Evan Biederstedt
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/scde |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7cdd70a |
| git_last_commit_date: 2025-04-15 10:56:24 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1902/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scde 2.36.0 (landing page) Evan Biederstedt
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the scde package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scde.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: scde |
| Version: 2.36.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scde |
| StartedAt: 2025-10-15 15:12:14 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 15:13:07 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 53.3 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scde
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘scde’ ...
** this is package ‘scde’ version ‘2.36.0’
** 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-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function ‘void set_random_matrix(arma::mat&, arma::mat&)’:
bwpca.cpp:24:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
24 | for(int j=0;j<target.n_rows;j++) {
| ~^~~~~~~~~~~~~~
bwpca.cpp:31:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
31 | for(int i=0;i<target.n_cols;i++) {
| ~^~~~~~~~~~~~~~
bwpca.cpp:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
34 | for(int j=0;j<target.n_rows;j++) {
| ~^~~~~~~~~~~~~~
bwpca.cpp: In function ‘void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)’:
bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
44 | for(int j=0;j<target1.n_rows;j++) {
| ~^~~~~~~~~~~~~~~
bwpca.cpp:51:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
51 | for(int i=0;i<target1.n_cols;i++) {
| ~^~~~~~~~~~~~~~~
bwpca.cpp:54:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
54 | for(int j=0;j<target1.n_rows;j++) {
| ~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function ‘SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
jpmatLogBoot.cpp:200:36: warning: ‘eT arma::Mat<eT>::max(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations]
200 | double maxv=nbp.max(maxij);
| ~~~~~~~^~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo:201,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from jpmatLogBoot.h:4,
from jpmatLogBoot.cpp:1:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:545:56: note: declared here
545 | [[deprecated("use .index_max() instead")]] inline eT max(uword& index_of_max_val) const;
| ^~~
jpmatLogBoot.cpp:200:24: warning: unused variable ‘maxv’ [-Wunused-variable]
200 | double maxv=nbp.max(maxij);
| ^~~~
jpmatLogBoot.cpp: In function ‘SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
jpmatLogBoot.cpp:443:36: warning: ‘eT arma::Mat<eT>::max(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations]
443 | double maxv=nbp.max(maxij);
| ~~~~~~~^~~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo:692:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7850:1: note: declared here
7850 | Mat<eT>::max(uword& index_of_max_val) const
| ^~~~~~~
jpmatLogBoot.cpp:443:24: warning: unused variable ‘maxv’ [-Wunused-variable]
443 | double maxv=nbp.max(maxij);
| ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c matSlideMult.cpp -o matSlideMult.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c pagoda.cpp -o pagoda.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -lpthread -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-scde/00new/scde/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (scde)