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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1552/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PICS 2.50.0  (landing page)
Renan Sauteraud
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/PICS
git_branch: RELEASE_3_20
git_last_commit: 2ffb0c3
git_last_commit_date: 2024-10-29 09:33:53 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


BUILD BIN results for PICS on lconway

To the developers/maintainers of the PICS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PICS.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: PICS
Version: 2.50.0
Command: rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PICS.buildbin-libdir
StartedAt: 2024-11-20 04:42:39 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:43:36 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 57.0 seconds
RetCode: 0
Status:   OK  
PackageFile: PICS_2.50.0.tgz
PackageFileSize: 1.642 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PICS.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_2.50.0.tar.gz'
>>>>>>> 

* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /opt/R/x86_64/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 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 pics.c -o pics.o
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
        double chiSum, etaF, etaR, dd, cc;
               ^
pics.c:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^~~~~~~
pics.c:1307:97: note: uninitialized use occurs here
        bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
                                                                                                       ^~~~~~~
pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning
        double bic, tmp, muF[K], muR[K], penalty, distance;
                                                ^
                                                 = 0.0
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
          double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                           ^
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
          double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                                  ^
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
  int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
          ^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
      ^
6 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 segment.c -o segment.o
segment.c:406:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
                                        pp++;
                                        ^
segment.c:395:27: note: incremented here
                                for (pp=start; pp<=p; pp++) {
                                                      ^
segment.c:536:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
                                        pp++;
                                        ^
segment.c:525:27: note: incremented here
                                for (pp=start; pp<=p; pp++) {
                                                      ^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
  SEXP ans, x, y, chr, names;
                  ^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
  SEXP filter1;
       ^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
  double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
          ^
5 warnings generated.
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 PICS.so pics.o segment.o -L/opt/R/x86_64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/PICS.buildbin-libdir/00LOCK-PICS/00new/PICS/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 (PICS)


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

>>>>>>> Paths before fix:
PICS.buildbin-libdir/PICS/libs/PICS.so:
	PICS.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-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"

>>>>>>> Paths after fix:
PICS.buildbin-libdir/PICS/libs/PICS.so:
	PICS.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-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)