Back to Multiple platform build/check report for BioC 3.21:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 313/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 3.43.0  (landing page)
Justin Lee
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/CGEN
git_branch: devel
git_last_commit: a8ad56a
git_last_commit_date: 2024-10-29 10:58:46 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for CGEN on lconway

To the developers/maintainers of the CGEN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.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: CGEN
Version: 3.43.0
Command: rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_3.43.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CGEN.buildbin-libdir
StartedAt: 2024-12-24 00:17:21 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 00:17:59 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:   OK  
PackageFile: CGEN_3.43.0.tgz
PackageFileSize: 1.938 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_3.43.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CGEN.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CGEN.buildbin-libdir CGEN_3.43.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CGEN’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
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 Additive.c -o Additive.o
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 CML.c -o CML.o
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 ccl.c -o ccl.o
ccl.c:430:16: warning: variable 'det' set but not used [-Wunused-but-set-variable]
        double temp , det = 1.0 ;
                      ^
1 warning generated.
/opt/gfortran/bin/gfortran -arch x86_64  -fPIC  -Wall -g -O2  -c csclust.f -o csclust.o
f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs]
csclust.f:72:72:

   72 |  10      FLAG(I)=.TRUE.
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
csclust.f:222:3:

  222 | 650   RETURN
      |   1
Warning: Label 650 at (1) defined but not used [-Wunused-label]
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 fsclust.c -o fsclust.o
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 hcl.c -o hcl.o
hcl.c:419:16: warning: variable 'det' set but not used [-Wunused-but-set-variable]
        double temp , det = 1.0 ;
                      ^
1 warning 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 pmatch.c -o pmatch.o
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 score.c -o score.o
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 CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/CGEN/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 (CGEN)


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

>>>>>>> Paths before fix:
CGEN.buildbin-libdir/CGEN/libs/CGEN.so:
	CGEN.so (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs/CGEN.so"

>>>>>>> Paths after fix:
CGEN.buildbin-libdir/CGEN/libs/CGEN.so:
	CGEN.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)