Multiple platform build/check report for BioC 3.21 - BUILD BIN results for puma on merida1

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*

BUILD BIN results for puma on merida1

To the developers/maintainers of the puma package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/puma.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: puma

Version: 3.50.0

Command: rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R puma.buildbin-libdir

StartedAt: 2025-10-14 14:26:20 -0400 (Tue, 14 Oct 2025)

EndedAt: 2025-10-14 14:28:20 -0400 (Tue, 14 Oct 2025)

EllapsedTime: 119.9 seconds

RetCode: 0

Status: OK

PackageFile: puma_3.50.0.tgz

PackageFileSize: 4.116 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R puma.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=puma.buildbin-libdir puma_3.50.0.tar.gz'
>>>>>>> 

* installing *source* package ‘puma’ ...
** this is package ‘puma’ version ‘3.50.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cregistration.c -o cregistration.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c donlp2.c -o donlp2.o
donlp2.c:471:33: warning: variable 'infiny' set but not used [-Wunused-but-set-variable]
    static DDOUBLE   tol1,term, infiny;
                                ^
donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive  
^
donlp2.c:2079:44: warning: variable 'iumin' set but not used [-Wunused-but-set-variable]
    static DDOUBLE   delsig,delx,sum,term, iumin;
                                           ^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gme.c -o gme.o
gme.c:266:9: warning: variable 'fstart' set but not used [-Wunused-but-set-variable]
        double fstart;
               ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ipplr_c.c -o ipplr_c.o
ipplr_c.c:255:118: warning: '&&' within '||' [-Wlogical-op-parentheses]
                   while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000))
                                                                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
ipplr_c.c:255:118: note: place parentheses around the '&&' expression to silence this warning
                   while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000))
                                                                                                                                   ^
                                                                              (                                                               )
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c multimgmos.c -o multimgmos.o
multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4;
                                                                                                     ^~~
                                                                                                     {  }
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c newx.c -o newx.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pplr_c.c -o pplr_c.o
pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable]
        double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
                                                                   ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pumaclust_c.c -o pumaclust_c.o
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^
pumaclust_c.c:181:24: note: use function 'fabs' instead
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^~~
                              fabs
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pumaclustii_c.c -o pumaclustii_c.o
pumaclustii_c.c:255:42: warning: variable 'temp2' set but not used [-Wunused-but-set-variable]
        double  *exprs=NULL, *vars=NULL, temp, *temp2, temp3, **t3=NULL, *t4=NULL;
                                                ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c user_eval.c -o user_eval.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/puma.buildbin-libdir/00LOCK-puma/00new/puma/libs
** R
** data
** demo
** 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 (puma)


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

>>>>>>> Paths before fix:
puma.buildbin-libdir/puma/libs/puma.so:
	puma.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "puma.buildbin-libdir/puma/libs/puma.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "puma.buildbin-libdir/puma/libs/puma.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "puma.buildbin-libdir/puma/libs/puma.so"

>>>>>>> Paths after fix:
puma.buildbin-libdir/puma/libs/puma.so:
	puma.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)