##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:postNet.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings postNet_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/postNet.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-18 07:17:06 UTC
* checking for file ‘postNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘postNet’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 40 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘postNet’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.3Mb
    libs      2.2Mb
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'motifAnalysis.Rd':
  ‘[postNet]{ptn_motifgeneList}’

Non-topic package-anchored link(s) in Rd file 'postNetData-class.Rd':
  ‘[postNet]{ptn_motifgeneList}’

Non-topic package-anchored link(s) in Rd file 'postNetStart.Rd':
  ‘[postNet]{ptn_motifgeneList}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
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
featureIntegration 52.989  2.155  32.016
goAnalysis         44.132  2.168  46.333
ptn_GO             42.701  0.962  43.878
rfPred             30.851  1.484  18.303
ptn_codonSelection 12.387  0.303  12.674
ptn_codonAnalysis  11.084  0.522  11.588
codonCalc          11.331  0.202  11.517
codonUsage         10.718  0.201  10.901
postNetStart        9.250  0.253   9.507
plotSignatures_ads  8.921  0.157   9.070
slopeFilt           6.256  0.507   6.764
plotFeaturesMap     5.539  0.236   5.797
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/postNet.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL postNet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘postNet’ ...
** this is package ‘postNet’ version ‘0.99.8’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pqsfinder.cpp -o pqsfinder.o
pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const boost::regex&, const opts_t&, const scoring&, const std::__cxx11::basic_string<char>::const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’:
pqsfinder.cpp:583:53: warning: ‘loop_len’ may be used uninitialized [-Wmaybe-uninitialized]
  583 |           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
      |                                      ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
pqsfinder.cpp:488:14: note: ‘loop_len’ was declared here
  488 |   int score, loop_len;
      |              ^~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o postNet.so RcppExports.o pqsfinder.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/static_mutex.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-postNet/00new/postNet/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 (postNet)

R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(postNet)
> 
> test_check("postNet")
Warning: stack imbalance in '{', 73 then 75

No motifs found in: UTR3_comparisonA
No motifs passed thresholds in: UTR3_comparisonA
A does not have any sites
0 genes removed because of NAs
0 genes removed because of NAs
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1

adding rname '/home/biocbuild/.cache/R/postNet/1585e879ddd575_CCDS.current.txt'

adding rname '/home/biocbuild/.cache/R/postNet/1585e8c12e143_CCDS_nucleotide.current.fna.gz'
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1

adding rname '/home/biocbuild/.cache/R/postNet/1585e85cda5d71_CCDS.current.txt'

adding rname '/home/biocbuild/.cache/R/postNet/1585e87d561d42_CCDS_nucleotide.current.fna.gz'
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
There are no significant codons for the comparison 1
0 genes removed because of NAs
Found more than one class "Anota2seqDataSet" in cache; using the first, from namespace 'postNet'
Also defined by 'anota2seq'
Found more than one class "Anota2seqDataSet" in cache; using the first, from namespace 'postNet'
Also defined by 'anota2seq'
Found more than one class "Anota2seqDataSet" in cache; using the first, from namespace 'postNet'
Also defined by 'anota2seq'
Found more than one class "Anota2seqDataSet" in cache; using the first, from namespace 'postNet'
Also defined by 'anota2seq'
Found more than one class "Anota2seqDataSet" in cache; using the first, from namespace 'postNet'
Also defined by 'anota2seq'
Found more than one class "Anota2seqDataSet" in cache; using the first, from namespace 'postNet'
Also defined by 'anota2seq'
found 2 rows with classes: character, character, character, integer, integer, character, character, character, character
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 524 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 524 ]
> 
> proc.time()
   user  system elapsed 
 23.862   2.014  29.320