flipflop 1.2.2
Elsa Bernard
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flipflop | | Last Changed Rev: 94109 / Revision: 95116 | | Last Changed Date: 2014-09-13 23:29:35 -0700 (Sat, 13 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flipflop_1.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.2.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flipflop’ can be installed ... [36s/36s] WARNING
Found the following significant warnings:
Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘flipflop’
Found the following additional warnings:
auxiliaryio.cpp:157:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
-fopenmp -stdlib=libstdc++ -O3 -mtune=native -Wall
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so’:
Found ‘__ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Object: ‘spams.o’
Found ‘__ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘spams.o’
Found ‘_exit’, possibly from ‘exit’ (C)
Object: ‘spams.o’
Found ‘_printf’, possibly from ‘printf’ (C)
Object: ‘spams.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘GenomicFeatures’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/00check.log’
for details.
* installing *source* package ‘flipflop’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_init_flipflop.c -o R_init_flipflop.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c align.cpp -o align.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c auxiliaryio.cpp -o auxiliaryio.o
auxiliaryio.cpp:157:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
auxiliaryio.cpp:892:9: warning: unused variable 'id' [-Wunused-variable]
int id;
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c bed2sam.cpp -o bed2sam.o
bed2sam.cpp:149:9: warning: unused variable 'xs' [-Wunused-variable]
char xs;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c bedio.cpp -o bedio.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c common.cpp -o common.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c cvganalysis.cpp -o cvganalysis.o
cvganalysis.cpp:156:12: warning: unused variable 'prevjump' [-Wunused-variable]
bool prevjump=false;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c ffProcesssam.cpp -o ffProcesssam.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c instanceio.cpp -o instanceio.o
instanceio.cpp:125:9: warning: unused variable 'currenttypeorder' [-Wunused-variable]
int currenttypeorder=-1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c parseopt.cpp -o parseopt.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c rangeset.cpp -o rangeset.o
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
long t=0;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c readgroup.cpp -o readgroup.o
readgroup.cpp:1098:14: warning: unused variable 'nneg' [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1098:7: warning: unused variable 'npos' [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1097:7: warning: unused variable 'r' [-Wunused-variable]
int r=0;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c samio.cpp -o samio.o
samio.cpp:102:7: warning: unused variable 'rangecounter' [-Wunused-variable]
int rangecounter=1;
^
samio.cpp:106:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
int currentreadlen=0;
^
samio.cpp:98:11: warning: unused variable 'dp2' [-Wunused-variable]
range_t dp2=dp;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c spams.cpp -o spams.o
spams.cpp:2515:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c structdef.cpp -o structdef.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flipflop.so R_init_flipflop.o align.o auxiliaryio.o bed2sam.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o spams.o structdef.o -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -stdlib=libstdc++ -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘flipflop’
Creating a generic function for ‘print’ from package ‘base’ in package ‘flipflop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)