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This page was generated on 2022-06-24 11:08:25 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 lconway


To the developers/maintainers of the puma package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1506/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
puma 3.39.0  (landing page)
Xuejun Liu
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/puma
git_branch: master
git_last_commit: 42f60dd
git_last_commit_date: 2022-04-26 10:59:55 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: puma
Version: 3.39.0
Command: rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R puma.buildbin-libdir
StartedAt: 2022-06-23 23:51:13 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:52:09 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 56.0 seconds
RetCode: 0
Status:   OK  
PackageFile: puma_3.39.0.tgz
PackageFileSize: 4.108 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.39.0.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_3.39.0.tar.gz'
>>>>>>> 

* installing *source* package ‘puma’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cregistration.c -o cregistration.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c newx.c -o newx.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c user_eval.c -o user_eval.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-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 LINKS FOR puma.buildbin-libdir/puma/libs/puma.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "puma.buildbin-libdir/puma/libs/puma.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/lib/libquadmath.0.dylib" "puma.buildbin-libdir/puma/libs/puma.so"