| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2228/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.24.2 (landing page) Benjamin Jean-Marie Tremblay
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the universalmotif package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/universalmotif.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: universalmotif |
| Version: 1.24.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings universalmotif_1.24.2.tar.gz |
| StartedAt: 2024-11-20 13:35:08 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 13:38:21 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 193.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: universalmotif.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings universalmotif_1.24.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/universalmotif.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.24.2’
* 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
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* 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 ... 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 14.234 0.483 14.744
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/universalmotif.Rcheck/00check.log’
for details.
universalmotif.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL universalmotif
###
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##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppThread/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppThread/include' -I/usr/local/include -fPIC -g -O2 -Wall -c calc_complexity.cpp -o calc_complexity.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppThread/include' -I/usr/local/include -fPIC -g -O2 -Wall -c compare_motifs.cpp -o compare_motifs.o
In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/aarch64-conda-linux-gnu/bits/c++allocator.h:33,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/allocator.h:46,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:39,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/ext/alloc_traits.h:34,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/hashtable_policy.h:39,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/hashtable.h:35,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unordered_map.h:33,
from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/unordered_map:41,
from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/r/headers.h:66,
from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:30,
from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
from compare_motifs.cpp:1:
In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]',
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:513:23,
inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:389:19,
inlined from 'std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:368:15,
inlined from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:738:7,
inlined from 'double compare_eucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&)' at compare_motifs.cpp:406:28:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/new_allocator.h:172:33: warning: 'void operator delete(void*)' called on pointer '<unknown>' with nonzero offset [8, 9223372036854775800] [-Wfree-nonheap-object]
172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
| ^
In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]',
inlined from 'static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = double]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:478:28,
inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:380:33,
inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:398:44,
inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:334:26,
inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:571:47,
inlined from 'double compare_eucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&)' at compare_motifs.cpp:406:47:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)'
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]',
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:513:23,
inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:389:19,
inlined from 'std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:368:15,
inlined from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:738:7,
inlined from 'double compare_weucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&)' at compare_motifs.cpp:604:28:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/new_allocator.h:172:33: warning: 'void operator delete(void*)' called on pointer '<unknown>' with nonzero offset [8, 9223372036854775800] [-Wfree-nonheap-object]
172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
| ^
In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]',
inlined from 'static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = double]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:478:28,
inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:380:33,
inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:398:44,
inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:334:26,
inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:571:47,
inlined from 'double compare_weucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&)' at compare_motifs.cpp:604:47:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)'
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/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/R/R-4.4.1/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/R/R-4.4.1/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)
universalmotif.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.277 0.034 0.209
universalmotif.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
11.262 0.570 11.772
universalmotif.Rcheck/universalmotif-Ex.timings
| name | user | system | elapsed | |
| add_multifreq | 0.015 | 0.008 | 0.023 | |
| compare_motifs | 0.194 | 0.008 | 0.202 | |
| convert_motifs | 14.234 | 0.483 | 14.744 | |
| convert_type | 0.009 | 0.000 | 0.009 | |
| create_motif | 0.372 | 0.012 | 0.385 | |
| create_sequences | 0.007 | 0.000 | 0.007 | |
| enrich_motifs | 1.546 | 0.112 | 1.663 | |
| filter_motifs | 0.021 | 0.000 | 0.021 | |
| get_bkg | 0.279 | 0.000 | 0.320 | |
| make_DBscores | 0 | 0 | 0 | |
| merge_motifs | 0.280 | 0.004 | 0.285 | |
| merge_similar | 0.000 | 0.000 | 0.001 | |
| motif_peaks | 0.319 | 0.008 | 0.327 | |
| motif_pvalue | 0.223 | 0.008 | 0.232 | |
| motif_rc | 0.006 | 0.000 | 0.006 | |
| motif_tree | 0.475 | 0.020 | 0.497 | |
| read_cisbp | 0.004 | 0.000 | 0.006 | |
| read_homer | 0.289 | 0.000 | 0.290 | |
| read_jaspar | 0.004 | 0.000 | 0.004 | |
| read_matrix | 0.001 | 0.002 | 0.004 | |
| read_meme | 0.019 | 0.001 | 0.021 | |
| read_transfac | 0.012 | 0.000 | 0.012 | |
| read_uniprobe | 0.007 | 0.000 | 0.008 | |
| run_meme | 0.001 | 0.000 | 0.000 | |
| sample_sites | 0.024 | 0.000 | 0.024 | |
| scan_sequences | 1.205 | 0.039 | 1.249 | |
| sequence_complexity | 1.044 | 0.028 | 1.074 | |
| shuffle_sequences | 0.007 | 0.000 | 0.007 | |
| switch_alph | 0.002 | 0.000 | 0.002 | |
| tidy-motifs | 0 | 0 | 0 | |
| trim_motifs | 0.009 | 0.000 | 0.008 | |
| universalmotif-class | 0.014 | 0.003 | 0.017 | |
| utils-motif | 0.092 | 0.024 | 0.117 | |
| utils-sequence | 0.908 | 0.020 | 0.930 | |
| view_logo | 0.249 | 0.000 | 0.250 | |
| view_motifs | 0.298 | 0.000 | 0.299 | |
| write_homer | 0.004 | 0.000 | 0.004 | |
| write_jaspar | 0.013 | 0.000 | 0.014 | |
| write_matrix | 0.003 | 0.000 | 0.003 | |
| write_meme | 0.020 | 0.000 | 0.019 | |
| write_transfac | 0.006 | 0.003 | 0.009 | |