Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1716/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REBET 1.22.0  (landing page)
Bill Wheeler
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/REBET
git_branch: RELEASE_3_19
git_last_commit: 02bac5f
git_last_commit_date: 2024-04-30 11:08:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


BUILD BIN results for REBET on kjohnson3

To the developers/maintainers of the REBET package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/REBET.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: REBET
Version: 1.22.0
Command: rm -rf REBET.buildbin-libdir && mkdir REBET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh REBET_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R REBET.buildbin-libdir
StartedAt: 2024-06-11 12:44:31 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 12:44:47 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 16.4 seconds
RetCode: 0
Status:   OK  
PackageFile: REBET_1.22.0.tgz
PackageFileSize: 329.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf REBET.buildbin-libdir && mkdir REBET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh REBET_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R REBET.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=REBET.buildbin-libdir REBET_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘REBET’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c source.c -o source.o
source.c:58:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double * dVec_alloc(n, initFlag, initVal)
                ^
source.c:76:18: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double ** dMat_alloc(nrow, ncol, initFlag, initVal)
                 ^
source.c:92:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void matrix_free(x, n)
            ^
source.c:105:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void vecIntoMat(vec, nrow, ncol, ret)
            ^
source.c:123:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void mult_stVec_stVec(X, invXtX, n, m, ret)
            ^
source.c:149:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void mult_stVec_scalar(X, n, col, c, ret)
            ^
source.c:165:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void mult_vec_TstVec(vec, TstVec, n, m, ret)
            ^
source.c:189:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double dotProd(v1, v2, n)
              ^
source.c:205:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void SIGMA2_cont(G, p_nsub, p_nsnp, X, p_ncov, invXtX, p_tildeSigma, ret)
     ^
source.c:297:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void SIGMA2_binary(G, p_nsub, p_nsnp, X, p_ncov, invXtX, d, ret)
     ^
source.c:388:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void computeXtDX(X, d, p_nsub, p_ncov, ret)
     ^
11 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o REBET.so source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/REBET.buildbin-libdir/00LOCK-REBET/00new/REBET/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 (REBET)


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

>>>>>>> Paths before fix:
REBET.buildbin-libdir/REBET/libs/REBET.so:
	REBET.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/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" "REBET.buildbin-libdir/REBET/libs/REBET.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "REBET.buildbin-libdir/REBET/libs/REBET.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "REBET.buildbin-libdir/REBET/libs/REBET.so"

>>>>>>> Paths after fix:
REBET.buildbin-libdir/REBET/libs/REBET.so:
	REBET.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)