Bioconductor Single Package Builder - Build History

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

 R CMD BUILD

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

* checking for file ‘scMitoMut/DESCRIPTION’ ... OK
* preparing ‘scMitoMut’:
* 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 ‘scMitoMut_0.99.1.tar.gz’

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

 BiocCheckGitClone('scMitoMut')

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

─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: scMitoMut
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3095/scMitoMut_20230825175123/scMitoMut
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * WARNING: System files in '/inst' should not be Git tracked.
      inst/extdata/mini_mgatk_out/.DS_Store
* 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 | 1 WARNINGS | 0 NOTES

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




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

 R CMD CHECK

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

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3095/scMitoMut_20230825175123/scMitoMut.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 ‘scMitoMut/DESCRIPTION’ ... OK
* this is package ‘scMitoMut’ 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scMitoMut’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/5s] NOTE
export_dt: no visible binding for global variable ‘af’
export_dt: no visible binding for global variable ‘fwd_depth’
export_dt: no visible binding for global variable ‘rev_depth’
export_dt: no visible binding for global variable ‘coverage’
export_dt: no visible binding for global variable ‘mut_status’
export_dt: no visible binding for global variable ‘cell_barcode’
export_dt: no visible binding for global variable ‘n’
export_dt: no visible binding for global variable ‘loc’
filter_loc: no visible binding for global variable ‘mut_cell_n’
plot_locus: no visible binding for global variable ‘alt_depth’
plot_locus: no visible binding for global variable ‘depth’
plot_locus: no visible binding for global variable ‘af’
plot_locus: no visible binding for global variable ‘highlight’
process_locus_bb: no visible binding for global variable ‘alt_depth’
process_locus_bb: no visible binding for global variable ‘fwd_depth’
process_locus_bb: no visible binding for global variable ‘rev_depth’
process_locus_bm: no visible binding for global variable ‘alt_depth’
process_locus_bm: no visible binding for global variable ‘fwd_depth’
process_locus_bm: no visible binding for global variable ‘rev_depth’
process_locus_summary: no visible binding for global variable
  ‘alt_depth’
process_locus_summary: no visible binding for global variable
  ‘fwd_depth’
process_locus_summary: no visible binding for global variable
  ‘rev_depth’
read_locus: no visible binding for global variable ‘cell_barcode’
read_locus: no visible binding for global variable ‘fwd_depth’
read_locus: no visible binding for global variable ‘rev_depth’
read_locus: no visible binding for global variable ‘coverage’
read_locus: no visible binding for global variable ‘alt’
read_locus: no visible binding for global variable ‘af’
read_mgatk: no visible binding for global variable ‘fwd_depth’
read_mgatk: no visible binding for global variable ‘rev_depth’
Undefined global functions or variables:
  af alt alt_depth cell_barcode coverage depth fwd_depth highlight loc
  mut_cell_n mut_status n rev_depth
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* 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 ... [18s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [3s/3s] 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 ... [4s/4s] OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3095/scMitoMut_20230825175123/scMitoMut.Rcheck/00check.log’
for details.






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

 BiocCheck('scMitoMut_0.99.1.tar.gz')

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

─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: scMitoMut
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmprBMtgz/file193e1393a130/scMitoMut
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmprBMtgz/file193e2132d62b
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3095/scMitoMut_20230825175123/scMitoMut.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...
    * NOTE: Update R version dependency from 4.1.0 to 4.3.0.
* 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:
      SingleCell
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: Invalid ORCID iD for Wenjie SUN
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* 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 scMitoMut...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 4 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* 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; 176 lines (7%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 453 lines
      (19%) 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 | 12 NOTES

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

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir scMitoMut_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘scMitoMut’ ...
** 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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c em_bm.cpp -o em_bm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/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/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mle_bb.cpp -o mle_bb.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 scMitoMut.so RcppExports.o em_bm.o mle_bb.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3095/scMitoMut_20230825175123/libdir/00LOCK-scMitoMut/00new/scMitoMut/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 (scMitoMut)


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

>>>>>>> Paths before fix:
libdir/scMitoMut/libs/scMitoMut.so:
	scMitoMut.so (compatibility version 0.0.0, current version 0.0.0)
	/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)
	/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/scMitoMut/libs/scMitoMut.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/scMitoMut/libs/scMitoMut.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/scMitoMut/libs/scMitoMut.so"

>>>>>>> Paths after fix:

libdir/scMitoMut/libs/scMitoMut.so:
	scMitoMut.so (compatibility version 0.0.0, current version 0.0.0)
	/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)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)