Zachary Kurtz
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 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 2025-11-21 11:39 -0500 (Fri, 21 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" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpiecEasi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpiecEasi_1.99.3.tar.gz |
| StartedAt: 2025-11-21 00:24:52 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 00:32:10 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 437.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpiecEasi.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpiecEasi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpiecEasi_1.99.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SpiecEasi.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 111.838 0.565 112.961
getOptInd 110.219 0.542 111.274
pval.sparccboot 21.696 0.329 22.125
sparccboot 21.129 0.276 21.532
multi.spiec.easi 16.101 0.083 16.254
spiec.easi 16.065 0.085 16.234
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/SpiecEasi.Rcheck/00check.log’
for details.
SpiecEasi.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpiecEasi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘SpiecEasi’ ...
** this is package ‘SpiecEasi’ version ‘1.99.3’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ADMM.cpp -o ADMM.o
In file included from ADMM.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: 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. [-W#pragma-messages]
#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.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: 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. [-W#pragma-messages]
#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.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matops.cpp -o matops.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sqrtNewton.cpp -o sqrtNewton.o
In file included from sqrtNewton.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: 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. [-W#pragma-messages]
#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.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c svthresh.cpp -o svthresh.o
In file included from svthresh.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: 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. [-W#pragma-messages]
#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.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SpiecEasi.so ADMM.o RcppExports.o matops.o sqrtNewton.o svthresh.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
52.542 1.031 53.945
SpiecEasi.Rcheck/SpiecEasi-Ex.timings
| name | user | system | elapsed | |
| adj2igraph | 0.005 | 0.001 | 0.005 | |
| alr | 0.001 | 0.001 | 0.002 | |
| as.data.frame.graph | 0.003 | 0.001 | 0.004 | |
| as.matrix.graph | 0.001 | 0.001 | 0.001 | |
| clr | 0.001 | 0.001 | 0.002 | |
| coat | 0.020 | 0.002 | 0.022 | |
| cor2cov | 0.001 | 0.000 | 0.000 | |
| cov2prec | 0.001 | 0.000 | 0.001 | |
| ebic | 0.000 | 0.001 | 0.001 | |
| edge.diss | 0.020 | 0.002 | 0.022 | |
| fitdistr | 0.004 | 0.000 | 0.005 | |
| getOptInd | 110.219 | 0.542 | 111.274 | |
| get_comm_params | 0.002 | 0.000 | 0.002 | |
| graph2prec | 0.005 | 0.000 | 0.005 | |
| make_graph | 0.016 | 0.001 | 0.017 | |
| multi.spiec.easi | 16.101 | 0.083 | 16.254 | |
| neff | 0.000 | 0.000 | 0.001 | |
| neighborhood.net | 0.030 | 0.001 | 0.031 | |
| norm_pseudo | 0.001 | 0.000 | 0.000 | |
| norm_rdiric | 0 | 0 | 0 | |
| norm_to_total | 0 | 0 | 0 | |
| prec2cov | 0.001 | 0.000 | 0.001 | |
| pval.sparccboot | 21.696 | 0.329 | 22.125 | |
| qqdplot_comm | 0.023 | 0.002 | 0.025 | |
| rmvnegbin | 0.002 | 0.000 | 0.003 | |
| rmvnorm | 0.001 | 0.000 | 0.001 | |
| rmvpois | 0 | 0 | 0 | |
| rmvzinegbin | 0.001 | 0.000 | 0.002 | |
| rmvzipois | 0.001 | 0.000 | 0.001 | |
| robustPCA | 0.114 | 0.007 | 0.121 | |
| rzipois | 0.000 | 0.001 | 0.001 | |
| shannon | 0.000 | 0.000 | 0.001 | |
| sparcc | 0.115 | 0.004 | 0.121 | |
| sparccboot | 21.129 | 0.276 | 21.532 | |
| sparseLowRankiCov | 0.056 | 0.002 | 0.059 | |
| sparseiCov | 2.518 | 0.017 | 2.546 | |
| spiec.easi | 16.065 | 0.085 | 16.234 | |
| stars.roc | 111.838 | 0.565 | 112.961 | |
| symBeta | 0.058 | 0.000 | 0.058 | |
| synth_comm_from_counts | 0.003 | 0.001 | 0.004 | |
| triu | 0.001 | 0.000 | 0.000 | |