Package: DeMixT

Version: 1.3.1

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_1.3.1.tar.gz

StartedAt: 2020-01-16 03:38:25 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:42:53 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 267.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DeMixT.Rcheck

Warnings: 1

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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_1.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DeMixT.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.1’
* 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 ... NOTE
DeMixT_S1: no visible binding for global variable ‘sd’
DeMixT_S2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
DeMixT          37.996  1.048   3.565
DeMixT_S1       32.786  0.806   3.115
Optimum_KernelC 17.715  0.360  17.525
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Located more than one ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘demixt’: ‘demixt.html’ (NA bytes), ‘demixt.pdf’ (NA bytes)
Package vignette without corresponding single PDF/HTML:
   ‘demixt.Rmd’

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DeMixT.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 DeMixT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c DeMixT.c -o DeMixT.o
DeMixT.c:255:26: 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:436:21: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
  if (nHavepi != 1) Rprintf("There are  %d normals and %d tumors\n", fNorm,intx);
                    ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/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	37.996	1.048	3.565
DeMixT_S1	32.786	0.806	3.115
DeMixT_S2	4.236	0.231	0.380
Optimum_KernelC	17.715	0.360	17.525
test.data1.comp1	0.029	0.010	0.039
test.data1.truth	0.004	0.004	0.007
test.data1.y	0.013	0.004	0.018
test.data2.comp1	0.014	0.004	0.017
test.data2.comp2	0.014	0.004	0.018
test.data2.truth	0.003	0.003	0.006
test.data2.y	0.013	0.004	0.017
test.data3.comp1	0.019	0.006	0.025
test.data3.comp2	0.018	0.007	0.025
test.data3.truth	0.003	0.003	0.006
test.data3.y	0.046	0.009	0.055