Zheng Wei
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/esATAC |
| git_branch: RELEASE_3_18 |
| git_last_commit: fc5274b |
| git_last_commit_date: 2023-10-24 11:01:27 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:09 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 | ||||
| Package 667/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| esATAC 1.24.0 (landing page) Zheng Wei
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the esATAC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: esATAC |
| Version: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2024-04-17 13:16:44 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 13:25:51 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 547.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: esATAC.Rcheck |
| Warnings: 0 |
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###
### 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/esATAC.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘esATAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esATAC’ version ‘1.24.0’
* 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
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 startup messages can be suppressed ... 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
FindAdapter 0.504 0.098 24.523
Renamer 0.494 0.068 24.497
* 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
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/esATAC.Rcheck/00check.log’
for details.
esATAC.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL esATAC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘esATAC’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedLine.cpp -o BedLine.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedUtils.cpp -o BedUtils.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChrDivi.cpp -o ChrDivi.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CutCountPre.cpp -o CutCountPre.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CutSiteCount.cpp -o CutSiteCount.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibComplexQC.cpp -o LibComplexQC.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SortBed.cpp -o SortBed.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c renamer.cpp -o renamer.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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)
esATAC.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, aperm, 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 object is masked from 'package:utils':
findMatches
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] "2024-04-17 13:25:40 EDT"
[1] "2024-04-17 13:25:40 EDT"
[1] "2024-04-17 13:25:40 EDT"
[1] "2024-04-17 13:25:40 EDT"
[1] "2024-04-17 13:25:40 EDT"
[1] "2024-04-17 13:25:40 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
23.183 0.985 24.281
esATAC.Rcheck/esATAC-Ex.timings
| name | user | system | elapsed | |
| BamToBed | 0 | 0 | 0 | |
| BedToBigWig | 0.077 | 0.005 | 0.082 | |
| BedUtils | 0.474 | 0.039 | 0.516 | |
| Bowtie2Mapping | 1.282 | 0.276 | 1.092 | |
| CutSiteCountR | 0.568 | 0.052 | 0.629 | |
| CutSitePre | 0.289 | 0.021 | 0.312 | |
| FRiPQC | 2.559 | 0.196 | 2.350 | |
| FastQC | 0.901 | 0.037 | 0.949 | |
| FindAdapter | 0.504 | 0.098 | 24.523 | |
| FragLenDistr | 0.071 | 0.003 | 0.074 | |
| LibComplexQC | 0.176 | 0.018 | 0.195 | |
| PeakCallingFseq | 0.359 | 0.030 | 0.391 | |
| PeakCallingMACS2 | 0.363 | 0.026 | 0.391 | |
| PeakQC | 0.569 | 0.043 | 0.614 | |
| RGo | 0 | 0 | 0 | |
| RMotifScan | 0.000 | 0.000 | 0.001 | |
| RMotifScanPair | 0.000 | 0.001 | 0.000 | |
| RPeakAnno | 0.229 | 0.014 | 0.247 | |
| RPeakComp | 0.074 | 0.004 | 0.078 | |
| RSNPs | 0.146 | 0.010 | 0.157 | |
| RemoveAdapter | 0.186 | 0.044 | 0.237 | |
| Renamer | 0.494 | 0.068 | 24.497 | |
| Rsortbam | 0.073 | 0.014 | 0.105 | |
| SamToBam | 0.196 | 0.025 | 0.227 | |
| SamToBed | 0.248 | 0.021 | 0.270 | |
| TSSQC | 2.008 | 0.078 | 2.087 | |
| UnzipAndMerge | 0.018 | 0.006 | 0.025 | |
| atacPipe2 | 0 | 0 | 0 | |
| atacRepsPipe | 0.000 | 0.001 | 0.000 | |
| atacRepsPipe2 | 0.000 | 0.000 | 0.001 | |
| esATAC-package | 0.000 | 0.000 | 0.001 | |
| getMotifInfo | 0.012 | 0.001 | 0.014 | |