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CHECK report for DeMixT on tokay2

This page was generated on 2019-10-16 12:43:51 -0400 (Wed, 16 Oct 2019).

Package 415/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeMixT 1.0.4
Zeya Wang , Fan Gao
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/DeMixT
Branch: RELEASE_3_9
Last Commit: 70e4f40
Last Changed Date: 2019-08-15 01:33:35 -0400 (Thu, 15 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DeMixT
Version: 1.0.4
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeMixT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DeMixT_1.0.4.tar.gz
StartedAt: 2019-10-16 03:09:43 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:15:32 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 349.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DeMixT.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeMixT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DeMixT_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.0.4'
* 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 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
* 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_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 compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
DeMixT          109.98   0.05    9.19
DeMixT_S1       100.46   0.03    8.25
Optimum_KernelC  54.91   0.03   54.94
DeMixT_S2        10.28   0.06    0.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
DeMixT          110.31   0.02    9.00
DeMixT_S1        99.36   0.01    8.02
Optimum_KernelC  57.46   0.00   57.47
DeMixT_S2        10.39   0.02    0.89
* 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', 'demixt.pdf'
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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck/00check.log'
for details.

Installation output

DeMixT.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DeMixT_1.0.4.tar.gz && rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMixT.buildbin-libdir DeMixT_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DeMixT_1.0.4.zip && rm DeMixT_1.0.4.tar.gz DeMixT_1.0.4.zip
###
##############################################################################
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  % 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 1447k  100 1447k    0     0  19.8M      0 --:--:-- --:--:-- --:--:-- 22.0M

install for i386

* installing *source* package 'DeMixT' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:255:7: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
       if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\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:542:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:542:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpi':
DeMixT.c:1231:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1231:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpiT':
DeMixT.c:1261:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1261:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'Tdemix':
DeMixT.c:190:11: 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/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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_S1                               html  
    DeMixT_S2                               html  
    Optimum_KernelC                         html  
    test.data1.comp1                        html  
    test.data1.truth                        html  
    test.data1.y                            html  
    test.data2.comp1                        html  
    test.data2.comp2                        html  
    test.data2.truth                        html  
    test.data2.y                            html  
    test.data3.comp1                        html  
    test.data3.comp2                        html  
    test.data3.truth                        html  
    test.data3.y                            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-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:255:7: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
       if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\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:542:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:542:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpi':
DeMixT.c:1231:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1231:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'getpiT':
DeMixT.c:1261:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
                     ^
DeMixT.c:1261:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
     double obj_old, obj_new;
            ^
DeMixT.c: In function 'Tdemix':
DeMixT.c:190:11: 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/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DeMixT.buildbin-libdir/DeMixT/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeMixT' as DeMixT_1.0.4.zip
* DONE (DeMixT)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DeMixT' successfully unpacked and MD5 sums checked

Tests output

Example timings

DeMixT.Rcheck/examples_i386/DeMixT-Ex.timings

nameusersystemelapsed
DeMixT109.98 0.05 9.19
DeMixT_S1100.46 0.03 8.25
DeMixT_S210.28 0.06 0.87
Optimum_KernelC54.91 0.0354.94
test.data1.comp10.020.020.03
test.data1.truth0.000.020.01
test.data1.y0.010.010.04
test.data2.comp10.020.000.01
test.data2.comp20.010.020.03
test.data2.truth0.000.010.02
test.data2.y0.030.000.03
test.data3.comp10.020.020.03
test.data3.comp20.020.010.03
test.data3.truth0.000.020.02
test.data3.y0.010.020.03

DeMixT.Rcheck/examples_x64/DeMixT-Ex.timings

nameusersystemelapsed
DeMixT110.31 0.02 9.00
DeMixT_S199.36 0.01 8.02
DeMixT_S210.39 0.02 0.89
Optimum_KernelC57.46 0.0057.47
test.data1.comp10.040.000.03
test.data1.truth000
test.data1.y0.010.010.03
test.data2.comp10.020.000.02
test.data2.comp20.010.000.01
test.data2.truth0.020.000.02
test.data2.y0.010.020.03
test.data3.comp10.020.000.02
test.data3.comp20.020.020.03
test.data3.truth0.010.000.01
test.data3.y0.000.010.02