nebbiolo2 Summary
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Package: beachmat.hdf5 |
Version: 0.99.1 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data beachmat.hdf5 |
BuildTime: 1 minutes 45.62 seconds |
CheckCommand: BiocCheckGitClone('beachmat.hdf5') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3072/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.install-out.txt beachmat.hdf5_0.99.1.tar.gz && BiocCheck('beachmat.hdf5_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 27.01 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 316.14 KiB |
BuildID:: beachmat.hdf5_20230807205743 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: beachmat.hdf5. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘beachmat.hdf5/DESCRIPTION’ ... OK
* preparing ‘beachmat.hdf5’:
* 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
* building ‘beachmat.hdf5_0.99.1.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('beachmat.hdf5')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: beachmat.hdf5
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat.hdf5/DESCRIPTION’ ... OK
* this is package ‘beachmat.hdf5’ version ‘0.99.1’
* 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 ‘beachmat.hdf5’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 40.4Mb
sub-directories of 1Mb or more:
libs 40.1Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... 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 ... [18s/18s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/pkgbuild/packagebuilder/workers/jobs/3072/R-libs/beachmat.hdf5/libs/beachmat.hdf5.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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 files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[7s/7s] 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 ... [2s/2s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.Rcheck/00check.log’
for details.
===============================
BiocCheck('beachmat.hdf5_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: beachmat.hdf5
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpkHEUEt/file2667aa498b724/beachmat.hdf5
─ installDir: /tmp/RtmpkHEUEt/file2667aa2a98fe64
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 beachmat.hdf5...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 48 lines (18%) are > 80 characters
long.
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: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 3 NOTES
See the beachmat.hdf5.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
[top]
Package: beachmat.hdf5 |
Version: 0.99.1 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data beachmat.hdf5 |
BuildTime: 1 minutes 15.38 seconds |
CheckCommand: BiocCheckGitClone('beachmat.hdf5') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3072/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.install-out.txt beachmat.hdf5_0.99.1.tar.gz && BiocCheck('beachmat.hdf5_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 17.68 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh beachmat.hdf5_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 1 minutes 12.86 seconds |
PackageFileSize: 316.03 KiB |
BuildID:: beachmat.hdf5_20230807205743 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: beachmat.hdf5. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘beachmat.hdf5/DESCRIPTION’ ... OK
* preparing ‘beachmat.hdf5’:
* 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
* building ‘beachmat.hdf5_0.99.1.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('beachmat.hdf5')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: beachmat.hdf5
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat.hdf5/DESCRIPTION’ ... OK
* this is package ‘beachmat.hdf5’ version ‘0.99.1’
* 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 ‘beachmat.hdf5’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
libs 7.1Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking use of S3 registration ... 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 ... [18s/18s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Users/pkgbuild/packagebuilder/workers/jobs/3072/R-libs/beachmat.hdf5/libs/beachmat.hdf5.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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)
Found ‘_rand_r’, possibly from ‘rand_r’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (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 files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/6s]
[7s/7s] 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 ... [5s/6s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.Rcheck/00check.log’
for details.
===============================
BiocCheck('beachmat.hdf5_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: beachmat.hdf5
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpCL2X0l/file61e64fa964e6/beachmat.hdf5
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpCL2X0l/file61e622129906
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/beachmat.hdf5.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 beachmat.hdf5...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 48 lines (18%) are > 80 characters
long.
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: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 3 NOTES
See the beachmat.hdf5.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir beachmat.hdf5_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘beachmat.hdf5’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/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../inst/include -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c initialize_from_hdf5.cpp -o initialize_from_hdf5.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_into_memory.cpp -o load_into_memory.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o beachmat.hdf5.so RcppExports.o initialize_from_hdf5.o load_into_memory.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3072/735cc52792fabd31671fba7b49685325967bcad1/libdir/00LOCK-beachmat.hdf5/00new/beachmat.hdf5/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 (beachmat.hdf5)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/beachmat.hdf5/libs/beachmat.hdf5.so
>>>>>>>
>>>>>>> Paths before fix:
libdir/beachmat.hdf5/libs/beachmat.hdf5.so:
beachmat.hdf5.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/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)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/beachmat.hdf5/libs/beachmat.hdf5.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/beachmat.hdf5/libs/beachmat.hdf5.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/beachmat.hdf5/libs/beachmat.hdf5.so"
>>>>>>> Paths after fix:
libdir/beachmat.hdf5/libs/beachmat.hdf5.so:
beachmat.hdf5.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/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)