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This page was generated on 2023-06-06 11:00:40 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1659/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Repitools 1.47.0 (landing page) Mark Robinson
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: Repitools |
| Version: 1.47.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Repitools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Repitools_1.47.0.tar.gz |
| StartedAt: 2023-06-06 05:10:34 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 05:21:15 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 641.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Repitools.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Repitools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Repitools_1.47.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Repitools.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.47.0’
* 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
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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: (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
methylEst 83.512 10.037 29.097
empBayes 44.350 7.790 24.380
sequenceCalc 11.191 0.710 11.929
cpgDensityCalc 11.028 0.263 11.337
BayMethList-class 8.719 0.280 9.018
determineOffset 7.618 0.136 7.766
maskOut 5.576 0.359 5.945
* 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 ...
‘Repitools_vignette.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.18-bioc/meat/Repitools.Rcheck/00check.log’
for details.
Repitools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Repitools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘Repitools’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fPIC -g -O2 -c const.c -o const.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fPIC -g -O2 -c hyp2f1.c -o hyp2f1.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fPIC -g -O2 -c mtherr.c -o mtherr.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
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, sort, 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
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
112.539 2.935 115.722
Repitools.Rcheck/Repitools-Ex.timings
| name | user | system | elapsed | |
| BAM2GRanges | 0.178 | 0.008 | 0.187 | |
| BayMethList-class | 8.719 | 0.280 | 9.018 | |
| GCadjustCopy | 0.000 | 0.000 | 0.001 | |
| GCbiasPlots | 0 | 0 | 0 | |
| QdnaData | 0.109 | 0.003 | 0.112 | |
| abcdDNA | 0.001 | 0.000 | 0.001 | |
| absoluteCN | 0 | 0 | 0 | |
| annoDF2GR | 0.026 | 0.000 | 0.026 | |
| annoGR2DF | 0.134 | 0.020 | 0.154 | |
| annotationBlocksCounts | 0.178 | 0.016 | 0.194 | |
| annotationBlocksLookup | 0.070 | 0.002 | 0.073 | |
| annotationCounts | 0.161 | 0.004 | 0.165 | |
| annotationLookup | 0.138 | 0.000 | 0.138 | |
| binPlots | 1.709 | 0.028 | 1.740 | |
| blocksStats | 0.251 | 0.004 | 0.255 | |
| checkProbes | 0.169 | 0.000 | 0.170 | |
| chromosomeCNplots | 0.001 | 0.000 | 0.000 | |
| clusterPlots | 0.971 | 0.012 | 0.984 | |
| cpgDensityCalc | 11.028 | 0.263 | 11.337 | |
| cpgDensityPlot | 4.001 | 0.060 | 4.068 | |
| determineOffset | 7.618 | 0.136 | 7.766 | |
| empBayes | 44.35 | 7.79 | 24.38 | |
| enrichmentCalc | 1.354 | 0.160 | 1.517 | |
| enrichmentPlot | 2.098 | 0.229 | 2.331 | |
| featureBlocks | 0.035 | 0.000 | 0.036 | |
| featureScores | 0.707 | 0.032 | 0.740 | |
| findClusters | 2.136 | 0.208 | 2.348 | |
| gcContentCalc | 2.468 | 0.172 | 2.644 | |
| genQC | 0.001 | 0.000 | 0.000 | |
| genomeBlocks | 0.080 | 0.004 | 0.084 | |
| getProbePositionsDf | 0 | 0 | 0 | |
| getSampleOffsets | 0.001 | 0.000 | 0.000 | |
| hyper | 0.000 | 0.001 | 0.001 | |
| loadPairFile | 0 | 0 | 0 | |
| loadSampleDirectory | 0 | 0 | 0 | |
| makeWindowLookupTable | 0.078 | 0.005 | 0.083 | |
| mappabilityCalc | 0 | 0 | 0 | |
| maskOut | 5.576 | 0.359 | 5.945 | |
| mergeReplicates | 1.484 | 0.136 | 1.623 | |
| methylEst | 83.512 | 10.037 | 29.097 | |
| multiHeatmap | 0.055 | 0.000 | 0.055 | |
| plotClusters | 0.176 | 0.004 | 0.181 | |
| plotQdnaByCN | 0 | 0 | 0 | |
| processNDF | 0 | 0 | 0 | |
| profilePlots | 0 | 0 | 0 | |
| regionStats | 0.000 | 0.000 | 0.001 | |
| relativeCN | 0.103 | 0.004 | 0.108 | |
| sequenceCalc | 11.191 | 0.710 | 11.929 | |
| setCNVOffsets | 0 | 0 | 0 | |
| summarizeScores | 0.754 | 0.036 | 0.792 | |
| writeWig | 0 | 0 | 0 | |