Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/HiCParser

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
lconway	macOS 12.7.1 Monterey/x86_64	OK	ERROR	OK	OK

lconway Summary

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Package: HiCParser

Version: 0.99.0

RVersion: 4.4

BiocVersion: 3.20

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiCParser

BuildTime: 0 minutes 29.78 seconds

CheckCommand: BiocCheckGitClone('HiCParser') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3498/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser.install-out.txt HiCParser_0.99.0.tar.gz && BiocCheck('HiCParser_0.99.0.tar.gz', `new-package`=TRUE)

CheckTime: 0 minutes 3.95 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh HiCParser_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 20.26 seconds

PackageFileSize: 377.03 KiB

BuildID:: HiCParser_20240806125511

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiCParser. Starting Build package. Starting Check package. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 1. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0.

lconway BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘HiCParser/DESCRIPTION’ ... OK
* preparing ‘HiCParser’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘HiCParser_0.99.0.tar.gz’

lconway CHECK output

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===============================

 BiocCheckGitClone('HiCParser')

===============================

─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser
─ BiocVersion: 3.20
─ Package: HiCParser
─ PackageVersion: 0.99.0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      src/HiCParser.so
      src/parseHiCFile.o
      src/RcppExports.o
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
    * WARNING: Unable to read CITATION file with
      'utils::readCitationFile()'

─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCParser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCParser’ version ‘0.99.0’
* 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 serialization versions ... OK
* checking whether package ‘HiCParser’ can be installed ... ERROR
Installation failed.
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser.Rcheck/00check.log’
for details.





===============================

 BiocCheck('HiCParser_0.99.0.tar.gz')

===============================

* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpSZDQNU/filee6a5febcb76/HiCParser
─ BiocVersion: 3.20
─ Package: HiCParser
─ PackageVersion: 0.99.0
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/HiCParser.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpSZDQNU/filee6a5febcb76/HiCParser
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpSZDQNU/filee6a717ae12c
─ isTarBall: TRUE
─ platform: unix

* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (60%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCParser...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 2 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 14 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 18 lines
      (1%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    * ERROR: Add package to Watched Tags in your Support Site profile;
      visit https://support.bioconductor.org/accounts/edit/profile

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 4 NOTES

See the HiCParser.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

lconway BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir HiCParser_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HiCParser’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c parseHiCFile.cpp -o parseHiCFile.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o HiCParser.so RcppExports.o parseHiCFile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3498/HiCParser_20240806125511/libdir/00LOCK-HiCParser/00new/HiCParser/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 (HiCParser)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/HiCParser/libs/HiCParser.so
>>>>>>> 

>>>>>>> Paths before fix:
libdir/HiCParser/libs/HiCParser.so:
	HiCParser.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/HiCParser/libs/HiCParser.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/HiCParser/libs/HiCParser.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/HiCParser/libs/HiCParser.so"

>>>>>>> Paths after fix:
libdir/HiCParser/libs/HiCParser.so:
	HiCParser.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)