| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:29 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 2209/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.20.0 (landing page) Benjamin Jean-Marie Tremblay
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: universalmotif |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings universalmotif_1.20.0.tar.gz |
| StartedAt: 2024-04-16 05:03:01 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 05:09:57 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 415.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: universalmotif.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings universalmotif_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/universalmotif.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.20.0’
* 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++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 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 9.522 0.492 10.015
* 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 ...
‘Introduction.Rmd’ using ‘UTF-8’... OK
‘IntroductionToSequenceMotifs.Rmd’ using ‘UTF-8’... OK
‘MotifComparisonAndPvalues.Rmd’ using ‘UTF-8’... OK
‘MotifManipulation.Rmd’ using ‘UTF-8’... failed
‘SequenceSearches.Rmd’ using ‘UTF-8’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘MotifManipulation.Rmd’
...
> data(examplemotif)
> examplemotif["consensus"]
[1] "TATAWAW"
> examplemotif["consensus"] <- "GGGAGAG"
When sourcing ‘MotifManipulation.R’:
Error: this slot is unmodifiable with [<-
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/universalmotif.Rcheck/00check.log’
for details.
universalmotif.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL universalmotif ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘universalmotif’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -c compare_motifs.cpp -o compare_motifs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-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-3.18-bioc/R/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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
0.154 0.031 0.171
universalmotif.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 240 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 240 ]
>
> proc.time()
user system elapsed
8.075 0.781 8.847
universalmotif.Rcheck/universalmotif-Ex.timings
| name | user | system | elapsed | |
| add_multifreq | 0.019 | 0.001 | 0.018 | |
| compare_motifs | 0.141 | 0.004 | 0.144 | |
| convert_motifs | 9.522 | 0.492 | 10.015 | |
| convert_type | 0.005 | 0.003 | 0.007 | |
| create_motif | 0.222 | 0.036 | 0.257 | |
| create_sequences | 0.008 | 0.000 | 0.007 | |
| enrich_motifs | 1.865 | 0.144 | 2.009 | |
| filter_motifs | 0.028 | 0.000 | 0.027 | |
| get_bkg | 0.178 | 0.012 | 0.189 | |
| make_DBscores | 0 | 0 | 0 | |
| merge_motifs | 0.334 | 0.012 | 0.346 | |
| merge_similar | 0 | 0 | 0 | |
| motif_peaks | 0.183 | 0.012 | 0.195 | |
| motif_pvalue | 0.086 | 0.008 | 0.094 | |
| motif_rc | 0.004 | 0.000 | 0.004 | |
| motif_tree | 0.355 | 0.003 | 0.359 | |
| read_cisbp | 0.003 | 0.000 | 0.004 | |
| read_homer | 0.205 | 0.000 | 0.205 | |
| read_jaspar | 0.003 | 0.000 | 0.003 | |
| read_matrix | 0.001 | 0.002 | 0.003 | |
| read_meme | 0.014 | 0.002 | 0.016 | |
| read_transfac | 0.008 | 0.000 | 0.009 | |
| read_uniprobe | 0.005 | 0.000 | 0.006 | |
| run_meme | 0.001 | 0.000 | 0.000 | |
| sample_sites | 0.019 | 0.000 | 0.018 | |
| scan_sequences | 0.718 | 0.032 | 0.750 | |
| sequence_complexity | 0.885 | 0.017 | 0.902 | |
| shuffle_sequences | 0.005 | 0.000 | 0.006 | |
| switch_alph | 0.001 | 0.001 | 0.001 | |
| tidy-motifs | 0 | 0 | 0 | |
| trim_motifs | 0.005 | 0.000 | 0.005 | |
| universalmotif-class | 0.011 | 0.000 | 0.012 | |
| utils-motif | 0.068 | 0.044 | 0.112 | |
| utils-sequence | 0.554 | 0.008 | 0.562 | |
| view_logo | 0.315 | 0.011 | 0.327 | |
| view_motifs | 0.207 | 0.001 | 0.208 | |
| write_homer | 0.002 | 0.000 | 0.002 | |
| write_jaspar | 0.009 | 0.000 | 0.009 | |
| write_matrix | 0.002 | 0.000 | 0.002 | |
| write_meme | 0.013 | 0.000 | 0.012 | |
| write_transfac | 0.006 | 0.000 | 0.006 | |