" "#0000FF" Plot saved in: F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf > TCGAvisualize_meanMethylation(data,groupCol = "group", subgroupCol="subgroup") ==================== DATA Summary ==================== groups Mean Median Max Min 1 group1 0.4935503 0.4844465 0.5193171 0.4690160 2 group2 0.4913444 0.4878388 0.5334364 0.4502542 3 group3 0.4970774 0.5012800 0.5218784 0.4649520 ==================== END DATA Summary ==================== ==================== T test results ==================== group1 group2 group3 group1 NA 0.8649153 0.7425559 group2 0.8649153 NA 0.6447791 group3 0.7425559 0.6447791 NA ==================== END T test results ==================== [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "#FF0000" "#00FF00" "#0000FF" Plot saved in: F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/groupMeanMet.pdf > TCGAvisualize_meanMethylation(data,groupCol = "group") ==================== DATA Summary ==================== groups Mean Median Max Min 1 group1 0.4935503 0.4844465 0.5193171 0.4690160 2 group2 0.4913444 0.4878388 0.5334364 0.4502542 3 group3 0.4970774 0.5012800 0.5218784 0.4649520 ==================== END DATA Summary ==================== ==================== T test results ==================== group1 group2 group3 group1 NA 0.8649153 0.7425559 group2 0.8649153 NA 0.6447791 group3 0.7425559 0.6447791 NA ==================== END T test results ==================== [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "group1" "group1" "group1" "group1" "group1" "group1" "group1" "group2" [9] "group2" "group2" "group2" "group2" "group2" "group2" "group3" "group3" [17] "group3" "group3" "group3" "group3" "group3" [1] "#FF0000" "#00FF00" "#0000FF" Error in grDevices::pdf(file = filename, ..., version = version) : cannot open file 'groupMeanMet.pdf' Calls: TCGAvisualize_meanMethylation -> ggsave -> dev -> Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * 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: 1 ERROR, 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAbiolinks.Rcheck/00check.log' for details.