Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:36 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
To the developers/maintainers of the genomation package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomation.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 746/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genomation 1.27.1 (landing page) Altuna Akalin
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: genomation |
Version: 1.27.1 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genomation.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings genomation_1.27.1.tar.gz |
StartedAt: 2022-03-17 19:10:28 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 19:14:38 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 250.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genomation.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genomation.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings genomation_1.27.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/genomation.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'genomation/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'genomation' version '1.27.1' * package encoding: latin1 * 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 'genomation' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' See 'D:/biocbuild/bbs-3.15-bioc/meat/genomation.Rcheck/00install.out' for details. * 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 ... NOTE Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ScoreMatrixBin,RleList-GRangesList: no visible binding for global variable 'id' ScoreMatrixBin,RleList-GRangesList: no visible global function definition for ':=' Undefined global functions or variables: := id * 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'D:/biocbuild/bbs-3.15-bioc/R/library/genomation/libs/x64/genomation.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (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. 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 ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'genomation_unit_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: 1 WARNING, 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/genomation.Rcheck/00check.log' for details.
genomation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL genomation ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'genomation' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c binSum.cpp -o binSum.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-genomation/00new/genomation/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** help *** installing help indices converting help for package 'genomation' finding HTML links ... done AnnotationByFeature-class html AnnotationByGeneParts-class html AnnotationByGeneParts-methods html Max_c html Mean_c html Median_c html Min_c html Ops-ScoreMatrix-ScoreMatrix-method html Ops-ScoreMatrixList-ScoreMatrixList-method html Ops-ScoreMatrixList-numeric-method html Ops-numeric-ScoreMatrixList-method html RandomEnrichment-class html ScoreMatrix-class html ScoreMatrix-methods html ScoreMatrixBin-methods html ScoreMatrixList-class html ScoreMatrixList-methods html Sum_c html annotatGrWithGeneParts html annotateWithFeature-methods html annotateWithFeatureFlank-methods html annotateWithFeatures-methods html annotateWithGeneParts-methods html finding level-2 HTML links ... done bed12ToExons html bed12ToIntrons html binMatrix-methods html binMax html binMean html binMedian html binMin html binSum html binner html c.ScoreMatrix html c.ScoreMatrixList html cage html calculateOverlapSignificance-methods html checkBedValidity html checkClass html compressedAndUrl2temp html constrainRanges html convertBed2Exons-methods html convertBed2Introns-methods html convertBedDf-methods html cpgi html detectUCSCheader html distance2NearestFeature html enrichmentMatrix-ScoreMatrix-method html enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method html enrichmentMatrix-ScoreMatrixList-method html file.ext html findFeatureComb-methods html galpTo2Ranges html genes html getColors html getFeatsWithTargetsStats-methods html getFlanks-methods html getMembers-methods html getRandomEnrichment-methods html getTargetAnnotationStats-methods html gffToGRanges html heatMatrix html heatMeta html heatTargetAnnotation-methods html intersectScoreMatrixList-methods html listSliceMax html listSliceMean html listSliceMedian html listSliceMin html listSliceSum html multiHeatMatrix html orderBy-methods html patternMatrix-methods html plotMeta html plotTargetAnnotation-methods html promoters html randomizeFeature-methods html read.zip html readBam html readBed html readBigWig html readBroadPeak html readFeatureFlank-methods html readGeneric html readNarrowPeak html readTableFast html readTranscriptFeatures-methods html scaleScoreMatrix-methods html scaleScoreMatrixList html show-methods html sub-ScoreMatrix-ANY-ANY-ANY-method html sub-ScoreMatrixList-ANY-ANY-ANY-method html target.type html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** testing if installed package keeps a record of temporary installation path * DONE (genomation) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'RJMCMCNucleosomes' is missing or broken done
genomation.Rcheck/tests/genomation_unit_tests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 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("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package") Loading required package: genomation Loading required package: grid Loading required package: GenomicRanges Loading required package: stats4 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 Loading required package: S4Vectors 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: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: rtracklayer Loading required package: readr [1] TRUE Warning message: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' > genomation:::.test() Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... testing:min testing:max testing:median Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Normalizing to rpm ... Rows: 2 Columns: 9 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (3): X1, X4, X6 dbl (5): X2, X3, X5, X7, X8 i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 9 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (3): X1, X4, X6 dbl (5): X2, X3, X5, X7, X8 i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. RUNIT TEST PROTOCOL -- Thu Mar 17 19:14:27 2022 *********************************************** Number of test functions: 24 Number of errors: 0 Number of failures: 0 1 Test Suite : genomation RUnit Tests - 24 test functions, 0 errors, 0 failures Number of test functions: 24 Number of errors: 0 Number of failures: 0 Warning messages: 1: In .local(target, windows, strand.aware) : 1 windows fall off the target 2: In .local(target, windows, strand.aware) : 2 windows fall off the target 3: In .local(target, windows, strand.aware) : 2 windows fall off the target 4: In .local(target, windows, strand.aware) : 2 windows fall off the target 5: In .local(target, windows, strand.aware) : 2 windows fall off the target 6: In .local(target, windows, strand.aware) : 2 windows fall off the target 7: In .local(target, windows, bin.num, bin.op, strand.aware) : 2 windows fall off the target 8: In .local(target, windows, bin.num, bin.op, strand.aware) : 2 windows fall off the target > > proc.time() user system elapsed 21.90 1.37 22.78
genomation.Rcheck/genomation-Ex.timings
name | user | system | elapsed | |
AnnotationByGeneParts-methods | 0.83 | 0.08 | 0.89 | |
ScoreMatrix-methods | 2.40 | 0.14 | 2.55 | |
ScoreMatrixBin-methods | 1.38 | 0.24 | 1.52 | |
ScoreMatrixList-methods | 0.37 | 0.08 | 0.45 | |
annotateWithFeature-methods | 0.03 | 0.01 | 0.05 | |
annotateWithFeatureFlank-methods | 0.2 | 0.0 | 0.2 | |
annotateWithFeatures-methods | 0.63 | 0.10 | 0.67 | |
annotateWithGeneParts-methods | 0.48 | 0.12 | 0.53 | |
binMatrix-methods | 0.21 | 0.02 | 0.22 | |
convertBed2Exons-methods | 0.07 | 0.00 | 0.06 | |
convertBed2Introns-methods | 0.06 | 0.00 | 0.06 | |
enrichmentMatrix-ScoreMatrix-method | 2.48 | 0.34 | 3.13 | |
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 3.39 | 0.67 | 4.09 | |
enrichmentMatrix-ScoreMatrixList-method | 3.33 | 0.63 | 3.96 | |
findFeatureComb-methods | 0.31 | 0.00 | 0.31 | |
getFeatsWithTargetsStats-methods | 0.31 | 0.11 | 0.33 | |
getFlanks-methods | 0.11 | 0.00 | 0.11 | |
getRandomEnrichment-methods | 0.00 | 0.01 | 0.02 | |
getTargetAnnotationStats-methods | 0.33 | 0.08 | 0.34 | |
gffToGRanges | 0.06 | 0.00 | 0.06 | |
heatMatrix | 0.77 | 0.11 | 0.88 | |
heatMeta | 0.28 | 0.06 | 0.34 | |
heatTargetAnnotation-methods | 0.40 | 0.06 | 0.47 | |
intersectScoreMatrixList-methods | 0.21 | 0.02 | 0.22 | |
multiHeatMatrix | 0.23 | 0.09 | 0.33 | |
orderBy-methods | 0.35 | 0.05 | 0.39 | |
patternMatrix-methods | 0.12 | 0.00 | 0.12 | |
plotMeta | 0.28 | 0.09 | 0.38 | |
plotTargetAnnotation-methods | 0.31 | 0.08 | 0.29 | |
readBed | 0.29 | 0.14 | 0.27 | |
readBroadPeak | 0.09 | 0.02 | 0.11 | |
readFeatureFlank-methods | 0.22 | 0.05 | 0.22 | |
readGeneric | 0.14 | 0.03 | 0.12 | |
readNarrowPeak | 0.14 | 0.06 | 0.13 | |
readTranscriptFeatures-methods | 0.23 | 0.03 | 0.25 | |
scaleScoreMatrix-methods | 0.16 | 0.00 | 0.15 | |
scaleScoreMatrixList | 0.38 | 0.03 | 0.41 | |