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This page was generated on 2022-03-18 11:07:23 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 522/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DirichletMultinomial 1.37.0  (landing page)
Martin Morgan
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/DirichletMultinomial
git_branch: master
git_last_commit: 13a0c2b
git_last_commit_date: 2021-10-26 12:03:07 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DirichletMultinomial
Version: 1.37.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DirichletMultinomial.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DirichletMultinomial_1.37.0.tar.gz
StartedAt: 2022-03-17 18:56:57 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 18:58:03 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 65.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DirichletMultinomial.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DirichletMultinomial.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DirichletMultinomial_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DirichletMultinomial.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DirichletMultinomial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DirichletMultinomial' version '1.37.0'
* 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 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 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/DirichletMultinomial/libs/x64/DirichletMultinomial.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
* 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/DirichletMultinomial.Rcheck/00check.log'
for details.



Installation output

DirichletMultinomial.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DirichletMultinomial' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dirichlet_fit.c -o dirichlet_fit.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
             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]
             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]
     int signum, status;
                 ^~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o DirichletMultinomial.dll tmp.def R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-DirichletMultinomial/00new/DirichletMultinomial/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DirichletMultinomial'
    finding HTML links ... done
    DMN-class                               html  
    DMNGroup-class                          html  
    finding level-2 HTML links ... done

    DirichletMultinomial-package            html  
    cvdmngroup                              html  
    dataobjects                             html  
    dmn                                     html  
    dmngroup                                html  
    fitted                                  html  
    heatmapdmn                              html  
    roc                                     html  
    util                                    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
* DONE (DirichletMultinomial)
Making 'packages.html' ... done

Tests output


Example timings

DirichletMultinomial.Rcheck/DirichletMultinomial-Ex.timings

nameusersystemelapsed
DMN-class0.000.020.01
DMNGroup-class0.030.000.03
cvdmngroup000
dataobjects0.020.000.01
dmn0.010.000.02
dmngroup000
fitted0.110.000.11
heatmapdmn0.050.000.05
roc0.170.020.18
util0.020.000.02