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This page was generated on 2022-08-15 13:20:07 -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 nebbiolo1


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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DeMixT_1.12.0.tar.gz
StartedAt: 2022-08-14 19:34:05 -0400 (Sun, 14 Aug 2022)
EndedAt: 2022-08-14 19:37:25 -0400 (Sun, 14 Aug 2022)
EllapsedTime: 200.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DeMixT.Rcheck
Warnings: 1

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/DeMixT.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 for sufficient/correct file permissions ... 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 ‘dprintf’? [-Wimplicit-function-declaration]
See ‘/home/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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
DeMixT_S2 107.052  0.094  55.386
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/DeMixT.Rcheck/00check.log’
for details.



Installation output

DeMixT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL DeMixT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c DeMixT.c -o DeMixT.o
DeMixT.c: In function ‘Tdemix’:
DeMixT.c:268:28: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
  268 |         if (nHavepi != 1)  Rprintf("Iteration %d: updating parameters\n", i+1);
      |                            ^~~~~~~
      |                            dprintf
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: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:
/usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here
  542 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Profile_2D.cpp -o Profile_2D.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)

Tests output


Example timings

DeMixT.Rcheck/DeMixT-Ex.timings

nameusersystemelapsed
DeMixT0.0010.0040.006
DeMixT_DE0.0030.0000.003
DeMixT_GS0.0020.0000.003
DeMixT_S2107.052 0.094 55.386
Optimum_KernelC0.0000.0020.002
simulate_2comp0.1130.0370.150
simulate_3comp0.1050.0400.145