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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings oppar_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/oppar.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘oppar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppar’ version ‘1.30.0’
* 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 ‘oppar’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Initial release
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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
compute.gene.density : <anonymous>: no visible global function
  definition for ‘ecdf’
compute.geneset.es: no visible global function definition for
  ‘txtProgressBar’
compute.geneset.es: no visible global function definition for
  ‘setTxtProgressBar’
ks_test_m: no visible global function definition for
  ‘setTxtProgressBar’
plage: no visible global function definition for ‘txtProgressBar’
plage : <anonymous>: no visible global function definition for ‘sd’
plage : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
plage: no visible global function definition for ‘setTxtProgressBar’
ssgsea: no visible global function definition for ‘txtProgressBar’
ssgsea : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
ssgsea: no visible global function definition for ‘setTxtProgressBar’
zscore: no visible global function definition for ‘txtProgressBar’
zscore : <anonymous>: no visible global function definition for ‘sd’
zscore : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
zscore: no visible global function definition for ‘setTxtProgressBar’
computeGeneSetsOverlap,list-ExpressionSet : <anonymous>: no visible
  global function definition for ‘na.omit’
computeGeneSetsOverlap,list-character : <anonymous>: no visible global
  function definition for ‘na.omit’
gsva,ExpressionSet-GeneSetCollection: no visible binding for global
  variable ‘sd’
gsva,ExpressionSet-GeneSetCollection : <anonymous>: no visible global
  function definition for ‘na.omit’
gsva,ExpressionSet-list: no visible binding for global variable ‘sd’
gsva,ExpressionSet-list : <anonymous>: no visible global function
  definition for ‘na.omit’
gsva,matrix-GeneSetCollection: no visible binding for global variable
  ‘sd’
gsva,matrix-GeneSetCollection : <anonymous>: no visible global function
  definition for ‘na.omit’
gsva,matrix-list: no visible binding for global variable ‘sd’
gsva,matrix-list : <anonymous>: no visible global function definition
  for ‘na.omit’
opa,matrix: no visible global function definition for ‘relevel’
opa,matrix : <anonymous>: no visible global function definition for
  ‘mad’
opa,matrix : <anonymous>: no visible global function definition for
  ‘median’
opa,matrix : <anonymous>: no visible binding for global variable
  ‘quantile’
opa,matrix : <anonymous>: no visible global function definition for
  ‘IQR’
show,OPPARList: no visible global function definition for ‘head’
Undefined global functions or variables:
  IQR ecdf head mad median na.omit quantile relevel sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "IQR", "ecdf", "mad", "median", "na.omit",
             "quantile", "relevel", "sd")
  importFrom("utils", "head", "setTxtProgressBar", "txtProgressBar")
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 ... WARNING
  LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... 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
getSampleOutlier 21.203  0.604  21.924
getSubtypeProbes 20.788  0.340  21.130
opa              14.935  0.156  15.090
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘oppar.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/oppar.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL oppar
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘oppar’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_oppar.c -o R_init_oppar.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c ks_test.c -o ks_test.o
ks_test.c: In function ‘ks_sample’:
ks_test.c:22:16: warning: unused variable ‘mx_value’ [-Wunused-variable]
   22 |         double mx_value = 0.0;
      |                ^~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o oppar.so R_init_oppar.o kernel_estimation.o ks_test.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-oppar/00new/oppar/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 (oppar)