| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:16:51 -0400 (Wed, 16 Oct 2019).
| Package 1702/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| universalmotif 1.2.1 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 | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: universalmotif |
| Version: 1.2.1 |
| 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_1.2.1.tar.gz |
| StartedAt: 2019-10-16 05:39:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:42:30 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 179.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: universalmotif.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/universalmotif.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.1’
* 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 9.622 0.317 10.362
filter_motifs 6.959 0.224 7.184
* 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
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL universalmotif
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* 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(x)[0] = object;
^~~~~~~~~~~~~~
motif_simil_helper.cpp:735:10: 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(x)[0] = object;
^~~~~~~~~~~~~~
motif_simil_helper.cpp:734:7: 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 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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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
0.253 0.015 0.254
universalmotif.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 (R.Version()$arch != "i386") {
+
+ library(testthat)
+ library(universalmotif)
+
+ test_check("universalmotif")
+
+ } else TRUE
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 213 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.925 0.362 15.315
universalmotif.Rcheck/universalmotif-Ex.timings
| name | user | system | elapsed | |
| add_multifreq | 0.650 | 0.001 | 1.313 | |
| compare_motifs | 0.005 | 0.000 | 0.005 | |
| convert_motifs | 9.622 | 0.317 | 10.362 | |
| convert_type | 0.006 | 0.000 | 0.006 | |
| create_motif | 0.270 | 0.004 | 0.274 | |
| create_sequences | 0.008 | 0.000 | 0.009 | |
| enrich_motifs | 1.337 | 0.020 | 1.406 | |
| filter_motifs | 6.959 | 0.224 | 7.184 | |
| get_bkg | 0.784 | 0.000 | 0.785 | |
| merge_motifs | 0.125 | 0.004 | 0.129 | |
| motif_peaks | 1.830 | 0.008 | 1.838 | |
| motif_pvalue | 0.034 | 0.004 | 0.038 | |
| motif_rc | 0.006 | 0.000 | 0.006 | |
| motif_tree | 0.079 | 0.000 | 0.079 | |
| read_cisbp | 0.002 | 0.003 | 0.005 | |
| read_homer | 0.006 | 0.000 | 0.005 | |
| read_jaspar | 0.005 | 0.000 | 0.004 | |
| read_matrix | 0.004 | 0.000 | 0.004 | |
| read_meme | 0.021 | 0.000 | 0.027 | |
| read_transfac | 0.012 | 0.000 | 0.011 | |
| read_uniprobe | 0.009 | 0.000 | 0.015 | |
| run_meme | 0 | 0 | 0 | |
| sample_sites | 0.022 | 0.000 | 0.022 | |
| scan_sequences | 0.341 | 0.012 | 0.353 | |
| shuffle_sequences | 0.304 | 0.001 | 0.304 | |
| switch_alph | 0.002 | 0.000 | 0.003 | |
| trim_motifs | 0.009 | 0.000 | 0.009 | |
| universalmotif-class | 0.024 | 0.000 | 0.024 | |
| utils-motif | 0.032 | 0.000 | 0.032 | |
| utils-sequence | 0.01 | 0.00 | 0.01 | |
| view_motifs | 0 | 0 | 0 | |
| write_homer | 0.008 | 0.000 | 0.008 | |
| write_jaspar | 0.022 | 0.000 | 0.022 | |
| write_matrix | 0.003 | 0.000 | 0.002 | |
| write_meme | 0.025 | 0.000 | 0.025 | |
| write_transfac | 0.008 | 0.000 | 0.009 | |