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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bcSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bcSeq_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/bcSeq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bcSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bcSeq’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package ‘bcSeq’ can be installed ... WARNING
Found the following significant warnings:
  ./helper/fastqCheck.h:54:26: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
  ./helper/fastqCheck.h:55:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
  ./helper/fastqCheck.h:56:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
  ./helper/count.h:37:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
  ./helper/count.h:38:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
  ./helper/count.h:72:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
  ./helper/count.h:73:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/bcSeq.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcSeq-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_bcSeq.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/bcSeq.Rcheck/00check.log’
for details.