Multiple platform build/check report for BioC 3.20 - BUILD BIN results for BASiCS on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

BUILD BIN results for BASiCS on kjohnson1

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.

raw results

Summary

Package: BASiCS

Version: 2.18.0

Command: rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BASiCS_2.18.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BASiCS.buildbin-libdir

StartedAt: 2024-12-21 13:56:25 -0500 (Sat, 21 Dec 2024)

EndedAt: 2024-12-21 13:57:45 -0500 (Sat, 21 Dec 2024)

EllapsedTime: 79.2 seconds

RetCode: 0

Status: OK

PackageFile: BASiCS_2.18.0.tgz

PackageFileSize: 3.861 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BASiCS_2.18.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BASiCS.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BASiCS.buildbin-libdir BASiCS_2.18.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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:357:9: 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
13 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++11 -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so
>>>>>>> 

>>>>>>> Paths before fix:
BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so:
	BASiCS.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so"

>>>>>>> Paths after fix:
BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so:
	BASiCS.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)