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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:postNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings postNet_0.99.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/postNet.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-18 01:29:38 UTC
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... INFO
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.7Mb
* 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 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
Package unavailable to check Rd xrefs: ‘pqsfinder’
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 30.403  4.692  19.525
rfPred             22.378  3.699  13.950
goAnalysis         18.931  0.986  20.171
ptn_GO             16.888  0.758  17.714
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/postNet.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL postNet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘postNet’ ...
** this is package ‘postNet’ version ‘0.99.8’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pqsfinder.cpp -o pqsfinder.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/regex.cpp -o boost_regex/regex.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o postNet.so RcppExports.o pqsfinder.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/static_mutex.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/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 (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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 '/Users/biocbuild/Library/Caches/org.R-project.R/R/postNet/ce0da5814df_CCDS.current.txt'

adding rname '/Users/biocbuild/Library/Caches/org.R-project.R/R/postNet/ce0d156c7e91_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 '/Users/biocbuild/Library/Caches/org.R-project.R/R/postNet/ce0d2e955c82_CCDS.current.txt'

adding rname '/Users/biocbuild/Library/Caches/org.R-project.R/R/postNet/ce0d2c5e2d1c_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 
  9.146   0.799  13.905