Catalina Vallejos
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BASiCS |
| git_branch: devel |
| git_last_commit: a6635d4 |
| git_last_commit_date: 2025-09-17 04:48:21 -0400 (Wed, 17 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:06 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 139/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCS 2.21.1 (landing page) Catalina Vallejos
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the BASiCS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.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: BASiCS |
| Version: 2.21.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BASiCS |
| StartedAt: 2025-10-22 15:29:32 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 15:29:57 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 24.6 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BASiCS’ ...
** this is package ‘BASiCS’ version ‘2.21.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BASiCS.cpp -o BASiCS.o
In file included from BASiCS.cpp:1:
In file included from ./updates.h:4:
./utils.h:357:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
if( arma::is_finite(log_aux(i)) & arma::is_finite(y(i)) ) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
[[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
^
In file included from BASiCS.cpp:1:
In file included from ./updates.h:4:
./utils.h:357:45: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
if( arma::is_finite(log_aux(i)) & arma::is_finite(y(i)) ) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
[[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
^
In file included from BASiCS.cpp:1:
In file included from ./updates.h:4:
./utils.h:357:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if( arma::is_finite(log_aux(i)) & arma::is_finite(y(i)) ) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./utils.h:357:9: note: cast one or both operands to int to silence this warning
./utils.h:358:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((log(u(i)) < log_aux(i)) & (y(i) > threshold)) { ind(i) = 1; }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./utils.h:358:10: note: cast one or both operands to int to silence this warning
In file included from BASiCS.cpp:1:
./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if(all(prop_var * phi1 < 2.5327372760800758e+305) &
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./updates.h:163:6: note: cast one or both operands to int to silence this warning
./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if(all(prop_var * phi1 < 2.5327372760800758e+305) &
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./updates.h:163:6: note: cast one or both operands to int to silence this warning
./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if(all(prop_var * phi1 < 2.5327372760800758e+305) &
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updates.h:163:6: note: cast one or both operands to int to silence this warning
./updates.h:258:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if (!R_IsNA(chi(j)) & (chi(j) > 0)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updates.h:258:11: note: cast one or both operands to int to silence this warning
./updates.h:266:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if (!(chi(j) < 0) & (lambda(j) > 0)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updates.h:266:13: note: cast one or both operands to int to silence this warning
In file included from BASiCS.cpp:3:
./updatesNoSpikes.h:76:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if ((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updatesNoSpikes.h:76:11: note: cast one or both operands to int to silence this warning
./updatesNoSpikes.h:102:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if ((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updatesNoSpikes.h:102:9: note: cast one or both operands to int to silence this warning
In file included from BASiCS.cpp:4:
./updatesRegNoSpikes.h:107:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updatesRegNoSpikes.h:107:10: note: cast one or both operands to int to silence this warning
./updatesRegNoSpikes.h:139:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if ((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./updatesRegNoSpikes.h:139:9: note: cast one or both operands to int to silence this warning
In file included from BASiCS.cpp:6:
./MCMCReg.h:383:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if ((det(V1) != 0) & all(arma::eig_sym(sigma2Aux * VAux) > 0)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./MCMCReg.h:383:9: note: cast one or both operands to int to silence this warning
In file included from BASiCS.cpp:8:
./MCMCRegNoSpikes.h:382:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((det(V1)!=0) & all(arma::eig_sym(sigma2Aux * VAux) > 0)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
./MCMCRegNoSpikes.h:382:8: note: cast one or both operands to int to silence this warning
15 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BASiCS.so BASiCS.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-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/4.5-arm64/Resources/library/00LOCK-BASiCS/00new/BASiCS/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 (BASiCS)