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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the esATAC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/esATAC.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 595/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
esATAC 1.14.0 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: esATAC |
Version: 1.14.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings esATAC_1.14.0.tar.gz |
StartedAt: 2021-10-14 22:55:06 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:05:04 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 598.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: esATAC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings esATAC_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/esATAC.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'esATAC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'esATAC' version '1.14.0' * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'esATAC' can be installed ... OK * checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: extdata 5.1Mb libs 1.2Mb * 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 ... NOTE Warning in options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'ShortRead:::.ShortReadQQA' 'ShortRead:::.qa_adapterContamination' 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 processing,BedToBigWig: no visible binding for global variable 'score' Undefined global functions or variables: score * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'RMotifScan.Rd': 'import' Missing link or links in documentation object 'RPeakAnno.Rd': 'import' Missing link or links in documentation object 'RPeakComp.Rd': 'import' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 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 ... NOTE Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/esATAC/libs/x64/esATAC.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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed CutSiteCountR 4.76 27.78 38.73 FastQC 3.37 27.35 32.34 CutSitePre 1.92 13.41 16.06 SamToBam 1.69 13.64 16.08 RSNPs 1.46 12.87 15.03 RPeakAnno 1.68 12.40 14.81 FindAdapter 0.81 0.04 24.42 Renamer 0.75 0.06 23.00 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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, 6 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/esATAC.Rcheck/00check.log' for details.
esATAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch esATAC ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' * installing *source* package 'esATAC' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BedLine.cpp -o BedLine.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BedUtils.cpp -o BedUtils.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChrDivi.cpp -o ChrDivi.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CutCountPre.cpp -o CutCountPre.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CutSiteCount.cpp -o CutSiteCount.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibComplexQC.cpp -o LibComplexQC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SortBed.cpp -o SortBed.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_wrapper.cpp -o rcpp_wrapper.o rcpp_wrapper.cpp: In function 'int CutSiteCount_wrapper(Rcpp::List)': rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable] int tmp_k; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c renamer.cpp -o renamer.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sam2bed.cc -o sam2bed.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o esATAC.dll tmp.def BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.13-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'esATAC' finding HTML links ... done ATACProc-class html BamToBed html BedToBigWig html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedToBigWig.html BedUtils html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedUtils.html Bowtie2Mapping html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bowtie2Mapping.html finding level-2 HTML links ... done CutSiteCountR html CutSitePre html FRiPQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fripQC.html FastQC html FindAdapter html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/findAdapter.html FragLenDistr html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fragLenDistr.html LibComplexQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/libComplexQC.html PeakCallingFseq html PeakQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/peakQC.html RGo html RMotifScan html RMotifScanPair html RPeakAnno html RPeakComp html RSNPs html RemoveAdapter html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/removeAdapter.html Renamer html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/renamer.html Rsortbam html SamToBam html SamToBed html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/samToBed.html SingleRepReport html TSSQC html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/tssQC.html UnzipAndMerge html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/unzipAndMerge.html atacPipe2 html atacRepsPipe html atacRepsPipe2 html esATAC-package html getMotifInfo html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled ** testing if installed package can be loaded from final location Warning in options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled ** testing if installed package keeps a record of temporary installation path * DONE (esATAC) Making 'packages.html' ... done
esATAC.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" 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. > library(testthat) > library(esATAC) Loading required package: Rsamtools Loading required package: GenomeInfoDb 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.max, which.min 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: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: ShortRead Loading required package: BiocParallel 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: pipeFrame Attaching package: 'pipeFrame' The following object is masked from 'package:ShortRead': report Warning message: In options(stringsAsFactors = TRUE) : 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled > > test_check("esATAC") [1] "2021-10-14 23:04:52 EDT" [1] "2021-10-14 23:04:52 EDT" [1] "2021-10-14 23:04:53 EDT" [1] "2021-10-14 23:04:53 EDT" [1] "2021-10-14 23:04:53 EDT" [1] "2021-10-14 23:04:53 EDT" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] > > proc.time() user system elapsed 18.95 0.92 22.56
esATAC.Rcheck/esATAC-Ex.timings
name | user | system | elapsed | |
BamToBed | 0.41 | 0.01 | 0.53 | |
BedToBigWig | 0.06 | 0.02 | 0.08 | |
BedUtils | 0.97 | 0.22 | 2.15 | |
Bowtie2Mapping | 0.16 | 0.06 | 2.86 | |
CutSiteCountR | 4.76 | 27.78 | 38.73 | |
CutSitePre | 1.92 | 13.41 | 16.06 | |
FRiPQC | 3.44 | 0.48 | 3.96 | |
FastQC | 3.37 | 27.35 | 32.34 | |
FindAdapter | 0.81 | 0.04 | 24.42 | |
FragLenDistr | 0.10 | 0.00 | 0.09 | |
LibComplexQC | 0.21 | 0.27 | 1.24 | |
PeakCallingFseq | 0.53 | 0.22 | 1.50 | |
PeakQC | 0.89 | 0.25 | 1.82 | |
RGo | 0 | 0 | 0 | |
RMotifScan | 0.01 | 0.00 | 0.02 | |
RMotifScanPair | 0 | 0 | 0 | |
RPeakAnno | 1.68 | 12.40 | 14.81 | |
RPeakComp | 0.07 | 0.02 | 0.10 | |
RSNPs | 1.46 | 12.87 | 15.03 | |
RemoveAdapter | 0.22 | 0.05 | 0.51 | |
Renamer | 0.75 | 0.06 | 23.00 | |
Rsortbam | 0.07 | 0.05 | 0.16 | |
SamToBam | 1.69 | 13.64 | 16.08 | |
SamToBed | 0.33 | 0.31 | 1.34 | |
TSSQC | 1.88 | 0.43 | 3.03 | |
UnzipAndMerge | 0.04 | 0.00 | 0.05 | |
atacPipe2 | 0 | 0 | 0 | |
atacRepsPipe | 0 | 0 | 0 | |
atacRepsPipe2 | 0 | 0 | 0 | |
esATAC-package | 0 | 0 | 0 | |
getMotifInfo | 0.00 | 0.01 | 0.02 | |