Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2022-07-07 11:11:53 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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 RNAdecay on kjohnson


To the developers/maintainers of the RNAdecay package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAdecay.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 1656/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAdecay 1.17.0  (landing page)
Reed Sorenson
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/RNAdecay
git_branch: master
git_last_commit: ec7cc2d
git_last_commit_date: 2022-04-26 11:48:58 -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    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    OK    NA    ERROR  

Summary

Package: RNAdecay
Version: 1.17.0
Command: rm -rf RNAdecay.buildbin-libdir && mkdir RNAdecay.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RNAdecay_1.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RNAdecay.buildbin-libdir
StartedAt: 2022-07-07 08:55:33 -0400 (Thu, 07 Jul 2022)
EndedAt: 2022-07-07 09:04:42 -0400 (Thu, 07 Jul 2022)
EllapsedTime: 549.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RNAdecay.buildbin-libdir && mkdir RNAdecay.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RNAdecay_1.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RNAdecay.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RNAdecay.buildbin-libdir RNAdecay_1.17.0.tar.gz'
>>>>>>> 

* installing *source* package ‘RNAdecay’ ...
** using staged installation
rm -rf *o
** libs
** arch - 
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_1sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_dExp_1sse.cpp -o general_dExp_1sse.o
In file included from general_dExp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_dExp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_1sse.so general_dExp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_1sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_Exp_1sse.cpp -o general_Exp_1sse.o
In file included from general_Exp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_Exp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_1sse.so general_Exp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_2sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_dExp_2sse.cpp -o general_dExp_2sse.o
In file included from general_dExp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_dExp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_2sse.so general_dExp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_2sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_Exp_2sse.cpp -o general_Exp_2sse.o
In file included from general_Exp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_Exp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_2sse.so general_Exp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_3sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_dExp_3sse.cpp -o general_dExp_3sse.o
In file included from general_dExp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_dExp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_3sse.so general_dExp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_3sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_Exp_3sse.cpp -o general_Exp_3sse.o
In file included from general_Exp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_Exp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_3sse.so general_Exp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_4sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_dExp_4sse.cpp -o general_dExp_4sse.o
In file included from general_dExp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_dExp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_4sse.so general_dExp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_4sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c general_Exp_4sse.cpp -o general_Exp_4sse.o
In file included from general_Exp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:34:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable]
        int sign;
            ^
In file included from general_Exp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/TMB.hpp:107:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/cppad.hpp:39:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable]
                size_t pow2 = 1;
                       ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_4sse.so general_Exp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
installing to /Users/biocbuild/bbs-3.16-bioc/meat/RNAdecay.buildbin-libdir/00LOCK-RNAdecay/00new/RNAdecay/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (RNAdecay)


>>>>>>> 
>>>>>>> FIXING LINKS FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so
>>>>>>> 

ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!