Zheng Wei
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/esATAC |
| Branch: RELEASE_3_9 |
| Last Commit: 6155826 |
| Last Changed Date: 2019-05-15 14:36:25 -0400 (Wed, 15 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:40:03 -0400 (Wed, 16 Oct 2019).
| Package 519/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| esATAC 1.6.1 Zheng Wei
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: esATAC |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings esATAC_1.6.1.tar.gz |
| StartedAt: 2019-10-16 03:34:24 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:44:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 586.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: esATAC.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings esATAC_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/esATAC.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.6.1'
* 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 7.4Mb
sub-directories of 1Mb or more:
extdata 5.1Mb
* 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 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 ... 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 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-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 or elapsed time > 5s
user system elapsed
RMotifScanPair 7.32 23.74 32.67
CutSiteCountR 2.61 22.69 34.62
FastQC 2.82 22.37 26.99
RSNPs 1.30 13.61 15.81
RPeakAnno 1.30 12.12 14.22
SamToBam 1.45 11.33 13.69
CutSitePre 1.43 11.14 13.36
ATACProc-class 1.86 0.64 7.28
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/esATAC.Rcheck/00check.log'
for details.
esATAC.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch esATAC
###
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* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
* installing *source* package 'esATAC' ...
** using staged installation
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BedLine.cpp -o BedLine.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BedUtils.cpp -o BedUtils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ChrDivi.cpp -o ChrDivi.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CutCountPre.cpp -o CutCountPre.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CutSiteCount.cpp -o CutSiteCount.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LibComplexQC.cpp -o LibComplexQC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SortBed.cpp -o SortBed.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c renamer.cpp -o renamer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sam2bed.cc -o sam2bed.o
C:/Rtools/mingw_64/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-3.9-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-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
BedUtils html
Bowtie2Mapping html
finding level-2 HTML links ... done
CutSiteCountR html
CutSitePre html
FastQC html
FragLenDistr html
FripQC html
LibComplexQC html
PeakCallingFseq html
PeakQC html
RGo html
RMotifScan html
RMotifScanPair html
RPeakAnno html
RPeakComp html
RSNPs html
RemoveAdapter html
Renamer html
Rsortbam html
SamToBam html
SamToBed html
TSSQC html
UnzipAndMerge html
atacPipe2 html
atacRepsPipe html
atacRepsPipe2 html
configureValue html
esATAC-package html
getMotifInfo html
** 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 (esATAC)
Making 'packages.html' ... done
esATAC.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, which.max, which.min
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
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: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("esATAC")
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_1.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_1.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_2.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_1.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_1.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\baseopr/reads_2.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\umr/reads_1.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\umr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\umr/reads_1.Renamer.fq'
Opening FASTQ file 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\umr/reads_2.Renamer.fq'
F-Seq Version 1.85
Settings:
window=2860
bandwidth=100
threshold = 8.616534
est. fragment size = 0
sequence length = 32
chr20: first=60385, last=13381774
....................
.....................
chr20: Completed in 0.641 seconds.
chr20: Found 1560 peaks.
-----------------------
finish temporary output:C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmpq0Ut1s\sam2bed/Example.SamToBed.bed.0
merge start
merge finish
finish
== testthat results ===========================================================
[ OK: 92 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
30.92 1.65 47.51
esATAC.Rcheck/esATAC-Ex.timings
| name | user | system | elapsed | |
| ATACProc-class | 1.86 | 0.64 | 7.28 | |
| BamToBed | 0.45 | 0.05 | 0.57 | |
| BedToBigWig | 0.09 | 0.02 | 0.11 | |
| BedUtils | 0.30 | 0.15 | 1.30 | |
| Bowtie2Mapping | 0.07 | 0.02 | 1.49 | |
| CutSiteCountR | 2.61 | 22.69 | 34.62 | |
| CutSitePre | 1.43 | 11.14 | 13.36 | |
| FastQC | 2.82 | 22.37 | 26.99 | |
| FragLenDistr | 0.09 | 0.00 | 0.09 | |
| FripQC | 2.46 | 0.28 | 3.26 | |
| LibComplexQC | 0.30 | 0.14 | 1.20 | |
| PeakCallingFseq | 0.48 | 0.14 | 1.39 | |
| PeakQC | 0.64 | 0.19 | 1.64 | |
| RGo | 0 | 0 | 0 | |
| RMotifScan | 0 | 0 | 0 | |
| RMotifScanPair | 7.32 | 23.74 | 32.67 | |
| RPeakAnno | 1.30 | 12.12 | 14.22 | |
| RPeakComp | 0.06 | 0.00 | 0.07 | |
| RSNPs | 1.30 | 13.61 | 15.81 | |
| RemoveAdapter | 0.34 | 0.02 | 0.36 | |
| Renamer | 0.05 | 0.00 | 0.05 | |
| Rsortbam | 0.06 | 0.01 | 0.08 | |
| SamToBam | 1.45 | 11.33 | 13.69 | |
| SamToBed | 0.36 | 0.14 | 1.23 | |
| TSSQC | 2.67 | 0.42 | 3.94 | |
| UnzipAndMerge | 0.02 | 0.00 | 0.02 | |
| atacPipe2 | 0 | 0 | 0 | |
| atacRepsPipe | 0 | 0 | 0 | |
| atacRepsPipe2 | 0 | 0 | 0 | |
| configureValue | 0 | 0 | 0 | |
| esATAC-package | 0 | 0 | 0 | |
| getMotifInfo | 0.01 | 0.00 | 0.03 | |