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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qsea_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/qsea.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qsea’ version ‘1.36.0’
* 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 for sufficient/correct file permissions ... 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 int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.22-bioc/meat/qsea.Rcheck/00install.out’ for details.
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 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 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
addNewSamples     19.718  0.336  20.128
addPatternDensity  7.215  0.051   7.285
addCNV             6.556  0.103   6.688
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/qsea.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL qsea
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘qsea’ ...
** this is package ‘qsea’ version ‘1.36.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c lm.c -o lm.o
In file included from lm.c:30:
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 int’} [-Wformat=]
   63 |     error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"),
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lm.c:63:11: note: in expansion of macro ‘_’
   63 |     error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"),
      |           ^
lm.c:63:50: note: format string is defined here
   63 |     error(_("dimensions of 'x' (%d,%d) and 'y' (%d) do not match"),
      |                                                 ~^
      |                                                  |
      |                                                  int
      |                                                 %ld
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o qsea.so lm.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-qsea/00new/qsea/libs
** 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
** 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 (qsea)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 15.006   0.748  15.832