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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings groHMM_1.35.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/groHMM.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'MASS', 'parallel', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'GenomicAlignments', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘groHMM’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives no person with maintainer role, valid email
address and non-empty name.
* 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 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘groHMM.Rnw’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Warnings in re-building vignettes:
  Warning: file stem ‘/home/biocbuild/bbs-3.18-bioc/meat/groHMM.Rcheck/vign_test/groHMM/vignettes/groHMM-fig2’ is not portable
  Warning: file stem ‘/home/biocbuild/bbs-3.18-bioc/meat/groHMM.Rcheck/vign_test/groHMM/vignettes/groHMM-fig3’ is not portable
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/groHMM.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 groHMM
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c MLEfit.c -o MLEfit.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Windowing.c -o Windowing.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c hmmEM.c -o hmmEM.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c hmmFwBw.c -o hmmFwBw.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c hmmMiscFunctions.c -o hmmMiscFunctions.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c hmmViterbi.c -o hmmViterbi.o
gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-groHMM/00new/groHMM/libs
** R
** 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 (groHMM)