##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FLAMES_1.1.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/FLAMES.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FLAMES/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FLAMES' version '1.1.2'
* 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 ... 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
* 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
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'
Undefined global functions or variables:
  FSM_match cell_id cnt gene_name is l tr_id
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 'D:/biocbuild/bbs-3.15-bioc/R/library/FLAMES/libs/x64/FLAMES.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (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 ... 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/FLAMES.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FLAMES
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'FLAMES' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
sh: D:/biocbuild/bbs-3.15-bioc/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc   -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
  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'
   if (k == b->core.n_cigar) return 0; // no 'B'
   ^~
bam.c:226:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   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'
    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'
     l = i;
     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c edit_dist.cpp -o edit_dist.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fastq_utils.cpp -o fastq_utils.o
In file included from fastq_utils.h:4,
                 from fastq_utils.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
fastq_utils.h: At global scope:
kseq.h:171:13: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
kseq.h:171:13: note: in definition of macro '__KSEQ_READ'
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c match_cell_barcode.cpp -o match_cell_barcode.o
In file included from fastq_utils.h:4,
                 from match_cell_barcode.cpp:13:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c merge_bulk.cpp -o merge_bulk.o
In file included from fastq_utils.h:4,
                 from merge_bulk.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
sh: D:/biocbuild/bbs-3.15-bioc/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc   -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ssw.c -o ssw.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ssw_cpp.cpp -o ssw_cpp.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o bam.o edit_dist.o fastq_utils.o match_cell_barcode.o merge_bulk.o ssw.o ssw_cpp.o D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-FLAMES/00new/FLAMES/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FLAMES'
    finding HTML links ... done
    bulk_long_pipeline                      html  
    finding level-2 HTML links ... done

    bulk_windows_pipeline_setup             html  
    callBasilisk                            html  
    create_config                           html  
    generate_umap                           html  
    generic_long_pipeline                   html  
    get_default_config_file                 html  
    gff3_to_bed12                           html  
    match_cell_barcode                      html  
    merge_bulk_fastq                        html  
    merge_bulk_fastq_cpp                    html  
    merge_bulk_fastq_python                 html  
    minimap2_align                          html  
    minimap2_check_callable                 html  
    parse_gff_tree                          html  
    parse_json_config                       html  
    print_config                            html  
    samtools_as_bam                         html  
    samtools_sort_index                     html  
    sc_DTU_analysis                         html  
    sc_long_pipeline                        html  
    sc_mutations                            html  
    sc_windows_pipeline_setup               html  
    windows_pipeline_isoforms               html  
    windows_pipeline_quantification         html  
    write_config                            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
* DONE (FLAMES)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MWASTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OncoSimulR' is missing or broken
 done