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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings FLAMES_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/FLAMES.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘FLAMES/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FLAMES’ version ‘1.4.3’
* 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 for sufficient/correct file permissions ... 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   7.8Mb
* 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 loading without being on the library search path ... 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
combine_sce: no visible global function definition for 'is'
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_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'
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 is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/FLAMES/libs/FLAMES.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ‘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 ...
  ‘FLAMES_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/FLAMES.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL FLAMES
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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:
/home/biocbuild/bbs-3.16-bioc/R/site-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) \
      |            ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:185:12: note: in definition of macro ‘__KSEQ_READ’
  185 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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)         \
      |             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:171:13: note: in definition of macro ‘__KSEQ_BASIC’
  171 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:16: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
  165 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:16: note: in definition of macro ‘__KSEQ_BASIC’
  165 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utility/edit_dist.cpp -o utility/edit_dist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utility/fastq_utils.cpp -o utility/fastq_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam.c -o bam.o
bam.c: In function ‘bam_remove_B’:
bam.c:164:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  164 |  for (k = 0; k < b->core.n_cigar; ++k)
      |  ^~~
bam.c:166:3: 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:227:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  227 |   for (k = 1; k < l; ++k)
      |   ^~~
bam.c:231:4: 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:231:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
bam.c:234:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  234 |     l = i;
      |     ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utility/ssw/ssw.c -o utility/ssw/ssw.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppFunctions.o RcppExports.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 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-FLAMES/00new/FLAMES/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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:  /tmp/RtmppzefiN/file2248ac72161ba2/config_file_2246828.json 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 19.869   1.013  20.867