Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘screenCounter/DESCRIPTION’ ... OK
* preparing ‘screenCounter’:
* 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 ‘screenCounter_0.99.0.tar.gz’

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 BiocCheckGitClone('screenCounter')

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─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: screenCounter
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2940/screenCounter_20230303161617/screenCounter
─ 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

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2940/screenCounter_20230303161617/screenCounter.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 ‘screenCounter/DESCRIPTION’ ... OK
* this is package ‘screenCounter’ version ‘0.99.0’
* 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 ‘screenCounter’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* checking installed package size ... OK
* 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 ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [20s/20s] 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 ... OK
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [15s/15s]
 [15s/15s] 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/5s] OK
* DONE

Status: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2940/screenCounter_20230303161617/screenCounter.Rcheck/00check.log’
for details.






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

 BiocCheck('screenCounter_0.99.0.tar.gz')

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─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: screenCounter
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpaNsdqF/filee8b1a9b3874/screenCounter
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpaNsdqF/filee8b2b625c05
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2940/screenCounter_20230303161617/screenCounter.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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Sequencing, Coverage, MultipleSequenceAlignment
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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 screenCounter...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 445 lines (25%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 89 lines
      (5%) 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 | 6 NOTES

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

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir screenCounter_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘screenCounter’ ...
** 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/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/usr/local/include    -fPIC  -Wall -g -O2  -c count_combo_barcodes_paired.cpp -o count_combo_barcodes_paired.o
In file included from count_combo_barcodes_paired.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:218:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:403:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_combo_barcodes_paired.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings 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/usr/local/include    -fPIC  -Wall -g -O2  -c count_combo_barcodes_single.cpp -o count_combo_barcodes_single.o
In file included from count_combo_barcodes_single.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:218:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:403:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_combo_barcodes_single.cpp:3:
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
In file included from count_combo_barcodes_single.cpp:3:
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable 'len' [-Wunused-variable]
                size_t len = current.second - current.first;
                       ^
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable 'len' [-Wunused-variable]
                size_t len = current.second - current.first;
                       ^
5 warnings 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/usr/local/include    -fPIC  -Wall -g -O2  -c count_dual_barcodes.cpp -o count_dual_barcodes.o
In file included from count_dual_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:218:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:403:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_dual_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings 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/usr/local/include    -fPIC  -Wall -g -O2  -c count_single_barcodes.cpp -o count_single_barcodes.o
In file included from count_single_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5:
../inst/include/kaori/handlers/../MismatchTrie.hpp:218:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
../inst/include/kaori/handlers/../MismatchTrie.hpp:403:22: warning: unused variable 'found' [-Wunused-variable]
                bool found = false;
                     ^
In file included from count_single_barcodes.cpp:3:
In file included from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4:
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: unused variable 'it' [-Wunused-variable]
        auto it = exact.find(current);
             ^
3 warnings 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/usr/local/include    -fPIC  -Wall -g -O2  -c utils.cpp -o utils.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 screenCounter.so RcppExports.o count_combo_barcodes_paired.o count_combo_barcodes_single.o count_dual_barcodes.o count_single_barcodes.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2940/screenCounter_20230303161617/libdir/00LOCK-screenCounter/00new/screenCounter/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 (screenCounter)


>>>>>>> 
>>>>>>> FIXING LINKS FOR libdir/screenCounter/libs/screenCounter.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/screenCounter/libs/screenCounter.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "libdir/screenCounter/libs/screenCounter.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "libdir/screenCounter/libs/screenCounter.so"