Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:07:49 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 esATAC on lconway


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? 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 617/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esATAC 1.19.0  (landing page)
Zheng Wei
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/esATAC
git_branch: master
git_last_commit: 1fb5e8e
git_last_commit_date: 2022-04-26 11:45:27 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: esATAC
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:esATAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings esATAC_1.19.0.tar.gz
StartedAt: 2022-06-23 20:07:46 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 20:15:11 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 444.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: esATAC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:esATAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings esATAC_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/esATAC.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.19.0’
* 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 ... OK
* 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  6.4Mb
  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 ... NOTE
atacPipe2: no visible global function definition for ‘getObjsInPipe’
atacPipe2: no visible binding for global variable ‘case.peak’
atacPipe2: no visible binding for global variable ‘ctrl.peak’
atacPipe2: no visible binding for global variable ‘pwm’
atacPipe2: no visible binding for global variable ‘bed.case’
atacPipe2: no visible binding for global variable ‘bed.ctrl’
atacPipe2: no visible binding for global variable ‘caselist’
atacPipe2: no visible binding for global variable ‘ctrllist’
atacPipe2: no visible global function definition for ‘.obtainConfigure’
atacPipe2: no visible binding for global variable ‘param.tmp’
atacPipe2: no visible binding for global variable ‘esATAC_report’
atacPipe2: no visible global function definition for ‘getReportVal’
atacPipe2: no visible binding for global variable ‘esATAC_result’
processing,BamToBed : <anonymous>: no visible global function
  definition for ‘readGAlignments’
processing,BedToBigWig: no visible binding for global variable ‘score’
Undefined global functions or variables:
  .obtainConfigure bed.case bed.ctrl case.peak caselist ctrl.peak
  ctrllist esATAC_report esATAC_result getObjsInPipe getReportVal
  param.tmp pwm readGAlignments 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 ... WARNING
Undocumented arguments in documentation object 'PeakCallingMACS2'
  ‘genomeSize’ ‘pvalueThreshold’
Documented arguments not in \usage in documentation object 'PeakCallingMACS2':
  ‘threshold’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
FindAdapter 0.500  0.094  22.335
Renamer     0.408  0.056  19.878
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/esATAC.Rcheck/00check.log’
for details.



Installation output

esATAC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL esATAC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘esATAC’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c BedLine.cpp -o BedLine.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c BedUtils.cpp -o BedUtils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ChrDivi.cpp -o ChrDivi.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CutCountPre.cpp -o CutCountPre.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CutSiteCount.cpp -o CutSiteCount.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c LibComplexQC.cpp -o LibComplexQC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SortBed.cpp -o SortBed.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c rcpp_wrapper.cpp -o rcpp_wrapper.o
rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable]
  int tmp_k;
      ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c renamer.cpp -o renamer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam2bed.cc -o sam2bed.o
sam2bed.cc:125:16: warning: unused variable 'xspm' [-Wunused-variable]
    regmatch_t xspm[1];
               ^
sam2bed.cc:294:16: warning: unused variable 'xspm' [-Wunused-variable]
    regmatch_t xspm[1];
               ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-esATAC/00new/esATAC/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (esATAC)

Tests output

esATAC.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

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
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

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: 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


> 
> test_check("esATAC")
[1] "2022-06-23 20:15:00 EDT"
[1] "2022-06-23 20:15:00 EDT"
[1] "2022-06-23 20:15:00 EDT"
[1] "2022-06-23 20:15:00 EDT"
[1] "2022-06-23 20:15:00 EDT"
[1] "2022-06-23 20:15:00 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 18.603   1.359  21.770 

Example timings

esATAC.Rcheck/esATAC-Ex.timings

nameusersystemelapsed
BamToBed0.0000.0010.001
BedToBigWig0.0810.0090.091
BedUtils0.5080.0440.572
Bowtie2Mapping0.8580.3461.755
CutSiteCountR0.5550.0660.696
CutSitePre1.3980.0311.437
FRiPQC2.3570.2682.154
FastQC0.8290.0600.914
FindAdapter 0.500 0.09422.335
FragLenDistr0.0850.0050.093
LibComplexQC0.1730.0210.205
PeakCallingFseq0.3610.0410.423
PeakCallingMACS20.3380.0420.401
PeakQC0.5630.0500.619
RGo0.0000.0010.001
RMotifScan000
RMotifScanPair0.0000.0000.001
RPeakAnno0.2250.0170.249
RPeakComp0.0780.0040.083
RSNPs0.1560.0100.170
RemoveAdapter0.1940.0450.276
Renamer 0.408 0.05619.878
Rsortbam0.0600.0150.086
SamToBam0.2040.0270.239
SamToBed0.2290.0220.262
TSSQC1.5050.0741.588
UnzipAndMerge0.0220.0080.031
atacPipe20.0010.0010.001
atacRepsPipe0.0000.0010.001
atacRepsPipe20.0000.0010.001
esATAC-package0.0000.0000.001
getMotifInfo0.0080.0010.010