############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings deepSNV_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/deepSNV.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 ‘deepSNV/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘deepSNV’ version ‘1.48.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'parallel', 'IRanges', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'VGAM', 'VariantAnnotation' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘deepSNV’ 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 5.9Mb sub-directories of 1Mb or more: libs 4.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2 * 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 ... NOTE Packages in Depends field not imported from: ‘GenomicRanges’ ‘SummarizedExperiment’ ‘VariantAnnotation’ ‘parallel’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘estimateRho’ ‘logbb’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .deepSNVsingle: no visible global function definition for ‘pchisq’ .estimateDispersion: no visible global function definition for ‘optimize’ .makeVCFheader: no visible global function definition for ‘splitAsList’ .makeVCFheader: no visible global function definition for ‘DataFrame’ .significantSNV: no visible global function definition for ‘p.adjust’ .significantSNV: no visible global function definition for ‘scanVcfHeader’ .significantSNV: no visible global function definition for ‘VCF’ .significantSNV: no visible global function definition for ‘GRanges’ .significantSNV: no visible global function definition for ‘IRanges’ .significantSNV: no visible global function definition for ‘DataFrame’ .significantSNV: no visible global function definition for ‘SimpleList’ .significantSNV: no visible global function definition for ‘VCFHeader’ .significantSNV: no visible global function definition for ‘reference’ .significantSNV: no visible global function definition for ‘header’ bbb: no visible global function definition for ‘na.omit’ betabinLRT: no visible global function definition for ‘pchisq’ betabinLRT: no visible global function definition for ‘p.adjust’ bf2Vcf: no visible global function definition for ‘scanVcfHeader’ bf2Vcf: no visible global function definition for ‘VCF’ bf2Vcf: no visible global function definition for ‘GRanges’ bf2Vcf: no visible global function definition for ‘IRanges’ bf2Vcf: no visible global function definition for ‘DataFrame’ bf2Vcf: no visible global function definition for ‘VCFHeader’ bf2Vcf: no visible global function definition for ‘reference’ bf2Vcf: no visible global function definition for ‘header’ bf2Vcf: no visible global function definition for ‘SimpleList’ loadAllData: no visible global function definition for ‘mclapply’ makePrior: no visible global function definition for ‘info’ manhattanPlot: no visible global function definition for ‘legend’ mcChunk: no visible global function definition for ‘mclapply’ mutID: no visible global function definition for ‘seqnames’ p.combine: no visible global function definition for ‘pgamma’ plot.deepSNV: no visible global function definition for ‘legend’ plot.deepSNV: no visible global function definition for ‘par’ plot.deepSNV: no visible global function definition for ‘abline’ qvals2Vcf: no visible global function definition for ‘scanVcfHeader’ qvals2Vcf: no visible global function definition for ‘VCF’ qvals2Vcf: no visible global function definition for ‘GRanges’ qvals2Vcf: no visible global function definition for ‘IRanges’ qvals2Vcf: no visible global function definition for ‘DataFrame’ qvals2Vcf: no visible global function definition for ‘VCFHeader’ qvals2Vcf: no visible global function definition for ‘reference’ qvals2Vcf: no visible global function definition for ‘header’ qvals2Vcf: no visible global function definition for ‘SimpleList’ PCRTest,matrix-matrix: no visible global function definition for ‘pnorm’ estimateDirichlet,matrix: no visible binding for global variable ‘dirichlet’ estimateDirichlet,matrix: no visible global function definition for ‘coefficients’ normalize,matrix-matrix : : no visible global function definition for ‘loess’ overDispersion,matrix-matrix: no visible global function definition for ‘optimize’ overDispersion,matrix-matrix : : no visible global function definition for ‘na.omit’ Undefined global functions or variables: DataFrame GRanges IRanges SimpleList VCF VCFHeader abline coefficients dirichlet header info legend loess mclapply na.omit optimize p.adjust par pchisq pgamma pnorm reference scanVcfHeader seqnames splitAsList Consider adding importFrom("graphics", "abline", "legend", "par") importFrom("stats", "coefficients", "loess", "na.omit", "optimize", "p.adjust", "pchisq", "pgamma", "pnorm") 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 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/deepSNV/libs/deepSNV.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 ‘deepSNV-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: RCC > ### Title: Example RCC data > ### Aliases: RCC > > ### ** Examples > > data("RCC", package="deepSNV") > summary(RCC, adjust.method="bonferroni")[,1:6] chr pos ref var p.val freq.var 6 chr10 89710231 C T 1.812318e-06 -0.0522069105 1 chr17 7512879 G A 4.923709e-03 0.0095680379 10 chr17 7513782 A G 6.137099e-57 0.0523098637 15 chr3 10158255 A - 7.414419e-27 0.0374605077 4 chr3 10158274 C T 6.596999e-152 -0.1420210172 2 chr3 10158337 G A 8.455105e-09 -0.1458150689 7 chr3 10163012 - C 2.512916e-211 0.1242571351 16 chr3 10163206 T - 0.000000e+00 0.2440387988 17 chr3 10163208 G - 1.908223e-02 0.0007724394 11 chr3 10163428 T G 1.026389e-79 -0.1111055718 8 chr3 10166219 G C 6.538408e-74 0.1591560973 3 chr3 10166943 G A 1.406981e-158 -0.1326056510 12 chr3 10167220 C G 2.960126e-36 0.0046531880 13 chr3 10167672 A G 0.000000e+00 0.1399833662 5 chr3 10167709 C T 6.203881e-304 -0.1440968910 9 chr3 10167762 T C 0.000000e+00 -0.1323353964 14 chr3 10168683 T G 2.134656e-304 -0.1324914089 > plot(RCC) > RCC.bb <- estimateDispersion(RCC, alternative="two.sided") Note: The initial object used a binomial model. Will be changed to beta-binomial. Estimated dispersion factor 136.926969822682 > summary(RCC.bb, adjust.method="bonferroni")[,1:6] chr pos ref var p.val freq.var 2 chr3 10158274 C T 4.185434e-03 -0.1420210172 7 chr3 10163206 T - 6.774267e-304 0.2440387988 8 chr3 10163208 G - 2.693886e-02 0.0007724394 1 chr3 10166943 G A 9.499952e-03 -0.1326056510 5 chr3 10167220 C G 5.461018e-30 0.0046531880 3 chr3 10167709 C T 3.466443e-02 -0.1440968910 4 chr3 10167762 T C 8.715616e-03 -0.1323353964 6 chr3 10168683 T G 4.237354e-02 -0.1324914089 > plot(RCC.bb) * 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, 6 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/deepSNV.Rcheck/00check.log’ for details.