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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 2222/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transite 1.27.0  (landing page)
Konstantin Krismer
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/transite
git_branch: devel
git_last_commit: 7895224
git_last_commit_date: 2025-04-15 11:38:14 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for transite on nebbiolo2

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: 1.27.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings transite_1.27.0.tar.gz
StartedAt: 2025-09-20 05:19:14 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 05:26:07 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 413.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: transite.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings transite_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/transite.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.27.0’
* 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 ‘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           44.009  0.325  46.791
run_kmer_spma           35.882  0.332  39.551
classify_spectrum        6.190  0.361   7.429
compute_kmer_enrichment  4.015  0.103   5.678
run_matrix_spma          2.989  0.031   5.030
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(transite)
  > 
  > test_check("transite")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 94 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-k-mer-based.R:43:5'): draw_volcano_plot ──────────────────────
  class(p) not equal to c("gg", "ggplot").
  Lengths differ: 5 is not 2
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 94 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/transite.Rcheck/00check.log’
for details.


Installation output

transite.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL transite
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘transite’ ...
** this is package ‘transite’ version ‘1.27.0’
** 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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -L/usr/local/lib -o transite.so RcppExports.o scoring.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "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 1 | WARN 2 | SKIP 0 | PASS 94 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-k-mer-based.R:43:5'): draw_volcano_plot ──────────────────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 94 ]
Error: Test failures
Execution halted

Example timings

transite.Rcheck/transite-Ex.timings

nameusersystemelapsed
RBPMotif-class0.0040.0000.004
SpectrumScore-class0.0010.0000.001
calculate_kmer_enrichment4.0430.0674.110
calculate_local_consistency0.7830.0450.828
calculate_motif_enrichment1.2530.0731.325
calculate_transcript_mc0.0040.0010.004
check_kmers0.0010.0000.000
classify_spectrum6.1900.3617.429
compute_kmer_enrichment4.0150.1035.678
create_kmer_motif0.0060.0000.016
create_matrix_motif0.0070.0000.014
draw_volcano_plot0.9910.0131.010
estimate_significance_core0.0040.0000.004
generate_iupac_by_kmers0.0010.0000.001
generate_iupac_by_matrix0.0040.0000.004
generate_kmers0.2770.0230.301
generate_kmers_from_iupac0.0050.0010.005
geometric_mean000
get_motif_by_id0.0080.0000.007
get_motif_by_rbp0.0080.0010.008
get_motifs0.0010.0000.001
get_motifs_meta_info0.0230.0020.025
get_ppm0.0090.0000.010
init_iupac_lookup_table0.0040.0010.005
p_combine0.0010.0000.002
run_kmer_spma35.882 0.33239.551
run_kmer_tsma44.009 0.32546.791
run_matrix_spma2.9890.0315.030
run_matrix_tsma0.0190.0000.019
score_sequences0.0030.0010.004
score_spectrum2.8370.0002.837
score_transcripts0.0060.0000.006
set_motifs0.0020.0000.002
subdivide_data0.0050.0000.005