Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:03 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 DirichletMultinomial on nebbiolo2


To the developers/maintainers of the DirichletMultinomial package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DirichletMultinomial.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 544/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DirichletMultinomial 1.40.0  (landing page)
Martin Morgan
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/DirichletMultinomial
git_branch: RELEASE_3_16
git_last_commit: 200176f
git_last_commit_date: 2022-11-01 11:06:58 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DirichletMultinomial
Version: 1.40.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DirichletMultinomial.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DirichletMultinomial_1.40.0.tar.gz
StartedAt: 2023-04-10 20:20:44 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:21:38 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 54.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DirichletMultinomial.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DirichletMultinomial.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DirichletMultinomial_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DirichletMultinomial.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DirichletMultinomial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DirichletMultinomial’ version ‘1.40.0’
* 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 ‘DirichletMultinomial’ 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 loading without being on the library search path ... 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 ... OK
* 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 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DirichletMultinomial.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DirichletMultinomial.Rcheck/00check.log’
for details.



Installation output

DirichletMultinomial.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DirichletMultinomial
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DirichletMultinomial’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c dirichlet_fit.c -o dirichlet_fit.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c dirichlet_fit_main.c -o dirichlet_fit_main.o
dirichlet_fit_main.c: In function ‘hessian’:
dirichlet_fit_main.c:391:34: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  391 |             adCJK0[j] += adPi[i] * n ? gsl_sf_psi(adAlpha[j] + n) : dPsiAlpha;
      |                          ~~~~~~~~^~~
dirichlet_fit_main.c:393:33: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  393 |             adCJK[j] += adPi[i] * n ? gsl_sf_psi_1(adAlpha[j] + n): dPsi1Alpha;
      |                         ~~~~~~~~^~~
dirichlet_fit_main.c: In function ‘dirichlet_fit_main’:
dirichlet_fit_main.c:542:17: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
  542 |     int signum, status;
      |                 ^~~~~~
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-DirichletMultinomial/00new/DirichletMultinomial/libs
** R
** data
** 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 (DirichletMultinomial)

Tests output


Example timings

DirichletMultinomial.Rcheck/DirichletMultinomial-Ex.timings

nameusersystemelapsed
DMN-class0.0160.0000.016
DMNGroup-class0.0090.0010.008
cvdmngroup0.0010.0020.003
dataobjects0.0100.0010.012
dmn0.0150.0000.015
dmngroup0.0050.0010.004
fitted0.0960.0030.100
heatmapdmn0.0480.0000.047
roc0.1760.0000.176
util0.0160.0000.016