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This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the universalmotif package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1990/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.10.2 (landing page) Benjamin Jean-Marie Tremblay
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: universalmotif |
| Version: 1.10.2 |
| 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_1.10.2.tar.gz |
| StartedAt: 2021-10-15 01:04:16 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:07:33 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 197.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: universalmotif.Rcheck |
| Warnings: 0 |
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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_1.10.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/universalmotif.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.2’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 12.054 0.36 12.423
* 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-3.13-bioc/meat/universalmotif.Rcheck/00check.log’
for details.
universalmotif.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL universalmotif ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppThread/include' -I/usr/local/include -fPIC -Wall -g -O2 -c get_bkg.cpp -o get_bkg.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppThread/include' -I/usr/local/include -fPIC -Wall -g -O2 -c motif_finder.cpp -o motif_finder.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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 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 -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/4.1/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 *** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
0.286 0.067 0.328
universalmotif.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 240 ]
>
> proc.time()
user system elapsed
11.008 0.643 11.629
universalmotif.Rcheck/universalmotif-Ex.timings
| name | user | system | elapsed | |
| add_multifreq | 0.029 | 0.005 | 0.033 | |
| compare_motifs | 0.269 | 0.006 | 0.276 | |
| convert_motifs | 12.054 | 0.360 | 12.423 | |
| convert_type | 0.012 | 0.002 | 0.014 | |
| create_motif | 0.457 | 0.034 | 0.491 | |
| create_sequences | 0.006 | 0.001 | 0.007 | |
| enrich_motifs | 0.290 | 0.009 | 0.300 | |
| filter_motifs | 0.009 | 0.001 | 0.010 | |
| get_bkg | 0.370 | 0.018 | 0.388 | |
| make_DBscores | 0.000 | 0.000 | 0.001 | |
| merge_motifs | 0.260 | 0.024 | 0.284 | |
| merge_similar | 0 | 0 | 0 | |
| motif_peaks | 0.219 | 0.036 | 0.255 | |
| motif_pvalue | 0.016 | 0.004 | 0.018 | |
| motif_rc | 0.009 | 0.001 | 0.010 | |
| motif_tree | 0.466 | 0.027 | 0.493 | |
| read_cisbp | 0.004 | 0.001 | 0.005 | |
| read_homer | 0.005 | 0.000 | 0.006 | |
| read_jaspar | 0.006 | 0.000 | 0.007 | |
| read_matrix | 0.006 | 0.001 | 0.006 | |
| read_meme | 0.032 | 0.002 | 0.035 | |
| read_transfac | 0.016 | 0.001 | 0.017 | |
| read_uniprobe | 0.011 | 0.001 | 0.012 | |
| run_meme | 0.000 | 0.001 | 0.000 | |
| sample_sites | 0.062 | 0.003 | 0.065 | |
| scan_sequences | 1.269 | 0.061 | 1.331 | |
| shuffle_sequences | 0.008 | 0.001 | 0.009 | |
| switch_alph | 0.001 | 0.000 | 0.002 | |
| tidy-motifs | 0.000 | 0.001 | 0.000 | |
| trim_motifs | 0.008 | 0.001 | 0.009 | |
| universalmotif-class | 0.023 | 0.008 | 0.031 | |
| utils-motif | 0.138 | 0.223 | 0.360 | |
| utils-sequence | 0.785 | 0.086 | 0.871 | |
| view_logo | 0.314 | 0.023 | 0.338 | |
| view_motifs | 0.143 | 0.006 | 0.148 | |
| write_homer | 0.004 | 0.001 | 0.004 | |
| write_jaspar | 0.017 | 0.001 | 0.017 | |
| write_matrix | 0.003 | 0.000 | 0.004 | |
| write_meme | 0.030 | 0.001 | 0.031 | |
| write_transfac | 0.013 | 0.000 | 0.014 | |