##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FLAMES.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FLAMES_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/FLAMES.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FLAMES/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FLAMES' version '1.6.0'
* 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 'FLAMES' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
* 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
barcode_info_plots: no visible global function definition for
  'everything'
barcode_info_plots: no visible binding for global variable 'name'
barcode_info_plots: no visible binding for global variable 'value'
barcode_info_plots: no visible binding for global variable
  'reads_demultiplexed'
combine_sce: no visible global function definition for 'is'
generate_sc_sce: no visible binding for global variable 'FSM_match'
plot_flagstat: no visible global function definition for 'everything'
plot_flagstat: no visible binding for global variable 'name'
plot_flagstat: no visible binding for global variable 'value'
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_plots: no visible binding for global variable 'gene_id'
sc_annotate_plots: no visible binding for global variable 'x'
sc_annotate_plots: no visible binding for global variable 'y'
sc_annotate_plots : plot_idx: no visible binding for global variable
  'x'
sc_annotate_plots : plot_idx: no visible binding for global variable
  'y'
sc_annotate_plots : plot_idx_impute: no visible binding for global
  variable 'x'
sc_annotate_plots : plot_idx_impute: no visible binding for global
  variable 'y'
sc_heatmap_expression: no visible binding for global variable
  'transcript_id'
sc_heatmap_expression: no visible binding for global variable 'gene_id'
sc_heatmap_expression : group_annotation: no visible binding for global
  variable 'heatmap_annotation_colors'
sc_umap_expression: no visible binding for global variable
  'transcript_id'
sc_umap_expression: no visible binding for global variable 'gene_id'
sc_umap_expression: no visible binding for global variable 'x'
sc_umap_expression: no visible binding for global variable 'y'
sc_umap_expression : plot_idx: no visible binding for global variable
  'x'
sc_umap_expression : plot_idx: no visible binding for global variable
  'y'
Undefined global functions or variables:
  FSM_match cell_id cnt everything gene_id gene_name
  heatmap_annotation_colors is l name reads_demultiplexed tr_id
  transcript_id value 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-3.17-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 nor [v]sprintf. 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
sc_heatmap_expression 300.54  10.01  315.14
sc_umap_expression    294.74   7.96  304.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/FLAMES.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL FLAMES
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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

using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/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:7,
                 from main-functions/match_cell_barcode.h:13,
                 from RcppFunctions.cpp:7:
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  185 |         SCOPE int kseq_read(kseq_t *seq) \
      |                   ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: note: in definition of macro '__KSEQ_READ'
  185 |         SCOPE int kseq_read(kseq_t *seq) \
      |                   ^~~~~~~~~
F:/biocbuild/bbs-3.17-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:12:1: note: in expansion of macro 'KSEQ_INIT'
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: note: in definition of macro '__KSEQ_BASIC'
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-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:12:1: note: in expansion of macro 'KSEQ_INIT'
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: 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-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: note: in definition of macro '__KSEQ_BASIC'
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
      |                       ^~~~~~~~~
F:/biocbuild/bbs-3.17-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:12:1: note: in expansion of macro 'KSEQ_INIT'
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/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
main-functions/match_cell_barcode.cpp: In function 'std::pair<int, int> get_bc_range(std::string, int, std::string, int)':
main-functions/match_cell_barcode.cpp:304:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  304 |     if (ix + 1 > vect.size()) {
      |         ~~~~~~~^~~~~~~~~~~~~
main-functions/match_cell_barcode.cpp:313:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  313 |     if (ix + 1 > vect_rev.size()) {
      |         ~~~~~~~^~~~~~~~~~~~~~~~~
main-functions/match_cell_barcode.cpp: In function 'Rcpp::List match_cell_barcode(Rcpp::String, Rcpp::String, Rcpp::String, Rcpp::String, int, int, Rcpp::String, int, bool, bool)':
main-functions/match_cell_barcode.cpp:601:24: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  601 |         if (seq.size() > min_length) {
      |             ~~~~~~~~~~~^~~~~~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/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-3.17-bioc/R/bin.R: No such file or directory
gcc   -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam.c -o bam.o
bam.c: In function 'bam_remove_B':
bam.c:164:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  164 |         for (k = 0; k < b->core.n_cigar; ++k)
      |         ^~~
bam.c:166:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  166 |                 if (k == b->core.n_cigar) return 0; // no 'B'
      |                 ^~
bam.c:227:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  227 |                 for (k = 1; k < l; ++k)
      |                 ^~~
bam.c:231:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  231 |                         for (k = i = 0; k < l; ++k)
      |                         ^~~
bam.c:231:25: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
bam.c:234:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  234 |                                 l = i;
      |                                 ^
/bin/sh: line 1: F:/biocbuild/bbs-3.17-bioc/R/bin.R: No such file or directory
gcc   -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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 utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/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
* DONE (FLAMES)

R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(FLAMES)
> 
> test_check("FLAMES")
Writing configuration parameters to:  F:\biocbuild\bbs-3.17-bioc\tmpdir\RtmpueLjdP\file2568441a142a/config_file_9576.json 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  18.48    1.45   21.65