Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:52:15 -0400 (Tue, 09 Apr 2019).
Package 1665/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
universalmotif 1.1.66 Benjamin Jean-Marie Tremblay
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: universalmotif |
Version: 1.1.66 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings universalmotif_1.1.66.tar.gz |
StartedAt: 2019-04-09 04:14:55 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 04:17:55 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 179.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: universalmotif.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings universalmotif_1.1.66.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/universalmotif.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘1.1.66’ * 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 ... NOTE Unexported object imported by a ':::' call: ‘TFBSTools:::schneider_correction’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE convert_to_tfbstools_tffmfirst: no visible binding for global variable ‘2’ motif_peaks: no visible binding for global variable ‘x’ motif_peaks: no visible binding for global variable ‘y’ motif_tree: no visible binding for global variable ‘group’ motif_tree: no visible binding for global variable ‘icscore’ Undefined global functions or variables: 2 group icscore x y * 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed convert_motifs 10.115 0.355 10.676 motif_peaks 9.218 0.092 9.313 filter_motifs 5.009 0.168 5.189 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/universalmotif.Rcheck/00check.log’ for details.
universalmotif.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL universalmotif ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘universalmotif’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c add_multifreq_helper.cpp -o add_multifreq_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c motif_peaks_helper.cpp -o motif_peaks_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c motif_pvalue_helper.cpp -o motif_pvalue_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c motif_simil_helper.cpp -o motif_simil_helper.o In file included from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:187:0, from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27, from motif_simil_helper.cpp:1: /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function ‘Rcpp::List merge_motifs_get_offset(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::String, double, Rcpp::NumericVector, Rcpp::NumericVector, double, bool)’: /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: ‘score’ may be used uninitialized in this function [-Wmaybe-uninitialized] r_vector_start<RTYPE>(x)[0] = object; ^˜˜˜˜˜˜˜˜˜˜˜˜˜ motif_simil_helper.cpp:734:10: note: ‘score’ was declared here double score; ^˜˜˜˜ In file included from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:187:0, from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27, from motif_simil_helper.cpp:1: /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: ‘offset’ may be used uninitialized in this function [-Wmaybe-uninitialized] r_vector_start<RTYPE>(x)[0] = object; ^˜˜˜˜˜˜˜˜˜˜˜˜˜ motif_simil_helper.cpp:733:7: note: ‘offset’ was declared here int offset; ^˜˜˜˜˜ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c scan_sequences_helper.cpp -o scan_sequences_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c shuffle_sequences_helper.cpp -o shuffle_sequences_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c trim_motifs_helper.cpp -o trim_motifs_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c universalmotif_helper.cpp -o universalmotif_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o universalmotif.so RcppExports.o add_multifreq_helper.o motif_peaks_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o shuffle_sequences_helper.o trim_motifs_helper.o universalmotif_helper.o utils.o -L/home/biocbuild/bbs-3.9-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-3.9-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 Loading required namespace: universalmotif Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang 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)
universalmotif.Rcheck/tests/spelling.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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 0.180 0.033 0.197
universalmotif.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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. > library(testthat) > library(universalmotif) > > test_check("universalmotif") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 212 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 13.646 0.227 13.915
universalmotif.Rcheck/universalmotif-Ex.timings
name | user | system | elapsed | |
add_multifreq | 0.640 | 0.000 | 0.649 | |
compare_motifs | 0.005 | 0.000 | 0.005 | |
convert_motifs | 10.115 | 0.355 | 10.676 | |
convert_type | 0.009 | 0.000 | 0.009 | |
create_motif | 0.559 | 0.004 | 0.563 | |
create_sequences | 0.013 | 0.000 | 0.013 | |
enrich_motifs | 0.169 | 0.004 | 0.172 | |
filter_motifs | 5.009 | 0.168 | 5.189 | |
get_bkg | 1.315 | 0.000 | 1.314 | |
merge_motifs | 0.204 | 0.000 | 0.203 | |
motif_peaks | 9.218 | 0.092 | 9.313 | |
motif_pvalue | 0.018 | 0.000 | 0.017 | |
motif_rc | 0.007 | 0.000 | 0.007 | |
motif_tree | 0.075 | 0.000 | 0.075 | |
read_cisbp | 0.005 | 0.000 | 0.016 | |
read_homer | 0.005 | 0.000 | 0.006 | |
read_jaspar | 0.005 | 0.000 | 0.004 | |
read_matrix | 0.005 | 0.000 | 0.004 | |
read_meme | 0.020 | 0.000 | 0.024 | |
read_transfac | 0.011 | 0.000 | 0.011 | |
read_uniprobe | 0.006 | 0.004 | 0.019 | |
run_meme | 0 | 0 | 0 | |
sample_sites | 0.025 | 0.000 | 0.024 | |
scan_sequences | 0.375 | 0.012 | 0.388 | |
shuffle_sequences | 0.013 | 0.000 | 0.012 | |
switch_alph | 0.002 | 0.000 | 0.003 | |
trim_motifs | 0.008 | 0.000 | 0.008 | |
universalmotif-class | 0.022 | 0.000 | 0.022 | |
utilities | 0.025 | 0.000 | 0.024 | |
view_motifs | 0.000 | 0.000 | 0.001 | |
write_homer | 0.008 | 0.000 | 0.008 | |
write_jaspar | 0.024 | 0.000 | 0.024 | |
write_matrix | 0.003 | 0.000 | 0.003 | |
write_meme | 0.024 | 0.004 | 0.027 | |
write_transfac | 0.012 | 0.000 | 0.012 | |