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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 838/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGPA 1.17.0  (landing page)
Dongjun Chung
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GGPA
git_branch: devel
git_last_commit: 8efbddb
git_last_commit_date: 2024-04-30 11:23:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for GGPA on palomino4

To the developers/maintainers of the GGPA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GGPA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GGPA
Version: 1.17.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GGPA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GGPA_1.17.0.tar.gz
StartedAt: 2024-06-10 03:19:41 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:26:24 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 402.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GGPA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GGPA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GGPA_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GGPA.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GGPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GGPA' version '1.17.0'
* 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 'GGPA' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code 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 ... NOTE
Packages in Depends field not imported from:
  'network' 'scales' 'sna'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... NOTE
checkRd: (-1) GGPA-class.Rd:37: Lost braces; missing escapes or markup?
    37 |     Nodes i and j are connected if the posterior probability of E_{ij} > \code{pCutoff} and the posterior probability of beta_{ij} > \code{betaCI}. }
       |                                                                   ^
checkRd: (-1) GGPA-class.Rd:37: Lost braces; missing escapes or markup?
    37 |     Nodes i and j are connected if the posterior probability of E_{ij} > \code{pCutoff} and the posterior probability of beta_{ij} > \code{betaCI}. }
       |                                                                                                                               ^
* 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
File 'GGPA/libs/x64/GGPA.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Object: '3_Param.o'

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 nor [v]sprintf.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GGPA-package  74.86   1.00   75.87
GGPA-class    40.75   3.44   44.58
assoc         37.27   0.63   37.92
GGPA          37.36   0.46   37.88
GGPA-internal 36.97   0.47   37.43
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/GGPA.Rcheck/00check.log'
for details.


Installation output

GGPA.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GGPA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'GGPA' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c 1_Main.cpp -o 1_Main.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c 3_Param.cpp -o 3_Param.o
3_Param.cpp: In member function 'void CParam::S6_G_beta_ij(CData&)':
3_Param.cpp:334:40: warning: 'logP_numer' may be used uninitialized [-Wmaybe-uninitialized]
  334 |           if ( w_prop > 0 ) logP_numer = logP_numer - log(w_prop) ; // f(G^q) // if w_prop=0, let 1/w_prop = 1, so that log(w_prop) = 0
      |                             ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
3_Param.cpp:226:10: note: 'logP_numer' was declared here
  226 |   double logP_numer, logP_denom ;
      |          ^~~~~~~~~~
3_Param.cpp:335:39: warning: 'logP_denom' may be used uninitialized [-Wmaybe-uninitialized]
  335 |           if ( w_cur > 0 ) logP_denom = logP_denom - log(w_cur) ; // f(G) // if w_cur=0, let 1/w_cur = 1, so that log(w_cur) = 0
      |                            ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
3_Param.cpp:226:22: note: 'logP_denom' was declared here
  226 |   double logP_numer, logP_denom ;
      |                      ^~~~~~~~~~
3_Param.cpp:350:47: warning: 'normC_prop' may be used uninitialized [-Wmaybe-uninitialized]
  350 |     Beta = Beta_prop ; G_mat = G_prop ; normC = normC_prop ;
      |                                         ~~~~~~^~~~~~~~~~~~
3_Param.cpp:227:10: note: 'normC_prop' was declared here
  227 |   double normC_prop ;
      |          ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Gibbs_e_it_no_ann.cpp -o Gibbs_e_it_no_ann.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -s -static-libgcc -o GGPA.dll tmp.def 1_Main.o 3_Param.o Gibbs_e_it_no_ann.o RcppExports.o -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-GGPA/00new/GGPA/libs/x64
** R
** data
** 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 (GGPA)

Tests output


Example timings

GGPA.Rcheck/GGPA-Ex.timings

nameusersystemelapsed
GGPA-class40.75 3.4444.58
GGPA-internal36.97 0.4737.43
GGPA-package74.86 1.0075.87
GGPA37.36 0.4637.88
assoc37.27 0.6337.92
simulation0.440.440.88