Package: DeMixT

Version: 1.2.5

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeMixT.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DeMixT_1.2.5.tar.gz

StartedAt: 2020-04-15 02:35:37 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:40:11 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 274.4 seconds

RetCode: 0

Status:  OK

CheckDir: DeMixT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeMixT.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DeMixT_1.2.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DeMixT.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeMixT/DESCRIPTION' ... OK
* this is package 'DeMixT' version '1.2.5'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth',
  'matrixcalc'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'DeMixT' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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_GS: no visible global function definition for 'qchisq'
simulate_2comp: no visible global function definition for 'SimpleList'
simulate_2comp: no visible global function definition for 'DataFrame'
simulate_3comp: no visible global function definition for 'SimpleList'
simulate_3comp: no visible global function definition for 'DataFrame'
Undefined global functions or variables:
  DataFrame SimpleList qchisq
Consider adding
  importFrom("stats", "qchisq")
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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/DeMixT/libs/i386/DeMixT.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/DeMixT/libs/x64/DeMixT.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
DeMixT_S2 380.8   0.03   26.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
DeMixT_S2 386.48   0.02   25.59
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/DeMixT.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DeMixT_1.2.5.tar.gz && rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMixT.buildbin-libdir DeMixT_1.2.5.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DeMixT_1.2.5.zip && rm DeMixT_1.2.5.tar.gz DeMixT_1.2.5.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2747k  100 2747k    0     0  42.3M      0 --:--:-- --:--:-- --:--:-- 44.7M

install for i386

* installing *source* package 'DeMixT' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:265:9: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
         if (nHavepi != 1)  Rprintf("Iteration %d: updating parameters\n", i+1);
         ^
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                             ^
DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                 ^
DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                      ^
DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
           ^
DeMixT.c: In function 'gettumor':
DeMixT.c:587:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:587:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpi':
DeMixT.c:1276:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1276:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getspikeinpi':
DeMixT.c:1303:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
  double obj_old, obj_new;
                  ^
DeMixT.c:1303:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
  double obj_old, obj_new;
         ^
DeMixT.c: In function 'getpiT':
DeMixT.c:1318:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1318:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'Tdemix':
DeMixT.c:191:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
           ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Profile_2D.cpp -o Profile_2D.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DeMixT'
    finding HTML links ... done
    DeMixT                                  html  
    DeMixT_GS                               html  
    DeMixT_S1                               html  
    DeMixT_S2                               html  
    Optimum_KernelC                         html  
    simulate_2comp                          html  
    simulate_3comp                          html  
    test.data.2comp                         html  
    test.data.3comp                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DeMixT' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:265:9: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
         if (nHavepi != 1)  Rprintf("Iteration %d: updating parameters\n", i+1);
         ^
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                             ^
DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                 ^
DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                      ^
DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
           ^
DeMixT.c: In function 'gettumor':
DeMixT.c:587:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:587:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpi':
DeMixT.c:1276:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1276:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getspikeinpi':
DeMixT.c:1303:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
  double obj_old, obj_new;
                  ^
DeMixT.c:1303:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
  double obj_old, obj_new;
         ^
DeMixT.c: In function 'getpiT':
DeMixT.c:1318:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1318:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'Tdemix':
DeMixT.c:191:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
           ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Profile_2D.cpp -o Profile_2D.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/DeMixT.buildbin-libdir/DeMixT/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeMixT' as DeMixT_1.2.5.zip
* DONE (DeMixT)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DeMixT' successfully unpacked and MD5 sums checked