Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
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 |
Package 1554/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PING 2.50.0 (landing page) Renan Sauteraud
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the PING package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PING.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. |
Package: PING |
Version: 2.50.0 |
Command: rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_2.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PING.buildbin-libdir |
StartedAt: 2024-12-21 15:59:54 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 16:01:11 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 77.0 seconds |
RetCode: 0 |
Status: OK |
PackageFile: PING_2.50.0.tgz |
PackageFileSize: 5.51 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_2.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PING.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PING.buildbin-libdir PING_2.50.0.tar.gz' >>>>>>> * installing *source* package ‘PING’ ... ** using staged installation checking for pkg-config... /opt/R/arm64/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ 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 init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ping.c -o ping.o ping.c:145:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ping.c:145:7: note: cast one or both operands to int to silence this warning ping.c:321:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha) ^ ping.c:321:10: note: use function 'fabs' instead if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha) ^~~ fabs ping.c:329:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha) ^ ping.c:329:10: note: use function 'fabs' instead if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha) ^~~ fabs ping.c:345:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha) ^ ping.c:345:12: note: use function 'fabs' instead if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha) ^~~ fabs ping.c:353:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha) ^ ping.c:353:12: note: use function 'fabs' instead if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha) ^~~ fabs ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] double chiSum = 0, etaF, etaR, dd, cc; ^ ping.c:3408:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if((gsl_matrix_get(Index,kMerge,k)==1) | (gsl_matrix_get(Index,kMerge+1,k)==1)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || ping.c:3408:10: note: cast one or both operands to int to silence this warning ping.c:3280:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable] double tstat=0.0,tstatMax=0.0; ^ 8 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 PING.so init.o ping.o -L/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/PING.buildbin-libdir/00LOCK-PING/00new/PING/libs ** R ** 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 (PING) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR PING.buildbin-libdir/PING/libs/PING.so >>>>>>> >>>>>>> Paths before fix: PING.buildbin-libdir/PING/libs/PING.so: PING.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /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) >>>>>>> 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" "PING.buildbin-libdir/PING/libs/PING.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "PING.buildbin-libdir/PING/libs/PING.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "PING.buildbin-libdir/PING/libs/PING.so" >>>>>>> Paths after fix: PING.buildbin-libdir/PING/libs/PING.so: PING.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /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)