##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings universalmotif_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/universalmotif.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.25.1’
* package encoding: UTF-8
* 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 ‘universalmotif’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ArabidopsisPromoters.Rd: DNAStringSet
  add_multifreq.Rd: XStringSet
  create_motif.Rd: XStringSet, DNAStringSet, RNAStringSet, AAStringSet,
    BStringSet
  create_sequences.Rd: XStringSet
  enrich_motifs.Rd: XStringSet
  fontDFroboto.Rd: DataFrame-class
  get_bkg.Rd: XStringSet
  run_meme.Rd: XStringSet
  sample_sites.Rd: XStringSet
  scan_sequences.Rd: XStringSet, DNAString, MaskedXString,
    DNAStringSet, RNAStringSet
  sequence_complexity.Rd: XStringSet
  shuffle_sequences.Rd: XStringSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... 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
convert_motifs 10.594  0.491  11.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/universalmotif.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL universalmotif
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c add_multifreq.cpp -o add_multifreq.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c calc_complexity.cpp -o calc_complexity.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from calc_complexity.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c compare_motifs.cpp -o compare_motifs.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from compare_motifs.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c get_bkg.cpp -o get_bkg.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from get_bkg.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c motif_finder.cpp -o motif_finder.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from motif_finder.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c motif_peaks.cpp -o motif_peaks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c motif_pvalue.cpp -o motif_pvalue.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from motif_pvalue.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c scan_sequences.cpp -o scan_sequences.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from scan_sequences.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c shuffle_sequences.cpp -o shuffle_sequences.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from shuffle_sequences.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c trim_motifs.cpp -o trim_motifs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c universalmotif-class.cpp -o universalmotif-class.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c utils-exported.cpp -o utils-exported.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c utils-internal.cpp -o utils-internal.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread.h:9,
                 from utils-internal.cpp:2:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppThread/include/RcppThread/RMonitor.hpp:10: warning: "R_NO_REMAP" redefined
   10 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o universalmotif.so RcppExports.o add_multifreq.o calc_complexity.o compare_motifs.o get_bkg.o motif_finder.o motif_peaks.o motif_pvalue.o scan_sequences.o shuffle_sequences.o trim_motifs.o universalmotif-class.o utils-exported.o utils-internal.o -latomic -lpthread -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.so; fi
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-universalmotif/00new/universalmotif/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘convert_motifs’ with signature ‘motifs="MotifList"’: no definition for class “MotifList”
in method for ‘convert_motifs’ with signature ‘motifs="TFFMFirst"’: no definition for class “TFFMFirst”
in method for ‘convert_motifs’ with signature ‘motifs="PFMatrix"’: no definition for class “PFMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="PWMatrix"’: no definition for class “PWMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="ICMatrix"’: no definition for class “ICMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="XMatrixList"’: no definition for class “XMatrixList”
in method for ‘convert_motifs’ with signature ‘motifs="pwm"’: no definition for class “pwm”
in method for ‘convert_motifs’ with signature ‘motifs="pcm"’: no definition for class “pcm”
in method for ‘convert_motifs’ with signature ‘motifs="pfm"’: no definition for class “pfm”
in method for ‘convert_motifs’ with signature ‘motifs="PWM"’: no definition for class “PWM”
in method for ‘convert_motifs’ with signature ‘motifs="Motif"’: no definition for class “Motif”
** 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 (universalmotif)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.140   0.037   0.166 

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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.

> if (R.Version()$arch != "i386") {
+ 
+   library(testthat)
+   library(universalmotif)
+ 
+   test_check("universalmotif") 
+ 
+ } else TRUE
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 240 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 240 ]
> 
> proc.time()
   user  system elapsed 
  7.909   0.556   8.464