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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings qsea_1.33.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/qsea.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.21-bioc/meat/qsea.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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     16.048  0.432  16.507
addPatternDensity  7.075  0.175   7.250
addCNV             5.336  0.239   5.587
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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