Zheng Wei
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/esATAC |
| Branch: RELEASE_3_10 |
| Last Commit: dca253f |
| Last Changed Date: 2019-10-29 13:10:54 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:32 -0400 (Wed, 15 Apr 2020).
| Package 540/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| esATAC 1.8.0 Zheng Wei
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: esATAC |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:esATAC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings esATAC_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:18:50 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:26:50 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 480.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: esATAC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:esATAC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings esATAC_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/esATAC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘esATAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esATAC’ version ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘esATAC’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.9Mb
sub-directories of 1Mb or more:
extdata 5.2Mb
libs 3.6Mb
* 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 ... 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RMotifScanPair 6.372 0.18 6.558
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/esATAC.Rcheck/00check.log’
for details.
esATAC.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL esATAC
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘esATAC’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c BedLine.cpp -o BedLine.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c BedUtils.cpp -o BedUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c ChrDivi.cpp -o ChrDivi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c CutCountPre.cpp -o CutCountPre.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c CutSiteCount.cpp -o CutSiteCount.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c LibComplexQC.cpp -o LibComplexQC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c SortBed.cpp -o SortBed.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -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;
^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c renamer.cpp -o renamer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c sam2bed.cc -o sam2bed.o
sam2bed.cc: In member function ‘int SamToBed::sam2bed(int, int, char**, int, bool, bool)’:
sam2bed.cc:125:16: warning: unused variable ‘xspm’ [-Wunused-variable]
regmatch_t xspm[1];
^~~~
sam2bed.cc: In member function ‘int SamToBed::sam2bed_merge(int, int, char**, int, bool, bool, int, int, bool)’:
sam2bed.cc:294:16: warning: unused variable ‘xspm’ [-Wunused-variable]
regmatch_t xspm[1];
^~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o esATAC.so BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-esATAC/00new/esATAC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
** testing if installed package keeps a record of temporary installation path
* DONE (esATAC)
esATAC.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> 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
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 objects are masked from 'package:base':
aperm, apply, rowsum
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
>
> test_check("esATAC")
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_2.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/baseopr/reads_2.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/umr/reads_1.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/umr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file '/tmp/RtmpKRHQri/umr/reads_1.Renamer.fq'
Opening FASTQ file '/tmp/RtmpKRHQri/umr/reads_2.Renamer.fq'
F-Seq Version 1.85
Settings:
window=2860
bandwidth=100
threshold = 8.7631645
est. fragment size = 0
sequence length = 32
chr20: first=60385, last=13381774
....................
.....................
chr20: Completed in 0.581 seconds.
chr20: Found 1494 peaks.
-----------------------
finish temporary output:/tmp/RtmpKRHQri/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
33.660 2.100 34.958
esATAC.Rcheck/esATAC-Ex.timings
| name | user | system | elapsed | |
| ATACProc-class | 0.740 | 0.244 | 1.309 | |
| BamToBed | 1.792 | 0.124 | 1.957 | |
| BedToBigWig | 0.100 | 0.000 | 0.103 | |
| BedUtils | 0.320 | 0.004 | 0.376 | |
| Bowtie2Mapping | 0.932 | 0.384 | 0.779 | |
| CutSiteCountR | 0.528 | 0.032 | 0.652 | |
| CutSitePre | 0.248 | 0.016 | 0.264 | |
| FastQC | 0.756 | 0.012 | 0.793 | |
| FragLenDistr | 0.060 | 0.000 | 0.062 | |
| FripQC | 1.804 | 0.084 | 1.417 | |
| LibComplexQC | 0.156 | 0.000 | 0.155 | |
| PeakCallingFseq | 0.264 | 0.000 | 0.264 | |
| PeakQC | 0.392 | 0.008 | 0.400 | |
| RGo | 0 | 0 | 0 | |
| RMotifScan | 0 | 0 | 0 | |
| RMotifScanPair | 6.372 | 0.180 | 6.558 | |
| RPeakAnno | 0.172 | 0.000 | 0.175 | |
| RPeakComp | 0.056 | 0.000 | 0.055 | |
| RSNPs | 0.164 | 0.000 | 0.165 | |
| RemoveAdapter | 0.212 | 0.000 | 0.211 | |
| Renamer | 0.024 | 0.000 | 0.023 | |
| Rsortbam | 0.044 | 0.000 | 0.042 | |
| SamToBam | 0.184 | 0.008 | 0.194 | |
| SamToBed | 0.324 | 0.004 | 0.327 | |
| TSSQC | 1.452 | 0.032 | 1.488 | |
| UnzipAndMerge | 0.008 | 0.000 | 0.006 | |
| atacPipe2 | 0.000 | 0.000 | 0.001 | |
| atacRepsPipe | 0 | 0 | 0 | |
| atacRepsPipe2 | 0 | 0 | 0 | |
| configureValue | 0.004 | 0.000 | 0.001 | |
| esATAC-package | 0 | 0 | 0 | |
| getMotifInfo | 0.008 | 0.004 | 0.059 | |