############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DiffBind_3.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DiffBind.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DiffBind/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DiffBind’ version ‘3.12.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘DiffBind’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 11.7Mb sub-directories of 1Mb or more: data 2.0Mb extra 1.3Mb libs 7.4Mb * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... 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 ... OK * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.3.1/site-library/DiffBind/libs/DiffBind.so’: Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘sprintf’, possibly from ‘sprintf’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘DiffBind-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dba.contrast > ### Title: Set up contrasts for differential binding affinity analysis > ### Aliases: dba.contrast > > ### ** Examples > > # Set up an explicit contrast > data(tamoxifen_counts) > tamoxifen <- dba.contrast(tamoxifen, contrast=c("Condition","Responsive","Resistant")) Computing results names... > tamoxifen 11 Samples, 2845 sites in matrix: ID Tissue Factor Condition Treatment Replicate Reads FRiP 1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16 2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15 3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31 4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19 5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25 6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11 7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06 8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22 9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14 10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33 11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22 Design: [~Condition] | 1 Contrast: Factor Group Samples Group2 Samples2 1 Condition Responsive 7 Resistant 4 > tamoxifen <- dba.analyze(tamoxifen) Normalize DESeq2 with defaults... Analyzing... gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates > dba.show(tamoxifen,bContrasts=TRUE) Factor Group Samples Group2 Samples2 DB.DESeq2 1 Condition Responsive 7 Resistant 4 246 > > # Add another contrast > tamoxifen <- dba.contrast(tamoxifen, contrast=c("Tissue","MCF7","BT474")) Replacing design and removing analysis. Computing results names... > dba.show(tamoxifen,bDesign=TRUE) [1] "~Condition + Tissue" > > # Change design > tamoxifen <- dba.contrast(tamoxifen,design="~Tissue + Condition") Replacing design. Computing results names... > tamoxifen <- dba.analyze(tamoxifen) Analyzing... gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates > tamoxifen 11 Samples, 2845 sites in matrix: ID Tissue Factor Condition Treatment Replicate Reads FRiP 1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16 2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15 3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31 4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19 5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25 6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11 7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06 8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22 9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14 10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33 11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22 Design: [~Tissue + Condition] | 2 Contrasts: Factor Group Samples Group2 Samples2 DB.DESeq2 1 Condition Responsive 7 Resistant 4 783 2 Tissue MCF7 5 BT474 2 988 > > # Automatically add all contrasts between sample groups > # where at least THREE samples have the same factor value > data(tamoxifen_counts) > tamoxifen <- dba.contrast(tamoxifen) Computing results names... > tamoxifen 11 Samples, 2845 sites in matrix: ID Tissue Factor Condition Treatment Replicate Reads FRiP 1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16 2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15 3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31 4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19 5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25 6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11 7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06 8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22 9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14 10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33 11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22 Design: [~Condition] | 1 Contrast: Factor Group Samples Group2 Samples2 1 Condition Resistant 4 Responsive 7 > > # Automatically add all contrasts between sample groups > # where at least TWO samples have the same factor value > tamoxifen <- dba.contrast(tamoxifen, minMembers=2) Clearing existing contrasts. > dba.show(tamoxifen,bContrasts=TRUE) Factor Group Samples Group2 Samples2 1 Condition Resistant 4 Responsive 7 > > ### Use of complex contrasts > data(tamoxifen_counts) > tamoxifen <- dba.contrast(tamoxifen, contrast=c("Tissue","BT474","MCF7")) Computing results names... > dba.contrast(tamoxifen, bGetCoefficients=TRUE) [1] "Intercept" "Tissue_MCF7_vs_BT474" "Tissue_T47D_vs_BT474" [4] "Tissue_ZR75_vs_BT474" > > #Change design and factor ordering > tamoxifen <- dba.contrast(tamoxifen,design="~Tissue + Condition", + reorderMeta=list(Condition="Responsive", + Tissue=c("MCF7","ZR75","T47D","BT474"))) Replacing design. Computing results names... > dba.contrast(tamoxifen, bGetCoefficients=TRUE) [1] "Intercept" "Tissue_ZR75_vs_MCF7" [3] "Tissue_T47D_vs_MCF7" "Tissue_BT474_vs_MCF7" [5] "Condition_Resistant_vs_Responsive" > tamoxifen <- dba.contrast(tamoxifen,contrast="Tissue_BT474_vs_MCF7") > tamoxifen <- dba.contrast(tamoxifen,contrast=list("Tissue_BT474_vs_MCF7")) > tamoxifen <- dba.contrast(tamoxifen,contrast=c(0,0,0,1,0)) > tamoxifen <- dba.contrast(tamoxifen, + contrast=list("Tissue_BT474_vs_MCF7","Tissue_T47D_vs_MCF7")) > tamoxifen <- dba.contrast(tamoxifen,contrast=c(0,0,-1,1,0)) > tamoxifen <- dba.contrast(tamoxifen,contrast=c(0,0,0,0,1)) > dba.show(tamoxifen,bContrasts=TRUE) Factor Group Samples Group2 Samples2 1 Tissue BT474 2 MCF7 5 2 Name Tissue_BT474_vs_MCF7 3 Results Tissue_BT474_vs_MCF7 4 Coefficient 0,0,0,1,0 5 Results Tissue_BT474_vs_MCF7 Tissue_T47D_vs_MCF7 6 Coefficient 0,0,-1,1,0 7 Coefficient 0,0,0,0,1 Intercept Tissue_ZR75_vs_MCF7 Tissue_T47D_vs_MCF7 Tissue_BT474_vs_MCF7 1 0 0 0 1 2 _ _ _ _ 3 _ _ _ _ 4 0 0 0 1 5 _ _ _ _ 6 0 0 -1 1 7 0 0 0 0 Condition_Resistant_vs_Responsive 1 0 2 _ 3 _ 4 0 5 _ 6 0 7 1 > tamoxifen <- dba.analyze(tamoxifen) Normalize DESeq2 with defaults... Analyzing... gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates > tamoxifen 11 Samples, 2845 sites in matrix: ID Tissue Factor Condition Treatment Replicate Reads FRiP 1 BT4741 BT474 ER Resistant Full-Media 1 652697 0.16 2 BT4742 BT474 ER Resistant Full-Media 2 663370 0.15 3 MCF71 MCF7 ER Responsive Full-Media 1 346429 0.31 4 MCF72 MCF7 ER Responsive Full-Media 2 368052 0.19 5 MCF73 MCF7 ER Responsive Full-Media 3 466273 0.25 6 T47D1 T47D ER Responsive Full-Media 1 399879 0.11 7 T47D2 T47D ER Responsive Full-Media 2 1475415 0.06 8 MCF7r1 MCF7 ER Resistant Full-Media 1 616630 0.22 9 MCF7r2 MCF7 ER Resistant Full-Media 2 593224 0.14 10 ZR751 ZR75 ER Responsive Full-Media 1 706836 0.33 11 ZR752 ZR75 ER Responsive Full-Media 2 2575408 0.22 Design: [~Tissue + Condition] | 7 Contrasts: Factor Group Samples Group2 Samples2 1 Tissue BT474 2 MCF7 5 2 Name Tissue_BT474_vs_MCF7 3 Results Tissue_BT474_vs_MCF7 4 Coefficient 0,0,0,1,0 5 Results Tissue_BT474_vs_MCF7 Tissue_T47D_vs_MCF7 6 Coefficient 0,0,-1,1,0 7 Coefficient 0,0,0,0,1 Intercept Tissue_ZR75_vs_MCF7 Tissue_T47D_vs_MCF7 Tissue_BT474_vs_MCF7 1 0 0 0 1 2 _ _ _ _ 3 _ _ _ _ 4 0 0 0 1 5 _ _ _ _ 6 0 0 -1 1 7 0 0 0 0 Condition_Resistant_vs_Responsive DB.DESeq2 1 0 988 2 _ 988 3 _ 988 4 0 988 5 _ 1096 6 0 1096 7 1 783 > tamoxifen <- dba.contrast(tamoxifen, + contrast=c("Condition","Responsive","Resistant")) > tamoxifen <- dba.analyze(tamoxifen) Analyzing... * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 947560 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians >>> DiffBind 3.12.0 > > test_check("DiffBind") * 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 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/DiffBind.Rcheck/00check.log’ for details.