Multiple platform build/check report for BioC 3.13 - CHECK results for universalmotif on nebbiolo1

Package: universalmotif

Version: 1.10.2

Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings universalmotif_1.10.2.tar.gz

StartedAt: 2021-10-14 11:59:30 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 12:01:39 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 128.9 seconds

RetCode: 0

Status: OK

CheckDir: universalmotif.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings universalmotif_1.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/universalmotif.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.10.2’
* 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
* 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 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 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 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 9.045  0.309   9.354
* 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 in ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/universalmotif.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL universalmotif
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c add_multifreq.cpp -o add_multifreq.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compare_motifs.cpp -o compare_motifs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c get_bkg.cpp -o get_bkg.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c motif_finder.cpp -o motif_finder.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c motif_peaks.cpp -o motif_peaks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c motif_pvalue.cpp -o motif_pvalue.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scan_sequences.cpp -o scan_sequences.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c shuffle_sequences.cpp -o shuffle_sequences.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c trim_motifs.cpp -o trim_motifs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c universalmotif-class.cpp -o universalmotif-class.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils-exported.cpp -o utils-exported.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppThread/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils-internal.cpp -o utils-internal.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o universalmotif.so RcppExports.o add_multifreq.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 -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 
  0.159   0.034   0.176


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 0 | SKIP 0 | PASS 240 ]
> 
> proc.time()
   user  system elapsed 
  7.146   0.463   7.589

name	user	system	elapsed
add_multifreq	0.017	0.001	0.019
compare_motifs	0.148	0.003	0.153
convert_motifs	9.045	0.309	9.354
convert_type	0.008	0.000	0.008
create_motif	0.332	0.016	0.348
create_sequences	0.009	0.000	0.009
enrich_motifs	0.188	0.003	0.191
filter_motifs	0.004	0.000	0.004
get_bkg	0.216	0.013	0.227
make_DBscores	0	0	0
merge_motifs	0.146	0.007	0.154
merge_similar	0	0	0
motif_peaks	0.172	0.023	0.196
motif_pvalue	0.009	0.005	0.012
motif_rc	0.005	0.000	0.004
motif_tree	0.340	0.015	0.357
read_cisbp	0.003	0.000	0.003
read_homer	0.004	0.000	0.004
read_jaspar	0.003	0.000	0.003
read_matrix	0.007	0.000	0.007
read_meme	0.017	0.000	0.017
read_transfac	0.008	0.000	0.008
read_uniprobe	0.002	0.003	0.006
run_meme	0.001	0.000	0.000
sample_sites	0.034	0.000	0.034
scan_sequences	0.742	0.056	0.798
shuffle_sequences	0.011	0.001	0.011
switch_alph	0.002	0.000	0.002
tidy-motifs	0.000	0.001	0.001
trim_motifs	0.004	0.002	0.006
universalmotif-class	0.014	0.003	0.018
utils-motif	0.118	0.341	0.462
utils-sequence	0.918	0.110	1.028
view_logo	0.442	0.028	0.470
view_motifs	0.177	0.000	0.177
write_homer	0.007	0.000	0.006
write_jaspar	0.018	0.000	0.018
write_matrix	0.003	0.000	0.003
write_meme	0.025	0.000	0.025
write_transfac	0.009	0.003	0.012

CHECK results for universalmotif on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings