Package: DeMixT

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeMixT_0.99.9.tar.gz

StartedAt: 2019-04-09 01:17:02 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:20:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 212.7 seconds

RetCode: 0

Status:  OK

CheckDir: DeMixT.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:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeMixT_0.99.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeMixT/DESCRIPTION’ ... OK
* this is package ‘DeMixT’ version ‘0.99.9’
* 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 ‘DeMixT’ 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 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
DeMixT          38.210  1.970   3.489
DeMixT_S1       34.435  1.599   3.031
Optimum_KernelC 22.871  1.142   2.069
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeMixT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c DeMixT.c -o DeMixT.o
DeMixT.c:253:26: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
      if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\n", i+1);
                         ^
DeMixT.c:43:9: warning: unused variable 'nthread' [-Wunused-variable]
    int nthread=*thread;
        ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.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 DeMixT.so DeMixT.o init.o registerDynamicSymbol.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (DeMixT)

name	user	system	elapsed
DeMixT	38.210	1.970	3.489
DeMixT_S1	34.435	1.599	3.031
DeMixT_S2	3.325	0.188	0.301
Optimum_KernelC	22.871	1.142	2.069
test.data1.comp1	0.066	0.062	0.022
test.data1.truth	0.024	0.027	0.009
test.data1.y	0.062	0.061	0.021
test.data2.comp1	0.067	0.065	0.020
test.data2.comp2	0.072	0.056	0.021
test.data2.truth	0.002	0.003	0.004
test.data2.y	0.009	0.003	0.011
test.data3.comp1	0.015	0.004	0.018
test.data3.comp2	0.016	0.006	0.021
test.data3.truth	0.002	0.003	0.004
test.data3.y	0.012	0.003	0.015