Zachary Kurtz
| Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SpiecEasi |
| git_branch: devel |
| git_last_commit: 18c9537 |
| git_last_commit_date: 2025-10-29 15:53:57 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-22 11:37 -0500 (Sat, 22 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4567 |
| 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 2070/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpiecEasi 1.99.3 (landing page) Zachary Kurtz
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SpiecEasi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpiecEasi.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: SpiecEasi |
| Version: 1.99.3 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SpiecEasi.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SpiecEasi_1.99.3.tar.gz |
| StartedAt: 2025-11-22 04:22:09 -0500 (Sat, 22 Nov 2025) |
| EndedAt: 2025-11-22 04:56:18 -0500 (Sat, 22 Nov 2025) |
| EllapsedTime: 2048.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpiecEasi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SpiecEasi.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SpiecEasi_1.99.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SpiecEasi.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘SpiecEasi/DESCRIPTION’ ... OK
* this is package ‘SpiecEasi’ version ‘1.99.3’
* 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 ‘SpiecEasi’ 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 ... OK
* 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 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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
stars.roc 129.940 0.153 128.591
getOptInd 128.699 0.516 127.563
pval.sparccboot 21.083 0.183 21.269
sparccboot 20.708 0.087 20.796
spiec.easi 15.849 0.003 15.852
multi.spiec.easi 15.427 0.006 15.434
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SpiecEasi.Rmd’ using rmarkdown
--- finished re-building ‘SpiecEasi.Rmd’
--- re-building ‘cross-domain-interactions.Rmd’ using rmarkdown
--- finished re-building ‘cross-domain-interactions.Rmd’
--- re-building ‘latent-variable-models.Rmd’ using rmarkdown
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
warning: sqrtmat_sympd(): given matrix is not symmetric
--- finished re-building ‘latent-variable-models.Rmd’
--- re-building ‘phyloseq-integration.Rmd’ using rmarkdown
--- finished re-building ‘phyloseq-integration.Rmd’
--- re-building ‘pulsar-parallel.Rmd’ using rmarkdown
Quitting from pulsar-parallel.Rmd:152-160 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'snow'
---
Backtrace:
▆
1. ├─parallel::makeCluster(4, type = "SOCK")
2. └─base::loadNamespace(x)
3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4. └─base (local) withOneRestart(expr, restarts[[1L]])
5. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pulsar-parallel.Rmd' failed with diagnostics:
there is no package called 'snow'
--- failed re-building ‘pulsar-parallel.Rmd’
--- re-building ‘troubleshooting.Rmd’ using rmarkdown
--- finished re-building ‘troubleshooting.Rmd’
SUMMARY: processing the following file failed:
‘pulsar-parallel.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/SpiecEasi.Rcheck/00check.log’
for details.
SpiecEasi.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SpiecEasi
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SpiecEasi’ ...
** this is package ‘SpiecEasi’ version ‘1.99.3’
** 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-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ADMM.cpp -o ADMM.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from ADMM.cpp:1:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c matops.cpp -o matops.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sqrtNewton.cpp -o sqrtNewton.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from sqrtNewton.cpp:1:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c svthresh.cpp -o svthresh.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from svthresh.cpp:1:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o SpiecEasi.so ADMM.o RcppExports.o matops.o sqrtNewton.o svthresh.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-SpiecEasi/00new/SpiecEasi/libs
** R
** data
** 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 (SpiecEasi)
SpiecEasi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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.
> suppressPackageStartupMessages(library(testthat))
> suppressPackageStartupMessages(library(SpiecEasi))
>
> testthat::test_check("SpiecEasi")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 149 ]
>
> proc.time()
user system elapsed
48.389 0.696 49.089
SpiecEasi.Rcheck/SpiecEasi-Ex.timings
| name | user | system | elapsed | |
| adj2igraph | 0.005 | 0.000 | 0.005 | |
| alr | 0.001 | 0.000 | 0.001 | |
| as.data.frame.graph | 0.003 | 0.000 | 0.003 | |
| as.matrix.graph | 0.000 | 0.001 | 0.001 | |
| clr | 0.001 | 0.000 | 0.001 | |
| coat | 0.014 | 0.002 | 0.015 | |
| cor2cov | 0 | 0 | 0 | |
| cov2prec | 0 | 0 | 0 | |
| ebic | 0 | 0 | 0 | |
| edge.diss | 0.015 | 0.000 | 0.015 | |
| fitdistr | 0.003 | 0.000 | 0.003 | |
| getOptInd | 128.699 | 0.516 | 127.563 | |
| get_comm_params | 0.002 | 0.000 | 0.003 | |
| graph2prec | 0.003 | 0.002 | 0.006 | |
| make_graph | 0.013 | 0.000 | 0.014 | |
| multi.spiec.easi | 15.427 | 0.006 | 15.434 | |
| neff | 0.001 | 0.000 | 0.000 | |
| neighborhood.net | 0.027 | 0.002 | 0.029 | |
| norm_pseudo | 0 | 0 | 0 | |
| norm_rdiric | 0.000 | 0.000 | 0.001 | |
| norm_to_total | 0.000 | 0.000 | 0.001 | |
| prec2cov | 0.000 | 0.000 | 0.001 | |
| pval.sparccboot | 21.083 | 0.183 | 21.269 | |
| qqdplot_comm | 0.021 | 0.000 | 0.021 | |
| rmvnegbin | 0.002 | 0.001 | 0.002 | |
| rmvnorm | 0.001 | 0.000 | 0.001 | |
| rmvpois | 0.001 | 0.000 | 0.001 | |
| rmvzinegbin | 0.002 | 0.001 | 0.002 | |
| rmvzipois | 0.002 | 0.000 | 0.002 | |
| robustPCA | 0.132 | 0.002 | 0.135 | |
| rzipois | 0.001 | 0.000 | 0.001 | |
| shannon | 0 | 0 | 0 | |
| sparcc | 0.111 | 0.003 | 0.115 | |
| sparccboot | 20.708 | 0.087 | 20.796 | |
| sparseLowRankiCov | 0.063 | 0.002 | 0.066 | |
| sparseiCov | 2.536 | 0.016 | 2.552 | |
| spiec.easi | 15.849 | 0.003 | 15.852 | |
| stars.roc | 129.940 | 0.153 | 128.591 | |
| symBeta | 0.062 | 0.001 | 0.063 | |
| synth_comm_from_counts | 0.004 | 0.000 | 0.005 | |
| triu | 0.000 | 0.000 | 0.001 | |