##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings FLAMES_1.3.3.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/FLAMES.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FLAMES/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FLAMES' version '1.3.3'
* 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 'FLAMES' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
* 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
* 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
generate_sc_sce: no visible binding for global variable 'FSM_match'
sc_DTU_analysis: no visible global function definition for 'is'
sc_DTU_analysis: no visible binding for global variable 'FSM_match'
sc_DTU_analysis: no visible binding for global variable 'gene_name'
sc_DTU_analysis: no visible binding for global variable 'cell_id'
sc_DTU_analysis: no visible binding for global variable 'cnt'
sc_DTU_analysis: no visible binding for global variable 'tr_id'
sc_DTU_analysis : get_rm: no visible binding for global variable
  'gene_name'
sc_DTU_analysis : get_rm: no visible binding for global variable 'l'
sc_annotate_umap: no visible binding for global variable 'FSM_match'
sc_annotate_umap: no visible binding for global variable 'gene_id'
sc_annotate_umap: no visible binding for global variable 'x'
sc_annotate_umap: no visible binding for global variable 'y'
sc_annotate_umap : plot_idx: no visible binding for global variable 'x'
sc_annotate_umap : plot_idx: no visible binding for global variable 'y'
sc_annotate_umap : plot_idx_impute: no visible binding for global
  variable 'x'
sc_annotate_umap : plot_idx_impute: no visible binding for global
  variable 'y'
Undefined global functions or variables:
  FSM_match cell_id cnt gene_id gene_name is l tr_id x y
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in shell scripts ... 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/FLAMES/libs/x64/FLAMES.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/FLAMES.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/FLAMES_1.3.3.tar.gz && rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FLAMES.buildbin-libdir FLAMES_1.3.3.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL FLAMES_1.3.3.zip && rm FLAMES_1.3.3.tar.gz FLAMES_1.3.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  652k  100  652k    0     0  6476k      0 --:--:-- --:--:-- --:--:-- 6522k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'FLAMES' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppFunctions.cpp -o RcppFunctions.o
In file included from main-functions/../utility/fastq_utils.h:9,
                 from main-functions/match_cell_barcode.h:16,
                 from RcppFunctions.cpp:7:
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:12: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  185 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:12: note: in definition of macro '__KSEQ_READ'
  185 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2'
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro 'KSEQ_INIT'
   15 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:13: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
  171 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:13: note: in definition of macro '__KSEQ_BASIC'
  171 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2'
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro 'KSEQ_INIT'
   15 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:16: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
  165 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:16: note: in definition of macro '__KSEQ_BASIC'
  165 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2'
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro 'KSEQ_INIT'
   15 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main-functions/merge_bulk.cpp -o main-functions/merge_bulk.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility/edit_dist.cpp -o utility/edit_dist.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility/fastq_utils.cpp -o utility/fastq_utils.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
/bin/sh: line 1: F:/biocbuild/bbs-3.16-bioc/R/bin.R: No such file or directory
gcc   -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam.c -o bam.o
bam.c: In function 'bam_remove_B':
bam.c:163:2: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  163 |  for (k = 0; k < b->core.n_cigar; ++k)
      |  ^~~
bam.c:165:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  165 |   if (k == b->core.n_cigar) return 0; // no 'B'
      |   ^~
bam.c:226:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  226 |   for (k = 1; k < l; ++k)
      |   ^~~
bam.c:230:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  230 |    for (k = i = 0; k < l; ++k)
      |    ^~~
bam.c:230:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
bam.c:233:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  233 |     l = i;
      |     ^
/bin/sh: line 1: F:/biocbuild/bbs-3.16-bioc/R/bin.R: No such file or directory
gcc   -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utility/ssw/ssw.c -o utility/ssw/ssw.o
g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o main-functions/merge_bulk.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/FLAMES.buildbin-libdir/00LOCK-FLAMES/00new/FLAMES/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'FLAMES' as FLAMES_1.3.3.zip
* DONE (FLAMES)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'FLAMES' successfully unpacked and MD5 sums checked