Zeya Wang
| 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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:17:49 -0400 (Wed, 16 Oct 2019).
| Package 415/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DeMixT 1.0.4 Zeya Wang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DeMixT |
| Version: 1.0.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DeMixT_1.0.4.tar.gz |
| StartedAt: 2019-10-16 01:04:49 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:08:11 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 202.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DeMixT.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DeMixT_1.0.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.4’
* 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 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DeMixT 89.641 0.074 10.838
DeMixT_S1 80.827 0.064 10.458
Optimum_KernelC 36.919 0.024 36.953
DeMixT_S2 8.223 0.040 1.169
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck/00check.log’
for details.
DeMixT.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DeMixT
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DeMixT.c -o DeMixT.o
DeMixT.c: In function ‘Tdemix’:
DeMixT.c:255:26: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
if (nHavepi != 1) Rprintf("Iteration %d: updating purities\n", i+1);
^~~~~~~
dprintf
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));
^
DeMixT.c:89:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
FD = calloc(nS ,sizeof(double *));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:0:
/usr/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here
extern void *calloc (size_t __nmemb, size_t __size)
^~~~~~
DeMixT.c:228:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
CD = calloc(intx ,sizeof(double *));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:0:
/usr/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here
extern void *calloc (size_t __nmemb, size_t __size)
^~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o DeMixT.so DeMixT.o init.o registerDynamicSymbol.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)
DeMixT.Rcheck/DeMixT-Ex.timings
| name | user | system | elapsed | |
| DeMixT | 89.641 | 0.074 | 10.838 | |
| DeMixT_S1 | 80.827 | 0.064 | 10.458 | |
| DeMixT_S2 | 8.223 | 0.040 | 1.169 | |
| Optimum_KernelC | 36.919 | 0.024 | 36.953 | |
| test.data1.comp1 | 0.028 | 0.012 | 0.041 | |
| test.data1.truth | 0.002 | 0.000 | 0.002 | |
| test.data1.y | 0.009 | 0.004 | 0.013 | |
| test.data2.comp1 | 0.013 | 0.000 | 0.013 | |
| test.data2.comp2 | 0.012 | 0.000 | 0.014 | |
| test.data2.truth | 0.000 | 0.002 | 0.002 | |
| test.data2.y | 0.006 | 0.002 | 0.008 | |
| test.data3.comp1 | 0.011 | 0.000 | 0.010 | |
| test.data3.comp2 | 0.011 | 0.000 | 0.011 | |
| test.data3.truth | 0.001 | 0.000 | 0.001 | |
| test.data3.y | 0.008 | 0.004 | 0.012 | |