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This page was generated on 2023-02-03 11:07:12 -0500 (Fri, 03 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

BUILD BIN results for snapCGH on merida1


To the developers/maintainers of the snapCGH package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snapCGH.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1892/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.69.0  (landing page)
John Marioni
Snapshot Date: 2023-02-02 14:00:21 -0500 (Thu, 02 Feb 2023)
git_url: https://git.bioconductor.org/packages/snapCGH
git_branch: master
git_last_commit: 29ab2bc
git_last_commit_date: 2022-11-01 10:40:32 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: snapCGH
Version: 1.69.0
Command: rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.69.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R snapCGH.buildbin-libdir
StartedAt: 2023-02-03 09:58:02 -0500 (Fri, 03 Feb 2023)
EndedAt: 2023-02-03 09:59:42 -0500 (Fri, 03 Feb 2023)
EllapsedTime: 99.7 seconds
RetCode: 0
Status:   OK  
PackageFile: snapCGH_1.69.0.tgz
PackageFileSize: 1.369 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.69.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R snapCGH.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=snapCGH.buildbin-libdir snapCGH_1.69.0.tar.gz'
>>>>>>> 

* installing *source* package ‘snapCGH’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using SDK: ‘’
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c optimizer.c -o optimizer.o
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                    ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                    ^
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                    ^
15 warnings generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/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 (snapCGH)


>>>>>>> 
>>>>>>> FIXING LINKS FOR snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so"