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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qsea.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings qsea_1.33.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/qsea.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'qsea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qsea' version '1.33.0'
* 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 'qsea' can be installed ... WARNING
Found the following significant warnings:
  lm.c:63:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
See 'E:/biocbuild/bbs-3.21-bioc/meat/qsea.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) fitNBglm.Rd:16: Lost braces
    16 | dQuote{log} link function is implemented. }
       |       ^
checkRd: (-1) fitNBglm.Rd:19: Lost braces
    19 | Allowed values are dQuote{region_wise} for independent window wise estimates, 
       |                          ^
checkRd: (-1) fitNBglm.Rd:20: Lost braces
    20 | dQuote{common} for a single estimate for all windows, 
       |       ^
checkRd: (-1) fitNBglm.Rd:21: Lost braces
    21 | dQuote{cutAtQuantiles} for window wise estimates trimmed at the 25\% and 75\% 
       |       ^
checkRd: (-1) fitNBglm.Rd:23: Lost braces
    23 | or dQuote{initial} for using the dispersion parameters provided with the 
       |          ^
checkRd: (-1) plotCNV.Rd:20: Lost braces
    20 | \item{dist}{distance measure for clustering. dQuote{euclid}ian 
       |                                                    ^
checkRd: (-1) plotCNV.Rd:21: Lost braces
    21 | or dQuote{cor}relation based (1-cor)}
       |          ^
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/qsea/libs/x64/qsea.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (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
addNewSamples     18.24   0.68   19.50
addCNV             8.31   0.25    8.92
addPatternDensity  7.85   0.41    8.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/qsea.Rcheck/00check.log'
for details.