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CHECK report for universalmotif on machv2

This page was generated on 2020-10-17 11:59:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE universalmotif PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1860/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
universalmotif 1.6.4
Benjamin Jean-Marie Tremblay
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/universalmotif
Branch: RELEASE_3_11
Last Commit: 91b2ec6
Last Changed Date: 2020-09-17 04:26:01 -0400 (Thu, 17 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: universalmotif
Version: 1.6.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings universalmotif_1.6.4.tar.gz
StartedAt: 2020-10-17 06:11:22 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:15:14 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 231.4 seconds
RetCode: 0
Status:  OK 
CheckDir: universalmotif.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings universalmotif_1.6.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/universalmotif.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.6.4’
* 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 ... NOTE
motif_clusters: no visible binding for global variable
  ‘target.sequences’
Undefined global functions or variables:
  target.sequences
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
convert_motifs 14.847  0.437  15.316
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/universalmotif.Rcheck/00check.log’
for details.



Installation output

universalmotif.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL universalmotif
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c add_multifreq.cpp -o add_multifreq.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c compare_motifs.cpp -o compare_motifs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c motif_peaks.cpp -o motif_peaks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c motif_pvalue.cpp -o motif_pvalue.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c motif_tree.cpp -o motif_tree.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c scan_sequences.cpp -o scan_sequences.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c shuffle_sequences.cpp -o shuffle_sequences.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c trim_motifs.cpp -o trim_motifs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c universalmotif-class.cpp -o universalmotif-class.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils-exported.cpp -o utils-exported.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppThread/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils-internal.cpp -o utils-internal.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o universalmotif.so RcppExports.o add_multifreq.o compare_motifs.o motif_peaks.o motif_pvalue.o motif_tree.o scan_sequences.o shuffle_sequences.o trim_motifs.o universalmotif-class.o utils-exported.o utils-internal.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.so; fi
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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
Loading required namespace: universalmotif
Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
*** 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)

Tests output

universalmotif.Rcheck/tests/spelling.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.266   0.064   0.307 

universalmotif.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 210 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.860   0.578  11.416 

Example timings

universalmotif.Rcheck/universalmotif-Ex.timings

nameusersystemelapsed
add_multifreq0.0230.0040.029
compare_motifs0.2570.0060.265
convert_motifs14.847 0.43715.316
convert_type0.0090.0010.010
create_motif0.3830.0360.420
create_sequences0.0080.0010.009
enrich_motifs0.3610.0350.396
filter_motifs0.0070.0010.009
get_bkg0.4110.0310.441
make_DBscores000
merge_motifs0.4820.0110.495
motif_peaks1.0320.0321.065
motif_pvalue0.0220.0030.024
motif_rc0.0080.0010.009
motif_tree0.1150.0030.119
read_cisbp0.0040.0010.005
read_homer0.0130.0010.014
read_jaspar0.0060.0000.007
read_matrix0.0050.0010.005
read_meme0.0260.0010.028
read_transfac0.0140.0010.015
read_uniprobe0.0090.0020.011
run_meme000
sample_sites0.0270.0010.028
scan_sequences2.4220.1692.634
shuffle_sequences0.0080.0010.009
switch_alph0.0020.0000.002
trim_motifs0.0100.0010.010
universalmotif-class0.0240.0060.031
utils-motif0.0450.0090.054
utils-sequence0.0040.0020.006
view_motifs0.0000.0010.001
write_homer0.0080.0010.009
write_jaspar0.0320.0010.033
write_matrix0.0030.0000.003
write_meme0.0270.0010.028
write_transfac0.0150.0010.015