Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1687/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Repitools 1.51.0 (landing page) Mark Robinson
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the Repitools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Repitools.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: Repitools |
Version: 1.51.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Repitools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Repitools_1.51.0.tar.gz |
StartedAt: 2024-06-10 08:07:46 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 08:20:45 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 778.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Repitools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Repitools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Repitools_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Repitools.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Repitools/DESCRIPTION' ... OK * this is package 'Repitools' version '1.51.0' * 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 whether package 'Repitools' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 code 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 ... OK * checking Rd files ... WARNING checkRd: (5) AdjustedCopyEstimate-class.Rd:16-34: \item in \describe must have non-empty label checkRd: (5) BayMethList-class.Rd:58-88: \item in \describe must have non-empty label checkRd: (-1) ChromaResults-class.Rd:25: Lost braces 25 | \code{blocks:}{\code{GRanges} of the blocks used across the genome, with their calculated RPKM} | ^ checkRd: (-1) ChromaResults-class.Rd:26: Lost braces 26 | \code{regions:}{\code{IRangesList} of regions determined to be enriched} | ^ checkRd: (-1) ChromaResults-class.Rd:27: Lost braces 27 | \code{FDRTable:}{\code{data.frame} showing the FDR at each cutoff tested} | ^ checkRd: (-1) ChromaResults-class.Rd:28: Lost braces 28 | \code{cutoff:}{The cutoff used to determine enrichment} | ^ checkRd: (5) ClusteredScoresList-class.Rd:29-50: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:57-60: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:61-64: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:65-68: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:75-78: \item in \describe must have non-empty label checkRd: (5) CopyEstimate-class.Rd:14-23: \item in \describe must have non-empty label checkRd: (5) GCAdjustParams-class.Rd:14-37: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:28-31: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:32-35: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:42-45: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:46-49: \item in \describe must have non-empty label * 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 ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed methylEst 57.86 5.66 63.58 empBayes 28.71 4.28 33.10 sequenceCalc 8.28 2.80 11.08 cpgDensityCalc 8.14 2.75 12.49 BayMethList-class 7.18 2.44 9.86 determineOffset 6.96 2.38 10.00 maskOut 4.45 2.30 6.87 gcContentCalc 2.48 2.43 5.01 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See 'F:/biocbuild/bbs-3.20-bioc/meat/Repitools.Rcheck/00check.log' for details.
Repitools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Repitools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Repitools' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c const.c -o const.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hyp2f1.c -o hyp2f1.o In file included from hyp2f1.c:81: ./mconf.h:100: warning: "DOMAIN" redefined 100 | #define DOMAIN 1 /* argument domain error */ | In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:43, from hyp2f1.c:80: C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:29: note: this is the location of the previous definition 29 | #define DOMAIN _DOMAIN | ./mconf.h:101: warning: "SING" redefined 101 | #define SING 2 /* argument singularity */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:30: note: this is the location of the previous definition 30 | #define SING _SING | ./mconf.h:102: warning: "OVERFLOW" redefined 102 | #define OVERFLOW 3 /* overflow range error */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:31: note: this is the location of the previous definition 31 | #define OVERFLOW _OVERFLOW | ./mconf.h:103: warning: "UNDERFLOW" redefined 103 | #define UNDERFLOW 4 /* underflow range error */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:32: note: this is the location of the previous definition 32 | #define UNDERFLOW _UNDERFLOW | ./mconf.h:104: warning: "TLOSS" redefined 104 | #define TLOSS 5 /* total loss of precision */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:33: note: this is the location of the previous definition 33 | #define TLOSS _TLOSS | ./mconf.h:105: warning: "PLOSS" redefined 105 | #define PLOSS 6 /* partial loss of precision */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:34: note: this is the location of the previous definition 34 | #define PLOSS _PLOSS | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mmeansd.cpp -o mmeansd.o mmeansd.cpp: In function 'SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)': mmeansd.cpp:33:24: warning: variable 'is' set but not used [-Wunused-but-set-variable] 33 | int * x, nval, hs, is, i; | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mtherr.c -o mtherr.o In file included from mtherr.c:58: ./mconf.h:100: warning: "DOMAIN" redefined 100 | #define DOMAIN 1 /* argument domain error */ | In file included from F:/biocbuild/bbs-3.20-bioc/R/include/R.h:45, from mtherr.c:56: C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:29: note: this is the location of the previous definition 29 | #define DOMAIN _DOMAIN | ./mconf.h:101: warning: "SING" redefined 101 | #define SING 2 /* argument singularity */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:30: note: this is the location of the previous definition 30 | #define SING _SING | ./mconf.h:102: warning: "OVERFLOW" redefined 102 | #define OVERFLOW 3 /* overflow range error */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:31: note: this is the location of the previous definition 31 | #define OVERFLOW _OVERFLOW | ./mconf.h:103: warning: "UNDERFLOW" redefined 103 | #define UNDERFLOW 4 /* underflow range error */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:32: note: this is the location of the previous definition 32 | #define UNDERFLOW _UNDERFLOW | ./mconf.h:104: warning: "TLOSS" redefined 104 | #define TLOSS 5 /* total loss of precision */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:33: note: this is the location of the previous definition 33 | #define TLOSS _TLOSS | ./mconf.h:105: warning: "PLOSS" redefined 105 | #define PLOSS 6 /* partial loss of precision */ | C:/rtools44/x86_64-w64-mingw32.static.posix/include/math.h:34: note: this is the location of the previous definition 34 | #define PLOSS _PLOSS | gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -D R_NO_REMAP -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ringo_stuff.c -o ringo_stuff.o ringo_stuff.c:13:24: warning: 'Ringo_calls' defined but not used [-Wunused-variable] 13 | static R_CallMethodDef Ringo_calls[] = { | ^~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mmeansd.o mtherr.o ringo_stuff.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-Repitools/00new/Repitools/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Repitools)
Repitools.Rcheck/tests/tests.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("Repitools") Loading required package: Repitools Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min > require("BSgenome.Hsapiens.UCSC.hg18") Loading required package: BSgenome.Hsapiens.UCSC.hg18 Loading required package: BSgenome Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat The following object is masked from 'package:Repitools': blocks > options(warn = -1) > > probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE) > genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE) > > crossMatch <- annotationLookup(probes, genes, 5000, 5000) Processing mapping between probes and features. Mapping done. > correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric())) > names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4) > names(correctCrossMatch$offsets$`Gene 2`) <- c(2) > names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4) > names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7) > names(correctCrossMatch$offsets$`Gene 8`) <- character() > names(correctCrossMatch$offsets$`Gene 9`) <- character() > > if(!isTRUE(all.equal(crossMatch, correctCrossMatch))) + stop("Error in annotationLookup function.") > cat("anontationLookup tested fine.\n") anontationLookup tested fine. > > lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100)) > correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100))) > correctLookupTable[1, c(50, 51)] <- 1 > correctLookupTable[1, c(60, 61)] <- 4 > correctLookupTable[2, c(90, 91)] <- 2 > correctLookupTable[4, c(45, 46)] <- 1 > correctLookupTable[4, c(55, 56)] <- 4 > correctLookupTable[6, c(49, 50)] <- 6 > correctLookupTable[6, c(51, 52)] <- 7 > > if(!all(lookupTable == correctLookupTable, na.rm = TRUE)) + stop("Error in makeWindowLookupTable function") > cat("makeWindowLookupTable tested fine.\n") makeWindowLookupTable tested fine. > > cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear") CpG density calculated for a sample. > if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000)))) + stop("cpgDensityCalc not working for window = 500, scaling = linear") > cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens) CpG density calculated for a sample. > if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000)))) + stop("cpgDensityCalc not working for window = 100, scaling = log") > cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens) CpG density calculated for a sample. > if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062)))) + stop("cpgDensityCalc not working for window = 1000, scaling = exp") > cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens) CpG density calculated for a sample. > if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0)))) + stop("cpgDensityCalc not working for window = 500, scaling = none") > cat("cpgDensityCalc tested fine.\n") cpgDensityCalc tested fine. > > GCpercent <- gcContentCalc(genes, Hsapiens, 500) Calculating GC content. > if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388)))) + stop("Error in gcContentCalc function") > cat("gcContentCalc tested fine.\n") gcContentCalc tested fine. > > findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT") > if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10)))) + stop("Error in sequenceCalc function counting task") > > findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE) > correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238)) > if(!isTRUE(all.equal(findsPlaces, correctPlaces))) + stop("Error in sequenceCalc function positions task") > cat("sequenceCalc tested fine.\n") sequenceCalc tested fine. > cat("All tests passed.\n") All tests passed. > > proc.time() user system elapsed 75.82 18.32 95.82
Repitools.Rcheck/Repitools-Ex.timings
name | user | system | elapsed | |
BAM2GRanges | 0.17 | 0.00 | 0.19 | |
BayMethList-class | 7.18 | 2.44 | 9.86 | |
GCadjustCopy | 0 | 0 | 0 | |
GCbiasPlots | 0 | 0 | 0 | |
QdnaData | 0.09 | 1.20 | 1.31 | |
abcdDNA | 0 | 0 | 0 | |
absoluteCN | 0 | 0 | 0 | |
annoDF2GR | 0.03 | 0.00 | 0.04 | |
annoGR2DF | 0.11 | 1.22 | 1.34 | |
annotationBlocksCounts | 0.14 | 1.16 | 1.36 | |
annotationBlocksLookup | 0.05 | 0.02 | 0.07 | |
annotationCounts | 0.20 | 1.10 | 1.34 | |
annotationLookup | 0.19 | 0.00 | 0.19 | |
binPlots | 1.31 | 0.13 | 1.45 | |
blocksStats | 0.22 | 1.19 | 1.45 | |
checkProbes | 0.23 | 0.01 | 0.25 | |
chromosomeCNplots | 0 | 0 | 0 | |
clusterPlots | 0.77 | 0.02 | 0.78 | |
cpgDensityCalc | 8.14 | 2.75 | 12.49 | |
cpgDensityPlot | 2.53 | 2.34 | 4.94 | |
determineOffset | 6.96 | 2.38 | 10.00 | |
empBayes | 28.71 | 4.28 | 33.10 | |
enrichmentCalc | 1.47 | 1.22 | 2.75 | |
enrichmentPlot | 2.28 | 0.17 | 2.46 | |
featureBlocks | 0.04 | 0.00 | 0.03 | |
featureScores | 0.76 | 0.02 | 0.79 | |
findClusters | 1.38 | 0.07 | 1.46 | |
gcContentCalc | 2.48 | 2.43 | 5.01 | |
genQC | 0 | 0 | 0 | |
genomeBlocks | 0.04 | 0.00 | 0.05 | |
getProbePositionsDf | 0 | 0 | 0 | |
getSampleOffsets | 0 | 0 | 0 | |
hyper | 0 | 0 | 0 | |
loadPairFile | 0 | 0 | 0 | |
loadSampleDirectory | 0 | 0 | 0 | |
makeWindowLookupTable | 0.05 | 0.00 | 0.04 | |
mappabilityCalc | 0 | 0 | 0 | |
maskOut | 4.45 | 2.30 | 6.87 | |
mergeReplicates | 1.16 | 1.09 | 2.25 | |
methylEst | 57.86 | 5.66 | 63.58 | |
multiHeatmap | 0.03 | 0.01 | 0.05 | |
plotClusters | 0.13 | 1.21 | 1.45 | |
plotQdnaByCN | 0 | 0 | 0 | |
processNDF | 0 | 0 | 0 | |
profilePlots | 0 | 0 | 0 | |
regionStats | 0 | 0 | 0 | |
relativeCN | 0.09 | 0.02 | 0.14 | |
sequenceCalc | 8.28 | 2.80 | 11.08 | |
setCNVOffsets | 0 | 0 | 0 | |
summarizeScores | 0.76 | 0.06 | 0.83 | |
writeWig | 0 | 0 | 0 | |