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INSTALL report for CALIB on machv2

This page was generated on 2020-10-17 11:58:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CALIB PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 220/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CALIB 1.54.0
Hui Zhao
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CALIB
Branch: RELEASE_3_11
Last Commit: 0e17e9d
Last Changed Date: 2020-04-27 14:14:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
machv2 macOS 10.14.6 Mojave / x86_64 [ OK ] OK  ERROR  OK 

Summary

Package: CALIB
Version: 1.54.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CALIB
StartedAt: 2020-10-16 16:09:34 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 16:09:58 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 24.5 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CALIB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CALIB’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Design.cpp -o Design.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Estimation.cpp -o Estimation.o
Estimation.cpp:147:19: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                         ^
Estimation.cpp:147:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                               ^
Estimation.cpp:147:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                    ^
Estimation.cpp:147:35: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                         ^
Estimation.cpp:147:40: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                              ^
Estimation.cpp:147:49: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                       ^
Estimation.cpp:147:58: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                                ^
Estimation.cpp:147:67: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                                         ^
Estimation.cpp:226:30: warning: 'readinparlist' has C-linkage specified, but returns incomplete type 'vector<ParameterofOneArray>' which could be incompatible with C [-Wreturn-type-c-linkage]
vector <ParameterofOneArray> readinparlist(SEXP parlist, int ncol)
                             ^
9 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c NormalizedData.cpp -o NormalizedData.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ParameterofOneArray.cpp -o ParameterofOneArray.o
In file included from ParameterofOneArray.cpp:4:
./ParameterofOneArray.h:11:9: warning: private field 'SpotErrorofOneSpot' is not used [-Wunused-private-field]
        double SpotErrorofOneSpot;
               ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c RawDataofOneArray.cpp -o RawDataofOneArray.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c SpikeofOneArray.cpp -o SpikeofOneArray.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CALIB/00new/CALIB/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
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (CALIB)