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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ppcseq.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ppcseq_1.7.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ppcseq.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ppcseq/DESCRIPTION' ... OK
* this is package 'ppcseq' version '1.7.0'
* 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 'ppcseq' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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
.identify_abundant: no visible binding for global variable '.'
.identify_abundant: no visible binding for global variable '.abundant'
add_exposure_rate: no visible binding for global variable '.variable'
add_exposure_rate: no visible binding for global variable 'S'
add_exposure_rate: no visible binding for global variable 'exposure
  rate'
add_partition: no visible binding for global variable '.'
add_scaled_counts_bulk.calcNormFactor: no visible binding for global
  variable 'transcript'
add_scaled_counts_bulk.get_low_expressed: no visible binding for global
  variable 'transcript'
check_if_within_posterior: no visible binding for global variable
  '.lower'
check_if_within_posterior: no visible binding for global variable
  '.upper'
check_if_within_posterior: no visible binding for global variable 'ppc'
do_inference: no visible binding for global variable 'idx_MPI'
do_inference: no visible binding for global variable 'read count MPI
  row'
do_inference: no visible binding for global variable '.'
do_inference: no visible binding for global variable 'symbol MPI row'
draws_to_tibble_x: no visible binding for global variable '.'
draws_to_tibble_x: no visible binding for global variable 'dummy'
draws_to_tibble_x: no visible binding for global variable '.variable'
draws_to_tibble_x: no visible binding for global variable '.chain'
draws_to_tibble_x: no visible binding for global variable '.iteration'
draws_to_tibble_x: no visible binding for global variable '.draw'
draws_to_tibble_x: no visible binding for global variable '.value'
draws_to_tibble_x_y: no visible binding for global variable '.'
draws_to_tibble_x_y: no visible binding for global variable 'dummy'
draws_to_tibble_x_y: no visible binding for global variable '.variable'
draws_to_tibble_x_y: no visible binding for global variable '.chain'
draws_to_tibble_x_y: no visible binding for global variable
  '.iteration'
draws_to_tibble_x_y: no visible binding for global variable '.draw'
draws_to_tibble_x_y: no visible binding for global variable '.value'
find_optimal_number_of_chains: no visible binding for global variable
  'cc'
find_optimal_number_of_chains: no visible binding for global variable
  'tot'
find_optimal_number_of_chains: no visible binding for global variable
  'chains'
fit_to_counts_rng: no visible binding for global variable '.variable'
fit_to_counts_rng: no visible binding for global variable 'S'
fit_to_counts_rng: no visible binding for global variable 'G'
fit_to_counts_rng: no visible binding for global variable '.'
fit_to_counts_rng_approximated: no visible binding for global variable
  '.'
fit_to_counts_rng_approximated: no visible binding for global variable
  'S'
fit_to_counts_rng_approximated: no visible binding for global variable
  'G'
fit_to_counts_rng_approximated: no visible binding for global variable
  'CI'
format_for_MPI: no visible binding for global variable '.'
format_for_MPI: no visible binding for global variable 'G'
format_for_MPI: no visible binding for global variable 'idx_MPI'
format_input: no visible binding for global variable '.'
format_results: no visible binding for global variable 'sample wise
  data'
get_outlier_data_to_exlude: no visible binding for global variable
  'idx_MPI'
get_outlier_data_to_exlude: no visible binding for global variable 's'
get_outlier_data_to_exlude: no visible binding for global variable
  'read count MPI row'
get_outlier_data_to_exlude: no visible binding for global variable '.'
get_outlier_data_to_exlude: no visible binding for global variable
  'rowid'
get_scaled_counts_bulk: no visible binding for global variable 'med'
get_scaled_counts_bulk: no visible binding for global variable
  'tot_filt'
get_scaled_counts_bulk: no visible binding for global variable 'nf'
get_scaled_counts_bulk: no visible binding for global variable '.'
get_scaled_counts_bulk: no visible binding for global variable 'tot'
identify_outliers: no visible binding for global variable '.'
identify_outliers: no visible binding for global variable 'multiplier'
identify_outliers: no visible binding for global variable 'TMM'
identify_outliers: no visible binding for global variable 'l'
identify_outliers: no visible binding for global variable 'l %>% sd'
identify_outliers: no visible binding for global variable 'cc'
identify_outliers: no visible binding for global variable
  'write_on_disk'
identify_outliers: no visible binding for global variable '.variable'
identify_outliers: no visible binding for global variable 'S'
identify_outliers: no visible binding for global variable 'G'
identify_outliers: no visible binding for global variable '.lower'
identify_outliers: no visible binding for global variable '.upper'
identify_outliers_1_step: no visible binding for global variable '.'
identify_outliers_1_step: no visible global function definition for
  'scale_abundance'
identify_outliers_1_step: no visible binding for global variable 'TMM'
identify_outliers_1_step: no visible binding for global variable
  'multiplier'
identify_outliers_1_step: no visible binding for global variable 'l'
identify_outliers_1_step: no visible binding for global variable 'l %>%
  sd'
identify_outliers_1_step: no visible binding for global variable 'cc'
identify_outliers_1_step: no visible binding for global variable
  'write_on_disk'
identify_outliers_1_step: no visible binding for global variable
  '.variable'
identify_outliers_1_step: no visible binding for global variable 'S'
identify_outliers_1_step: no visible binding for global variable 'G'
identify_outliers_1_step: no visible binding for global variable
  '.lower'
identify_outliers_1_step: no visible binding for global variable
  '.upper'
identify_outliers_1_step: no visible binding for global variable 'ppc'
identify_outliers_1_step: no visible binding for global variable
  'exposure rate'
inits_fx: no visible binding for global variable 'res_discovery'
inits_fx: no visible binding for global variable '.variable'
inits_fx: no visible binding for global variable 'S'
inits_fx: no visible binding for global variable 'G'
inits_fx: no visible binding for global variable 'init'
merge_results: no visible binding for global variable '.variable'
merge_results: no visible binding for global variable 'S'
merge_results: no visible binding for global variable 'G'
merge_results: no visible binding for global variable 'exposure rate'
merge_results: no visible binding for global variable 'slope'
merge_results: no visible binding for global variable '.lower'
merge_results: no visible binding for global variable '.upper'
merge_results: no visible binding for global variable 'ppc'
plot_credible_intervals: no visible binding for global variable 'sample
  wise data'
produce_plots: no visible binding for global variable '.upper_2'
select_to_check_and_house_keeping: no visible binding for global
  variable '.'
summary_to_tibble: no visible binding for global variable '.'
Undefined global functions or variables:
  . .abundant .chain .draw .iteration .lower .upper .upper_2 .value
  .variable CI G S TMM cc chains dummy exposure rate idx_MPI init l l
  %>% sd med multiplier nf ppc read count MPI row res_discovery rowid s
  sample wise data scale_abundance slope symbol MPI row tot tot_filt
  transcript write_on_disk
Consider adding
  importFrom("base", "row", "sample")
  importFrom("stats", "sd")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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/ppcseq/libs/x64/ppcseq.dll':
  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
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ppcseq.Rcheck/00check.log'
for details.