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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CGEN.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CGEN_3.37.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CGEN.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘3.37.1’
* 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 ‘CGEN’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used Fortran compiler: ‘GNU Fortran (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 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 ... 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 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
additive.test  77.241  0.211  77.601
snp.matched    22.497  0.004  22.535
getMatchedSets 18.518  0.056  18.602
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vignette.Rnw’... OK
  ‘vignette_GxE.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CGEN.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CGEN
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘CGEN’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using Fortran compiler: ‘GNU Fortran (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Additive.c -o Additive.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c CML.c -o CML.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c ccl.c -o ccl.o
gfortran  -fPIC  -g -O2  -c csclust.f -o csclust.o
csclust.f:72:72:

   72 |  10      FLAG(I)=.TRUE.
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c fsclust.c -o fsclust.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c hcl.c -o hcl.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c pmatch.c -o pmatch.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c score.c -o score.o
gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-CGEN/00new/CGEN/libs
** R
** data
** 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 (CGEN)