Mark Robinson
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/Repitools |
| Branch: RELEASE_3_11 |
| Last Commit: b9a0183 |
| Last Changed Date: 2020-04-27 14:26:02 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:23 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE Repitools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1464/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Repitools 1.34.0 Mark Robinson
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Repitools |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Repitools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Repitools_1.34.0.tar.gz |
| StartedAt: 2020-10-17 04:29:57 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:39:47 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 590.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Repitools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Repitools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Repitools_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.34.0’
* 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 ‘Repitools’ 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 ... 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 ... 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 78.521 9.594 28.577
empBayes 38.824 5.131 21.094
BayMethList-class 9.873 0.504 10.394
cpgDensityCalc 9.716 0.634 10.595
sequenceCalc 9.700 0.455 10.165
determineOffset 7.152 0.392 7.695
maskOut 6.163 0.299 6.467
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tests.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: OK
Repitools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Repitools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘Repitools’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fPIC -Wall -g -O2 -c const.c -o const.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fPIC -Wall -g -O2 -c hyp2f1.c -o hyp2f1.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fPIC -Wall -g -O2 -c mtherr.c -o mtherr.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Repitools/00new/Repitools/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, sort, table,
tapply, union, unique, unsplit, which, 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:base':
expand.grid
Loading required package: IRanges
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: rtracklayer
Attaching package: 'rtracklayer'
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
98.976 4.060 106.358
Repitools.Rcheck/Repitools-Ex.timings
| name | user | system | elapsed | |
| BAM2GRanges | 0.195 | 0.006 | 0.201 | |
| BayMethList-class | 9.873 | 0.504 | 10.394 | |
| GCadjustCopy | 0 | 0 | 0 | |
| GCbiasPlots | 0.000 | 0.001 | 0.001 | |
| QdnaData | 0.090 | 0.005 | 0.095 | |
| abcdDNA | 0 | 0 | 0 | |
| absoluteCN | 0.000 | 0.001 | 0.001 | |
| annoDF2GR | 0.031 | 0.001 | 0.032 | |
| annoGR2DF | 0.147 | 0.008 | 0.154 | |
| annotationBlocksCounts | 0.165 | 0.006 | 0.170 | |
| annotationBlocksLookup | 0.099 | 0.001 | 0.100 | |
| annotationCounts | 0.209 | 0.007 | 0.216 | |
| annotationLookup | 0.175 | 0.002 | 0.177 | |
| binPlots | 1.489 | 0.081 | 1.572 | |
| blocksStats | 0.308 | 0.008 | 0.317 | |
| checkProbes | 0.348 | 0.041 | 0.390 | |
| chromosomeCNplots | 0.000 | 0.001 | 0.001 | |
| clusterPlots | 1.014 | 0.027 | 1.044 | |
| cpgDensityCalc | 9.716 | 0.634 | 10.595 | |
| cpgDensityPlot | 3.812 | 0.238 | 4.054 | |
| determineOffset | 7.152 | 0.392 | 7.695 | |
| empBayes | 38.824 | 5.131 | 21.094 | |
| enrichmentCalc | 1.523 | 0.112 | 1.658 | |
| enrichmentPlot | 2.805 | 0.228 | 3.036 | |
| featureBlocks | 0.038 | 0.001 | 0.039 | |
| featureScores | 0.721 | 0.041 | 0.762 | |
| findClusters | 3.285 | 0.252 | 3.551 | |
| gcContentCalc | 3.426 | 0.276 | 3.707 | |
| genQC | 0.000 | 0.000 | 0.001 | |
| genomeBlocks | 0.155 | 0.001 | 0.156 | |
| getProbePositionsDf | 0 | 0 | 0 | |
| getSampleOffsets | 0.001 | 0.000 | 0.000 | |
| hyper | 0.001 | 0.001 | 0.002 | |
| loadPairFile | 0.001 | 0.000 | 0.001 | |
| loadSampleDirectory | 0.000 | 0.000 | 0.001 | |
| makeWindowLookupTable | 0.105 | 0.002 | 0.106 | |
| mappabilityCalc | 0 | 0 | 0 | |
| maskOut | 6.163 | 0.299 | 6.467 | |
| mergeReplicates | 1.152 | 0.055 | 1.209 | |
| methylEst | 78.521 | 9.594 | 28.577 | |
| multiHeatmap | 0.057 | 0.005 | 0.062 | |
| plotClusters | 0.221 | 0.009 | 0.230 | |
| plotQdnaByCN | 0 | 0 | 0 | |
| processNDF | 0.000 | 0.001 | 0.001 | |
| profilePlots | 0.000 | 0.001 | 0.001 | |
| regionStats | 0.000 | 0.001 | 0.001 | |
| relativeCN | 0.124 | 0.004 | 0.128 | |
| sequenceCalc | 9.700 | 0.455 | 10.165 | |
| setCNVOffsets | 0.001 | 0.001 | 0.001 | |
| summarizeScores | 0.876 | 0.071 | 0.955 | |
| writeWig | 0 | 0 | 0 | |