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This page was generated on 2022-08-15 13:21:19 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DeMixT on palomino3


To the developers/maintainers of the DeMixT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeMixT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 504/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeMixT 1.12.0  (landing page)
Shuai Guo
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/DeMixT
git_branch: RELEASE_3_15
git_last_commit: f7bf7d2
git_last_commit_date: 2022-04-26 11:54:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: DeMixT
Version: 1.12.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeMixT.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DeMixT_1.12.0.tar.gz
StartedAt: 2022-08-15 00:17:20 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 00:23:00 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 341.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DeMixT.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeMixT.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DeMixT_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/DeMixT.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DeMixT/DESCRIPTION' ... OK
* this is package 'DeMixT' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth',
  'matrixcalc', 'rmarkdown'
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 ... WARNING
Found the following significant warnings:
  DeMixT.c:268:28: warning: implicit declaration of function 'Rprintf'; did you mean 'wprintf'? [-Wimplicit-function-declaration]
See 'F:/biocbuild/bbs-3.15-bioc/meat/DeMixT.Rcheck/00install.out' for details.
* 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_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 LazyData ... 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/DeMixT/libs/x64/DeMixT.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
DeMixT_S2 271.93   0.03  138.69
* 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 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/DeMixT.Rcheck/00check.log'
for details.



Installation output

DeMixT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DeMixT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DeMixT' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:268:28: warning: implicit declaration of function 'Rprintf'; did you mean 'wprintf'? [-Wimplicit-function-declaration]
  268 |         if (nHavepi != 1)  Rprintf("Iteration %d: updating parameters\n", i+1);
      |                            ^~~~~~~
      |                            wprintf
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
   36 |   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]
   36 |   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]
   36 |   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]
   36 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |           ^~~~~~~~
DeMixT.c: In function 'gettumor':
DeMixT.c:590:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
  590 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:590:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
  590 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function 'getpi':
DeMixT.c:1279:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
 1279 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:1279:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
 1279 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function 'getspikeinpi':
DeMixT.c:1306:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
 1306 |  double obj_old, obj_new;
      |                  ^~~~~~~
DeMixT.c:1306:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
 1306 |  double obj_old, obj_new;
      |         ^~~~~~~
DeMixT.c: In function 'getpiT':
DeMixT.c:1321:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
 1321 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:1321:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
 1321 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function 'Tdemix':
DeMixT.c:194:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
  194 |         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
      |           ^
DeMixT.c:239:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  239 |   CD = calloc(intx ,sizeof(double *));
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here
  535 |   void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
      |                 ^~~~~~
DeMixT.c:93:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   93 |   FD = calloc(nS ,sizeof(double *));
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here
  535 |   void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
      |                 ^~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Profile_2D.cpp -o Profile_2D.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-DeMixT/00new/DeMixT/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DeMixT)

Tests output


Example timings

DeMixT.Rcheck/DeMixT-Ex.timings

nameusersystemelapsed
DeMixT0.000.020.02
DeMixT_DE0.000.000.08
DeMixT_GS000
DeMixT_S2271.93 0.03138.69
Optimum_KernelC0.000.020.01
simulate_2comp0.150.030.17
simulate_3comp0.120.010.14