flipflop 1.9.0
Elsa Bernard
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flipflop | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flipflop.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.9.0’
* 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 ... [45s/45s] OK
* 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 ... OK
* 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 ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
/usr/bin/nm: /home/biocbuild/bbs-3.3-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols
/usr/bin/nm: /home/biocbuild/bbs-3.3-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in vignettes ... OK
* 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
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/flipflop.Rcheck/00check.log’
for details.
* installing *source* package ‘flipflop’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c FileSplitter.cpp -o FileSplitter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_flipflop.c -o R_init_flipflop.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c align.cpp -o align.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c auxiliaryio.cpp -o auxiliaryio.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c bedio.cpp -o bedio.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c common.cpp -o common.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c cvganalysis.cpp -o cvganalysis.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c ffProcesssam.cpp -o ffProcesssam.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c instanceio.cpp -o instanceio.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c parseopt.cpp -o parseopt.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c rangeset.cpp -o rangeset.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c readgroup.cpp -o readgroup.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c samio.cpp -o samio.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c samples.cpp -o samples.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c spams.cpp -o spams.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -c structdef.cpp -o structdef.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o flipflop.so FileSplitter.o R_init_flipflop.o align.o auxiliaryio.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o samples.o spams.o structdef.o -s -fopenmp -lstdc++ -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
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)