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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qsea.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings qsea_1.32.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.32.0'
* 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 'F:/biocbuild/bbs-3.20-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 'F:/biocbuild/bbs-3.20-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     19.23   1.19   22.16
addPatternDensity  9.75   0.60   10.31
addCNV             8.32   0.39    8.87
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL qsea
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'qsea' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c lm.c -o lm.o
lm.c: In function 'Cdqrls':
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=]
   63 |     error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"),
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lm.c:31:38: note: in definition of macro '_'
   31 | #define _(String) dgettext ("stats", String)
      |                                      ^~~~~~
lm.c:63:50: note: format string is defined here
   63 |     error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"),
      |                                                 ~^
      |                                                  |
      |                                                  int
      |                                                 %lld
gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-qsea/00new/qsea/libs/x64
** R
** inst
** preparing 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 (qsea)

R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(qsea)
> 
> test_check("qsea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
  13.43    0.62   14.59