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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellBarcode.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CellBarcode_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CellBarcode.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellBarcode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellBarcode' version '1.0.0'
* 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 whether package 'CellBarcode' can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
bc_2matrix,BarcodeObj: no visible binding for global variable
  'barcode_seq'
bc_cure_depth,BarcodeObj : <anonymous>: no visible binding for global
  variable 'barcode_seq'
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable 'barcode_seq'
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable 'umi_seq'
bc_extract,character: no visible binding for global variable 'i'
bc_plot_seqQc,BarcodeQcSet: no visible binding for global variable
  'sample_name'
bc_subset,BarcodeObj : <anonymous>: no visible binding for global
  variable 'barcode_seq'
Undefined global functions or variables:
  barcode_seq i sample_name umi_seq
* checking Rd files ... OK
* checking Rd metadata ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/CellBarcode/libs/i386/CellBarcode.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/CellBarcode/libs/x64/CellBarcode.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
bc_summary_seqQc                    4.47   4.34    9.50
sub-BarcodeQcSet-ANY-ANY-ANY-method 4.17   3.05    7.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
sub-BarcodeQcSet-ANY-ANY-ANY-method 4.99   3.48    8.48
bc_summary_seqQc                    4.51   3.37    7.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CellBarcode.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CellBarcode_1.0.0.tar.gz && rm -rf CellBarcode.buildbin-libdir && mkdir CellBarcode.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellBarcode.buildbin-libdir CellBarcode_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CellBarcode_1.0.0.zip && rm CellBarcode_1.0.0.tar.gz CellBarcode_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 1495k    7  118k    0     0   504k      0  0:00:02 --:--:--  0:00:02  504k
100 1495k  100 1495k    0     0  1254k      0  0:00:01  0:00:01 --:--:-- 1254k

install for i386

* installing *source* package 'CellBarcode' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c lib.cpp -o lib.o
lib.cpp: In function 'int hamm_dist(std::__cxx11::string, std::__cxx11::string)':
lib.cpp:59:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (int i=0; i < s1.length(); i++) {
                   ~~^~~~~~~~~~~~~
lib.cpp: In function 'Rcpp::List seq_correct(std::vector<std::__cxx11::basic_string<char> >, Rcpp::IntegerVector, int, int, int, int, int, int)':
lib.cpp:123:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto i=0; i<seq.size(); i++) {
                    ~^~~~~~~~~~~
lib.cpp:159:18: warning: variable 'flag_is_connetcted' set but not used [-Wunused-but-set-variable]
             bool flag_is_connetcted = false;
                  ^~~~~~~~~~~~~~~~~~
lib.cpp:230:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<std::__cxx11::basic_string<char>, int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto i=0; i<res.size(); i++) {
                    ~^~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellBarcode.dll tmp.def RcppExports.o lib.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CellBarcode.buildbin-libdir/00LOCK-CellBarcode/00new/CellBarcode/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CellBarcode'
    finding HTML links ... done
    BarcodeObj                              html  
    CellBarcode                             html  
    bc_2df                                  html  
    bc_auto_cutoff                          html  
    bc_barcodes                             html  
    bc_cleanBc                              html  
    bc_cure_cluster                         html  
    bc_cure_depth                           html  
    bc_cure_umi                             html  
    bc_extract                              html  
    bc_messyBc                              html  
    bc_meta                                 html  
    bc_names                                html  
    bc_obj                                  html  
    bc_plot_mutual                          html  
    bc_plot_pair                            html  
    bc_plot_single                          html  
    bc_seq_filter                           html  
    bc_seq_qc                               html  
    bc_subset                               html  
    bc_summary_barcode                      html  
    bc_summary_seqQc                        html  
    format                                  html  
    show                                    html  
    sub-BarcodeQcSet-ANY-ANY-ANY-method     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CellBarcode' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c lib.cpp -o lib.o
lib.cpp: In function 'int hamm_dist(std::__cxx11::string, std::__cxx11::string)':
lib.cpp:59:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i=0; i < s1.length(); i++) {
                   ~~^~~~~~~~~~~~~
lib.cpp: In function 'Rcpp::List seq_correct(std::vector<std::__cxx11::basic_string<char> >, Rcpp::IntegerVector, int, int, int, int, int, int)':
lib.cpp:123:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto i=0; i<seq.size(); i++) {
                    ~^~~~~~~~~~~
lib.cpp:159:18: warning: variable 'flag_is_connetcted' set but not used [-Wunused-but-set-variable]
             bool flag_is_connetcted = false;
                  ^~~~~~~~~~~~~~~~~~
lib.cpp:230:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<std::__cxx11::basic_string<char>, int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto i=0; i<res.size(); i++) {
                    ~^~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellBarcode.dll tmp.def RcppExports.o lib.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CellBarcode.buildbin-libdir/CellBarcode/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellBarcode' as CellBarcode_1.0.0.zip
* DONE (CellBarcode)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CellBarcode' successfully unpacked and MD5 sums checked