Rory Stark
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/DiffBind |
| git_branch: RELEASE_3_20 |
| git_last_commit: da0b044 |
| git_last_commit_date: 2024-10-29 09:38:34 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 565/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DiffBind 3.16.0 (landing page) Rory Stark
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the DiffBind package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DiffBind.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: DiffBind |
| Version: 3.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffBind_3.16.0.tar.gz |
| StartedAt: 2024-11-09 00:54:18 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 01:01:10 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 411.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DiffBind.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffBind_3.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiffBind/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffBind’ version ‘3.16.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘DiffBind’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 2.0Mb
extra 1.3Mb
libs 1.1Mb
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 ... NOTE
checkRd: (-1) NEWS.Rd:106-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:431-438: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:440-446: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NEWS.Rd:450-456: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:96-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:102-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:126-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiffBind3.Rd:128-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:54-55: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dba.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:71: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dba.Rd:78: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dba.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:102-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:104-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:116-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:118-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:120-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.Rd:122-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.analyze.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:40: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dba.blacklist.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.blacklist.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:55-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:92-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:217-219: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:221: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:223-226: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:233-234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:236-237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:253: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:257-258: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:267-268: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.normalize.Rd:270-271: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.peakset.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotHeatmap.Rd:148: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) dba.plotHeatmap.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:58-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:64-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dba.plotProfile.rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:81-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:89-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:102-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:116-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:123-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:130-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:136-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:142-145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:148-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:153-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:158-159: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:162-163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:166-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:170-171: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:174-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:178-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:183-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:188-190: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:193-195: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:198-200: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:203-204: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:207-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:211-212: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:215-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:219-220: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:223-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:227-228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:231-232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.DBA.Rd:235-236: Lost braces in \itemize; meant \describe ?
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
GNU make is a SystemRequirements.
* 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
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DiffBind/libs/DiffBind.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (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 nor [v]sprintf. 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dba.contrast 9.632 0.206 9.838
dba.plotVenn 6.500 0.143 6.646
dba.normalize 6.113 0.135 6.249
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
‘/Users/biocbuild/bbs-3.20-bioc/meat/DiffBind.Rcheck/00check.log’
for details.
DiffBind.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DiffBind ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘DiffBind’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bamReader.cpp -o bamReader.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bedReader.cpp -o bedReader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bitBucket.cpp -o bitBucket.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c croi_func.cpp -o croi_func.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c croi_main.cpp -o croi_main.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densitySet.cpp -o densitySet.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c iBucket.cpp -o iBucket.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interval.cpp -o interval.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalDensity.cpp -o intervalDensity.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalNode.cpp -o intervalNode.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalSet.cpp -o intervalSet.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intervalTree.cpp -o intervalTree.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c merge.cpp -o merge.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mergeOne.c -o mergeOne.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nodeGroup.cpp -o nodeGroup.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c peakOrder.cpp -o peakOrder.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c reader.cpp -o reader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sequence.cpp -o sequence.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.cpp -o util.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DiffBind.so RcppExports.o bamReader.o bam_plbuf.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o merge.o mergeOne.o nodeGroup.o peakOrder.o reader.o sequence.o util.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-DiffBind/00new/DiffBind/libs ** R ** data ** 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 (DiffBind)
DiffBind.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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> library(testthat)
> library(DiffBind)
Loading required package: GenomicRanges
Loading required package: stats4
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, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
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: GenomeInfoDb
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
>>> DiffBind 3.16.0
>
> test_check("DiffBind")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 141 ]
>
> proc.time()
user system elapsed
27.119 0.541 27.666
DiffBind.Rcheck/DiffBind-Ex.timings
| name | user | system | elapsed | |
| dba | 0.137 | 0.014 | 0.156 | |
| dba.analyze | 3.537 | 0.105 | 3.642 | |
| dba.blacklist | 1.892 | 0.025 | 1.919 | |
| dba.contrast | 9.632 | 0.206 | 9.838 | |
| dba.count | 0.515 | 0.020 | 0.537 | |
| dba.load | 0.027 | 0.002 | 0.029 | |
| dba.mask | 0.020 | 0.004 | 0.024 | |
| dba.normalize | 6.113 | 0.135 | 6.249 | |
| dba.overlap | 0.184 | 0.009 | 0.194 | |
| dba.peakset | 0.356 | 0.028 | 0.387 | |
| dba.plotBox | 0.146 | 0.003 | 0.150 | |
| dba.plotHeatmap | 2.102 | 0.029 | 2.065 | |
| dba.plotMA | 3.428 | 0.060 | 3.491 | |
| dba.plotPCA | 0.384 | 0.009 | 0.394 | |
| dba.plotProfile | 0.094 | 0.003 | 0.097 | |
| dba.plotVenn | 6.500 | 0.143 | 6.646 | |
| dba.plotVolcano | 0.779 | 0.017 | 0.797 | |
| dba.report | 1.028 | 0.014 | 1.041 | |
| dba.save | 0 | 0 | 0 | |
| dba.show | 0.187 | 0.003 | 0.190 | |
| print.DBA | 0.032 | 0.001 | 0.033 | |
| tamoxifen | 0.182 | 0.005 | 0.188 | |