Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* preparing ‘alabaster.base’:
* 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 ‘alabaster.base_0.99.3.tar.gz’

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 BiocCheckGitClone('alabaster.base')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.base
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/4670811b234184fc3353ff870a9ac3bfdf2f5d82/alabaster.base
─ 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')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2894/4670811b234184fc3353ff870a9ac3bfdf2f5d82/alabaster.base.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘0.99.3’
* 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 ‘alabaster.base’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [15s/16s] OK
* checking Rd files ... [1s/1s] 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/2894/R-libs/alabaster.base/libs/alabaster.base.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)

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 ... [8s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [32s/32s]
 [32s/32s] 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 ... [10s/11s] OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2894/4670811b234184fc3353ff870a9ac3bfdf2f5d82/alabaster.base.Rcheck/00check.log’
for details.






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 BiocCheck('alabaster.base_0.99.3.tar.gz')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.base
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp5nwN7u/file16eb15ca9d40e/alabaster.base
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp5nwN7u/file16eb165d01e49
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/4670811b234184fc3353ff870a9ac3bfdf2f5d82/alabaster.base.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 alabaster.base...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in vignettes/applications.Rmd
    Found @ in vignettes/extensions.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 87 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* 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; 600 lines (15%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 49 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.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES

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

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir alabaster.base_0.99.3.tar.gz'
>>>>>>> 

* installing *source* package ‘alabaster.base’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++17
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c check_csv.cpp -o check_csv.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c check_list.cpp -o check_list.o
In file included from check_list.cpp:3:
In file included from ../inst/include/uzuki2/uzuki2.hpp:15:
In file included from ../inst/include/uzuki2/parse_json.hpp:15:
In file included from ../inst/include/byteme/SomeBufferReader.hpp:6:
../inst/include/byteme/ZlibBufferReader.hpp:47:24: warning: variable 'ret' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                       ^~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:51:17: note: uninitialized use occurs here
            if (ret != Z_OK) {
                ^~~
../inst/include/byteme/ZlibBufferReader.hpp:47:20: note: remove the 'if' if its condition is always true
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                   ^~~~~~~~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:40:20: note: initialize the variable 'ret' to silence this warning
            int ret;
                   ^
                    = 0
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c load_csv.cpp -o load_csv.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c load_list.cpp -o load_list.o
In file included from load_list.cpp:3:
In file included from ../inst/include/uzuki2/uzuki2.hpp:15:
In file included from ../inst/include/uzuki2/parse_json.hpp:15:
In file included from ../inst/include/byteme/SomeBufferReader.hpp:6:
../inst/include/byteme/ZlibBufferReader.hpp:47:24: warning: variable 'ret' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                       ^~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:51:17: note: uninitialized use occurs here
            if (ret != Z_OK) {
                ^~~
../inst/include/byteme/ZlibBufferReader.hpp:47:20: note: remove the 'if' if its condition is always true
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                   ^~~~~~~~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:40:20: note: initialize the variable 'ret' to silence this warning
            int ret;
                   ^
                    = 0
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c write_scalar.cpp -o write_scalar.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o load_csv.o load_list.o write_scalar.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2894/4670811b234184fc3353ff870a9ac3bfdf2f5d82/libdir/00LOCK-alabaster.base/00new/alabaster.base/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 (alabaster.base)


>>>>>>> 
>>>>>>> FIXING LINKS FOR libdir/alabaster.base/libs/alabaster.base.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "libdir/alabaster.base/libs/alabaster.base.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "libdir/alabaster.base/libs/alabaster.base.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "libdir/alabaster.base/libs/alabaster.base.so"