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This page was generated on 2025-09-29 11:38 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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 2227/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transite 1.26.1  (landing page)
Konstantin Krismer
Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/transite
git_branch: RELEASE_3_21
git_last_commit: 97876e2
git_last_commit_date: 2025-09-23 04:48:53 -0400 (Tue, 23 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for transite on nebbiolo1

To the developers/maintainers of the transite package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transite.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.

raw results


Summary

Package: transite
Version: 1.26.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings transite_1.26.1.tar.gz
StartedAt: 2025-09-29 04:32:32 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 04:39:32 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 420.6 seconds
RetCode: 0
Status:   OK  
CheckDir: transite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings transite_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/transite.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘transite/DESCRIPTION’ ... OK
* this is package ‘transite’ version ‘1.26.1’
* 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 ‘transite’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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 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
run_kmer_tsma   50.799  1.007  62.597
run_kmer_spma   35.774  0.307  40.064
run_matrix_spma  3.316  0.082   5.400
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/transite.Rcheck/00check.log’
for details.


Installation output

transite.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL transite
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘transite’ ...
** this is package ‘transite’ version ‘1.26.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c scoring.cpp -o scoring.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o transite.so RcppExports.o scoring.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-transite/00new/transite/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (transite)

Tests output

transite.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(transite)
> 
> test_check("transite")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
 78.599   2.248 180.679 

Example timings

transite.Rcheck/transite-Ex.timings

nameusersystemelapsed
RBPMotif-class0.0030.0000.005
SpectrumScore-class0.0010.0000.002
calculate_kmer_enrichment4.0810.0844.165
calculate_local_consistency0.5020.0200.522
calculate_motif_enrichment1.2960.0101.307
calculate_transcript_mc0.0040.0010.005
check_kmers0.0000.0010.000
classify_spectrum2.9300.1433.072
compute_kmer_enrichment1.9820.0302.011
create_kmer_motif0.0030.0000.003
create_matrix_motif0.0020.0020.003
draw_volcano_plot0.4500.0190.470
estimate_significance_core0.0020.0010.003
generate_iupac_by_kmers0.0000.0010.000
generate_iupac_by_matrix0.0010.0010.002
generate_kmers0.1290.0050.134
generate_kmers_from_iupac0.0020.0000.002
geometric_mean000
get_motif_by_id0.0030.0000.004
get_motif_by_rbp0.0040.0000.005
get_motifs000
get_motifs_meta_info0.0070.0100.019
get_ppm0.0050.0000.005
init_iupac_lookup_table0.0010.0000.003
p_combine0.0000.0000.001
run_kmer_spma35.774 0.30740.064
run_kmer_tsma50.799 1.00762.597
run_matrix_spma3.3160.0825.400
run_matrix_tsma0.0220.0000.022
score_sequences0.0030.0020.005
score_spectrum2.8820.0322.914
score_transcripts0.0060.0010.007
set_motifs0.0020.0000.002
subdivide_data0.0060.0000.005