Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:06:38 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for Repitools on palomino3


To the developers/maintainers of the Repitools package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1622/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Repitools 1.42.0  (landing page)
Mark Robinson
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/Repitools
git_branch: RELEASE_3_15
git_last_commit: 9936214
git_last_commit_date: 2022-04-26 11:08:15 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: Repitools
Version: 1.42.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Repitools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Repitools_1.42.0.tar.gz
StartedAt: 2022-06-24 04:08:06 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:24:05 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 958.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Repitools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Repitools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Repitools_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Repitools.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.42.0'
* 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
* 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         54.72   3.27   58.00
empBayes          30.85   2.00   32.86
cpgDensityCalc     8.74   0.64   99.60
sequenceCalc       8.22   0.27    8.49
BayMethList-class  7.97   0.33    8.38
determineOffset    5.90   0.27    6.19
* 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


Installation output

Repitools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Repitools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Repitools' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c const.c -o const.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -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-3.15-bioc/R/include/Rmath.h:43,
                 from hyp2f1.c:80:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:29: note: this is the location of the previous definition
   29 | #define DOMAIN  _DOMAIN
      | 
In file included from hyp2f1.c:81:
./mconf.h:101: warning: "SING" redefined
  101 | #define SING  2 /* argument singularity */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:43,
                 from hyp2f1.c:80:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:30: note: this is the location of the previous definition
   30 | #define SING  _SING
      | 
In file included from hyp2f1.c:81:
./mconf.h:102: warning: "OVERFLOW" redefined
  102 | #define OVERFLOW 3 /* overflow range error */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:43,
                 from hyp2f1.c:80:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:31: note: this is the location of the previous definition
   31 | #define OVERFLOW _OVERFLOW
      | 
In file included from hyp2f1.c:81:
./mconf.h:103: warning: "UNDERFLOW" redefined
  103 | #define UNDERFLOW 4 /* underflow range error */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:43,
                 from hyp2f1.c:80:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:32: note: this is the location of the previous definition
   32 | #define UNDERFLOW _UNDERFLOW
      | 
In file included from hyp2f1.c:81:
./mconf.h:104: warning: "TLOSS" redefined
  104 | #define TLOSS  5 /* total loss of precision */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:43,
                 from hyp2f1.c:80:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:33: note: this is the location of the previous definition
   33 | #define TLOSS  _TLOSS
      | 
In file included from hyp2f1.c:81:
./mconf.h:105: warning: "PLOSS" redefined
  105 | #define PLOSS  6 /* partial loss of precision */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/Rmath.h:43,
                 from hyp2f1.c:80:
c:\rtools42\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-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -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-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:29: note: this is the location of the previous definition
   29 | #define DOMAIN  _DOMAIN
      | 
In file included from mtherr.c:58:
./mconf.h:101: warning: "SING" redefined
  101 | #define SING  2 /* argument singularity */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:30: note: this is the location of the previous definition
   30 | #define SING  _SING
      | 
In file included from mtherr.c:58:
./mconf.h:102: warning: "OVERFLOW" redefined
  102 | #define OVERFLOW 3 /* overflow range error */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:31: note: this is the location of the previous definition
   31 | #define OVERFLOW _OVERFLOW
      | 
In file included from mtherr.c:58:
./mconf.h:103: warning: "UNDERFLOW" redefined
  103 | #define UNDERFLOW 4 /* underflow range error */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:32: note: this is the location of the previous definition
   32 | #define UNDERFLOW _UNDERFLOW
      | 
In file included from mtherr.c:58:
./mconf.h:104: warning: "TLOSS" redefined
  104 | #define TLOSS  5 /* total loss of precision */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:33: note: this is the location of the previous definition
   33 | #define TLOSS  _TLOSS
      | 
In file included from mtherr.c:58:
./mconf.h:105: warning: "PLOSS" redefined
  105 | #define PLOSS  6 /* partial loss of precision */
      | 
In file included from F:/biocbuild/bbs-3.15-bioc/R/include/R.h:47,
                 from mtherr.c:56:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\math.h:34: note: this is the location of the previous definition
   34 | #define PLOSS  _PLOSS
      | 
gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-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)

Tests output

Repitools.Rcheck/tests/tests.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 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: 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 
  79.60    3.54  435.78 

Example timings

Repitools.Rcheck/Repitools-Ex.timings

nameusersystemelapsed
BAM2GRanges0.980.011.00
BayMethList-class7.970.338.38
GCadjustCopy000
GCbiasPlots000
QdnaData0.090.030.13
abcdDNA000
absoluteCN000
annoDF2GR0.030.000.03
annoGR2DF0.130.020.14
annotationBlocksCounts0.140.010.16
annotationBlocksLookup0.040.000.05
annotationCounts0.160.000.16
annotationLookup0.110.000.11
binPlots1.170.101.28
blocksStats0.20.00.2
checkProbes0.270.000.27
chromosomeCNplots000
clusterPlots0.870.030.90
cpgDensityCalc 8.74 0.6499.60
cpgDensityPlot2.580.092.68
determineOffset5.900.276.19
empBayes30.85 2.0032.86
enrichmentCalc1.050.091.14
enrichmentPlot2.050.132.17
featureBlocks0.040.000.05
featureScores0.560.010.58
findClusters1.580.081.66
gcContentCalc2.740.242.96
genQC000
genomeBlocks0.060.000.07
getProbePositionsDf000
getSampleOffsets000
hyper000
loadPairFile000
loadSampleDirectory000
makeWindowLookupTable0.040.000.05
mappabilityCalc000
maskOut3.580.113.69
mergeReplicates1.110.011.12
methylEst54.72 3.2758.00
multiHeatmap0.050.000.05
plotClusters0.140.010.16
plotQdnaByCN000
processNDF000
profilePlots000
regionStats000
relativeCN0.090.000.10
sequenceCalc8.220.278.49
setCNVOffsets000
summarizeScores0.520.080.60
writeWig000