| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-26 11:57 -0500 (Thu, 26 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| 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 986/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiCPotts 1.0.0 (landing page) Itunu. Godwin Osuntoki
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for HiCPotts in R Universe. | ||||||||||||||
|
To the developers/maintainers of the HiCPotts package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCPotts.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: HiCPotts |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCPotts.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCPotts_1.0.0.tar.gz |
| StartedAt: 2026-02-26 00:55:09 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 01:01:23 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 374.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: HiCPotts.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCPotts.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCPotts_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCPotts.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘HiCPotts/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCPotts’ version ‘1.0.0’
* 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 ‘HiCPotts’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 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 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
get_data 31.209 0.677 31.892
* 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:
Iteration: 10
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 130 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-run_chain.R:59:5'): run_metropolis_MCMC_betas works for multiple distributions ──
Error in `(function (pred_combined, params, z, y, x_vars, component, theta, N, use_data_priors, user_fixed_priors, dist, size) { if (length(z[z == component]) == 0) { stop(sprintf("Invalid component: %s", component)) } likelihood <- likelihood_combined(pred_combined, params, z, y, x_vars, component, theta, N, dist = dist, size = size) prior <- prior_combined(params, component, y, x_vars, z, use_data_priors, user_fixed_priors) if (dist == "NB" || dist == "ZINB") { if (is.null(size) || component < 1 || component > 3) { stop("Invalid size or component for NB/ZINB distribution") } size_prior_value <- size_prior(size, component) return(likelihood + prior + size_prior_value) } else { return(likelihood + prior) } })(function (params, z, x_vars, component, N) { if (is.null(x_vars)) { stop("x_vars cannot be NULL") } if (!is.list(x_vars) || length(x_vars) != 4) { stop("x_vars must be a list of four matrices") } if (any(vapply(x_vars, function(x) !is.matrix(x[[1]]) || dim(x[[1]])[1] != N || dim(x[[1]])[2] != N, logical(1)))) { stop("Each x_vars matrix must have dimensions N x N") } a <- params[1] b <- params[2] c <- params[3] d <- params[4] e <- params[5] logical_mask <- z == component x1_sub <- x_vars[[1]][[1]][logical_mask] x2_sub <- x_vars[[2]][[1]][logical_mask] x3_sub <- x_vars[[3]][[1]][logical_mask] x4_sub <- x_vars[[4]][[1]][logical_mask] pred <- a + b * log(x1_sub + 1) + c * log(x2_sub + 1) + d * log(x3_sub + 1) + e * log(x4_sub + 1) return(pred) }, c(0, 0, 0, 0, 0), structure(c(1, 1, 1, 3, 1, 1, 1, 1, 3, 3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 3, 1, 1, 3, 1, 3), dim = c(5L, 5L)), structure(c(5, 2, 3, 6, 6, 9, 3, 2, 5, 9, 2, 5, 6, 5, 6, 5, 6, 2, 9, 6, 7, 2, 7, 4, 5), dim = c(5L, 5L)), list(distance = list(structure(c(0.861885093618184, 0.875864404253662, 0.552202206104994, 0.984846141189337, 0.495294772554189, 0.504002103349194, 0.956533525139093, 0.448340931674466, 0.947531301993877, 0.653985358774662, 0.899880526354536, 0.881625772221014, 0.335451656486839, 0.796499052550644, 0.0686217669863254, 0.989345502341166, 0.703007376054302, 0.521524257957935, 0.442783153383061, 0.841896589379758, 0.425814246293157, 0.819405316142365, 0.490663319593295, 0.884447664720938, 0.679605249548331), dim = c(5L, 5L))), GC = list(structure(c(0.788897418417037, 0.668381702853367, 0.200679884292185, 0.455776963848621, 0.484834906179458, 0.0921496951486915, 0.548566304380074, 0.276053926208988, 0.111801100429147, 0.789136520586908, 0.0585715237539262, 0.917311726137996, 0.263895244570449, 0.339755475288257, 0.868146962486207, 0.353476417250931, 0.888078905409202, 0.320560390828177, 0.266851098043844, 0.67000701255165, 0.683286143932492, 0.101791127119213, 0.469177683582529, 0.616231119260192, 0.688802394317463), dim = c(5L, 5L))), TES = list(structure(c(0.142699385527521, 0.258798165014014, 0.693456333596259, 0.0247734128497541, 0.181571253342554, 0.020440477412194, 0.807724815793335, 0.67230026749894, 0.741852616425604, 0.81996233202517, 0.485607676906511, 0.25090271467343, 0.666053034830838, 0.780140888644382, 0.0644880891777575, 0.717131999554113, 0.289241172838956, 0.53558460297063, 0.993963567307219, 0.825664751464501, 0.0206003240309656, 0.181431472767144, 0.896255719708279, 0.14827557024546, 0.415598868392408), dim = c(5L, 5L))), ACC = list(structure(c(0.480792825808749, 0.827646758873016, 0.0454979024361819, 0.165399262448773, 0.677076171152294, 0.00230608345009387, 0.255336100002751, 0.402137719327584, 0.978440625127405, 0.3393238929566, 0.499170589726418, 0.351387069793418, 0.907491780584678, 0.399671071674675, 0.788517370121554, 0.139001973206177, 0.335611990885809, 0.206896337680519, 0.40120611875318, 0.110172357177362, 0.351979855680838, 0.219380670459941, 0.319322561612353, 0.278262983076274, 0.311137101612985), dim = c(5L, 5L)))), 2L, NA_real_, 5L, TRUE, NULL, "NB", 1.45541038408495)`: Invalid component: 2
Backtrace:
▆
1. ├─HiCPotts::run_metropolis_MCMC_betas(...) at test-run_chain.R:59:5
2. └─HiCPotts (local) `<fn>`(...)
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 130 ]
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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/HiCPotts.Rcheck/00check.log’
for details.
HiCPotts.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HiCPotts ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘HiCPotts’ ... ** this is package ‘HiCPotts’ version ‘1.0.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c MCMC_chain.cpp -o MCMC_chain.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Neighbours_function.cpp -o Neighbours_function.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c potts_posterior.cpp -o potts_posterior.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o HiCPotts.so MCMC_chain.o Neighbours_function.o RcppExports.o potts_posterior.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-HiCPotts/00new/HiCPotts/libs ** R ** 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 (HiCPotts)
HiCPotts.Rcheck/tests/testthat.Rout.fail
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(HiCPotts)
>
> test_check("HiCPotts")
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Saving _problems/test-run_chain-70.R
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[ FAIL 1 | WARN 8 | SKIP 0 | PASS 130 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-run_chain.R:59:5'): run_metropolis_MCMC_betas works for multiple distributions ──
Error in `(function (pred_combined, params, z, y, x_vars, component, theta, N, use_data_priors, user_fixed_priors, dist, size) { if (length(z[z == component]) == 0) { stop(sprintf("Invalid component: %s", component)) } likelihood <- likelihood_combined(pred_combined, params, z, y, x_vars, component, theta, N, dist = dist, size = size) prior <- prior_combined(params, component, y, x_vars, z, use_data_priors, user_fixed_priors) if (dist == "NB" || dist == "ZINB") { if (is.null(size) || component < 1 || component > 3) { stop("Invalid size or component for NB/ZINB distribution") } size_prior_value <- size_prior(size, component) return(likelihood + prior + size_prior_value) } else { return(likelihood + prior) } })(function (params, z, x_vars, component, N) { if (is.null(x_vars)) { stop("x_vars cannot be NULL") } if (!is.list(x_vars) || length(x_vars) != 4) { stop("x_vars must be a list of four matrices") } if (any(vapply(x_vars, function(x) !is.matrix(x[[1]]) || dim(x[[1]])[1] != N || dim(x[[1]])[2] != N, logical(1)))) { stop("Each x_vars matrix must have dimensions N x N") } a <- params[1] b <- params[2] c <- params[3] d <- params[4] e <- params[5] logical_mask <- z == component x1_sub <- x_vars[[1]][[1]][logical_mask] x2_sub <- x_vars[[2]][[1]][logical_mask] x3_sub <- x_vars[[3]][[1]][logical_mask] x4_sub <- x_vars[[4]][[1]][logical_mask] pred <- a + b * log(x1_sub + 1) + c * log(x2_sub + 1) + d * log(x3_sub + 1) + e * log(x4_sub + 1) return(pred) }, c(0, 0, 0, 0, 0), structure(c(1, 1, 1, 3, 1, 1, 1, 1, 3, 3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 3, 1, 1, 3, 1, 3), dim = c(5L, 5L)), structure(c(5, 2, 3, 6, 6, 9, 3, 2, 5, 9, 2, 5, 6, 5, 6, 5, 6, 2, 9, 6, 7, 2, 7, 4, 5), dim = c(5L, 5L)), list(distance = list(structure(c(0.861885093618184, 0.875864404253662, 0.552202206104994, 0.984846141189337, 0.495294772554189, 0.504002103349194, 0.956533525139093, 0.448340931674466, 0.947531301993877, 0.653985358774662, 0.899880526354536, 0.881625772221014, 0.335451656486839, 0.796499052550644, 0.0686217669863254, 0.989345502341166, 0.703007376054302, 0.521524257957935, 0.442783153383061, 0.841896589379758, 0.425814246293157, 0.819405316142365, 0.490663319593295, 0.884447664720938, 0.679605249548331), dim = c(5L, 5L))), GC = list(structure(c(0.788897418417037, 0.668381702853367, 0.200679884292185, 0.455776963848621, 0.484834906179458, 0.0921496951486915, 0.548566304380074, 0.276053926208988, 0.111801100429147, 0.789136520586908, 0.0585715237539262, 0.917311726137996, 0.263895244570449, 0.339755475288257, 0.868146962486207, 0.353476417250931, 0.888078905409202, 0.320560390828177, 0.266851098043844, 0.67000701255165, 0.683286143932492, 0.101791127119213, 0.469177683582529, 0.616231119260192, 0.688802394317463), dim = c(5L, 5L))), TES = list(structure(c(0.142699385527521, 0.258798165014014, 0.693456333596259, 0.0247734128497541, 0.181571253342554, 0.020440477412194, 0.807724815793335, 0.67230026749894, 0.741852616425604, 0.81996233202517, 0.485607676906511, 0.25090271467343, 0.666053034830838, 0.780140888644382, 0.0644880891777575, 0.717131999554113, 0.289241172838956, 0.53558460297063, 0.993963567307219, 0.825664751464501, 0.0206003240309656, 0.181431472767144, 0.896255719708279, 0.14827557024546, 0.415598868392408), dim = c(5L, 5L))), ACC = list(structure(c(0.480792825808749, 0.827646758873016, 0.0454979024361819, 0.165399262448773, 0.677076171152294, 0.00230608345009387, 0.255336100002751, 0.402137719327584, 0.978440625127405, 0.3393238929566, 0.499170589726418, 0.351387069793418, 0.907491780584678, 0.399671071674675, 0.788517370121554, 0.139001973206177, 0.335611990885809, 0.206896337680519, 0.40120611875318, 0.110172357177362, 0.351979855680838, 0.219380670459941, 0.319322561612353, 0.278262983076274, 0.311137101612985), dim = c(5L, 5L)))), 2L, NA_real_, 5L, TRUE, NULL, "NB", 1.45541038408495)`: Invalid component: 2
Backtrace:
▆
1. ├─HiCPotts::run_metropolis_MCMC_betas(...) at test-run_chain.R:59:5
2. └─HiCPotts (local) `<fn>`(...)
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 130 ]
Error:
! Test failures.
Execution halted
HiCPotts.Rcheck/HiCPotts-Ex.timings
| name | user | system | elapsed | |
| Neighbours_combined | 0.000 | 0.000 | 0.001 | |
| compute_HMRFHiC_probabilities | 0.006 | 0.001 | 0.008 | |
| gamma_prior_value | 0.000 | 0.000 | 0.001 | |
| get_data | 31.209 | 0.677 | 31.892 | |
| likelihood_combined | 0.001 | 0.000 | 0.000 | |
| likelihood_gamma | 0.001 | 0.000 | 0.000 | |
| posterior_combined | 0.001 | 0.000 | 0.001 | |
| pred_combined | 0.001 | 0.001 | 0.000 | |
| prior_combined | 0.000 | 0.000 | 0.001 | |
| process_data | 0.002 | 0.000 | 0.002 | |
| proposaldensity_combined | 0.001 | 0.000 | 0.000 | |
| proposalfunction | 0 | 0 | 0 | |
| pz_123 | 0.002 | 0.001 | 0.003 | |
| run_chain_betas | 0.03 | 0.00 | 0.03 | |
| run_metropolis_MCMC_betas | 0.023 | 0.001 | 0.023 | |
| size_prior | 0 | 0 | 0 | |