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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 911/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harshlight 1.72.0  (landing page)
Maurizio Pellegrino
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Harshlight
git_branch: RELEASE_3_17
git_last_commit: 0ec7d5e
git_last_commit_date: 2023-04-25 09:44:01 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for Harshlight on kjohnson2


To the developers/maintainers of the Harshlight package:
- 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: Harshlight
Version: 1.72.0
Command: rm -rf Harshlight.buildbin-libdir && mkdir Harshlight.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Harshlight_1.72.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Harshlight.buildbin-libdir
StartedAt: 2023-10-19 13:57:43 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 13:58:20 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:   OK  
PackageFile: Harshlight_1.72.0.tgz
PackageFileSize: 307.8 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf Harshlight.buildbin-libdir && mkdir Harshlight.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Harshlight_1.72.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Harshlight.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Harshlight.buildbin-libdir Harshlight_1.72.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Harshlight’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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 Harshlight.c -o Harshlight.o
Harshlight.c:564:20: warning: variable 'p_num_points' set but not used [-Wunused-but-set-variable]
  int num_points, *p_num_points; //number of points inside the median kernel
                   ^
Harshlight.c:948:10: warning: variable 'cell_value' set but not used [-Wunused-but-set-variable]
  double cell_value;
         ^
Harshlight.c:1316:27: warning: unused variable 'sorted2' [-Wunused-variable]
  double *sorted; double *sorted2;
                          ^
Harshlight.c:1471:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 215, *diff_br);
                        ~^
Harshlight.c:1474:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_text_val, y_text - 230, *diff_dr);
                        ~^
Harshlight.c:1532:107: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                         ~^
Harshlight.c:1542:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_val_1, y_text - 100, *perc_c);
                        ~^
Harshlight.c:1543:26: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (%.2f%) show\n", x_val_2, y_text - 100, *perc_d);
                        ~^
Harshlight.c:1555:107: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
  PP "%d %d moveto (Extended defects: the variance of the Error Image explained by the background is %.2f%) show\n", x_text, y_text - 30, *var);
                                                                                                         ~^
9 warnings generated.
clang -arch arm64 -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 Harshlight.so Harshlight.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Harshlight.buildbin-libdir/00LOCK-Harshlight/00new/Harshlight/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 (Harshlight)


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

>>>>>>> Paths before fix:
Harshlight.buildbin-libdir/Harshlight/libs/Harshlight.so:
	Harshlight.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "Harshlight.buildbin-libdir/Harshlight/libs/Harshlight.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "Harshlight.buildbin-libdir/Harshlight/libs/Harshlight.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "Harshlight.buildbin-libdir/Harshlight/libs/Harshlight.so"

>>>>>>> Paths after fix:

Harshlight.buildbin-libdir/Harshlight/libs/Harshlight.so:
	Harshlight.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)