Package: GLAD

Version: 2.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GLAD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GLAD_2.46.0.tar.gz

StartedAt: 2019-04-16 00:18:20 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:18:50 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 29.8 seconds

RetCode: 0

Status:  OK

CheckDir: GLAD.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GLAD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GLAD_2.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GLAD.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.46.0’
* 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 ‘GLAD’ can be installed ... 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/GLAD/libs/GLAD.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GLAD.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GLAD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GLAD’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm  
PKG_CPPFLAGS = -DIS_MAC_OS

** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c BkpInfo.cpp -o BkpInfo.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c HaarSeg.cpp -o HaarSeg.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c MoveBkp.cpp -o MoveBkp.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c OutliersGNL.cpp -o OutliersGNL.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c cutree.cpp -o cutree.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c daglad.cpp -o daglad.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c distance.cpp -o distance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c filterBkp.cpp -o filterBkp.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c findCluster.cpp -o findCluster.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c glad-utils.cpp -o glad-utils.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c hclust.cpp -o hclust.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c laws.c -o laws.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/usr/local/include   -fPIC  -Wall -g -O2  -c loopRemove.cpp -o loopRemove.o
clang++ -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 GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/GLAD/libs
** R
** data
** demo
** 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
* DONE (GLAD)

name	user	system	elapsed
ChrNumeric	0	0	0
ColorBar	0.022	0.001	0.022
arrayCGH	0.029	0.005	0.033
arrayPersp	0	0	0
arrayPlot	0.061	0.008	0.070
as.data.frame.profileCGH	0.222	0.024	0.248
as.profileCGH	0.051	0.003	0.055
bladder	0.016	0.003	0.019
cytoband	0.018	0.008	0.027
daglad	0.597	0.029	0.637
glad	0.498	0.026	0.527
hclust	0.024	0.004	0.027
myPalette	0.008	0.001	0.009
plotProfile	0.547	0.020	0.579
profileCGH	0.084	0.006	0.094
snijders	0.070	0.004	0.076
veltman	0.159	0.060	0.224