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This page was generated on 2022-01-21 13:06:24 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 GGPA on tokay2


To the developers/maintainers of the GGPA package:
- Please 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 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 778/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGPA 1.6.0  (landing page)
Dongjun Chung
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/GGPA
git_branch: RELEASE_3_14
git_last_commit: 59e21a3
git_last_commit_date: 2021-10-26 12:58:56 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GGPA
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GGPA_1.6.0.tar.gz
StartedAt: 2022-01-20 20:42:41 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:51:34 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 533.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GGPA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GGPA_1.6.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GGPA.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GGPA' version '1.6.0'
* 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
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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
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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GGPA-package  74.95   2.31   77.34
GGPA-internal 37.25   1.19   38.72
GGPA-class    35.95   2.25   38.28
GGPA          35.97   1.25   37.25
assoc         36.05   1.00   37.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GGPA-package  69.06   1.11   70.18
assoc         37.04   0.55   37.58
GGPA          35.48   0.44   35.92
GGPA-internal 34.33   0.64   34.98
GGPA-class    33.32   1.17   34.50
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GGPA.Rcheck/00check.log'
for details.



Installation output

GGPA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GGPA_1.6.0.tar.gz && rm -rf GGPA.buildbin-libdir && mkdir GGPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GGPA.buildbin-libdir GGPA_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GGPA_1.6.0.zip && rm GGPA_1.6.0.tar.gz GGPA_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3161k  100 3161k    0     0  3867k      0 --:--:-- --:--:-- --:--:-- 3873k

install for i386

* installing *source* package 'GGPA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c 1_Main.cpp -o 1_Main.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/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:350:47: warning: 'normC_prop' may be used uninitialized in this function [-Wmaybe-uninitialized]
     Beta = Beta_prop ; G_mat = G_prop ; normC = normC_prop ;
                                         ~~~~~~^~~~~~~~~~~~
3_Param.cpp:335:32: warning: 'logP_denom' may be used uninitialized in this function [-Wmaybe-uninitialized]
    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:334:33: warning: 'logP_numer' may be used uninitialized in this function [-Wmaybe-uninitialized]
    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
                      ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Gibbs_e_it_no_ann.cpp -o Gibbs_e_it_no_ann.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GGPA.dll tmp.def 1_Main.o 3_Param.o Gibbs_e_it_no_ann.o RcppExports.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GGPA.buildbin-libdir/00LOCK-GGPA/00new/GGPA/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GGPA'
    finding HTML links ... done
    GGPA-class                              html  
    GGPA-internal                           html  
    GGPA-package                            html  
    GGPA                                    html  
    assoc                                   html  
    simulation                              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

install for x64

* installing *source* package 'GGPA' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c 1_Main.cpp -o 1_Main.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/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:350:47: warning: 'normC_prop' may be used uninitialized in this function [-Wmaybe-uninitialized]
     Beta = Beta_prop ; G_mat = G_prop ; normC = normC_prop ;
                                         ~~~~~~^~~~~~~~~~~~
3_Param.cpp:335:32: warning: 'logP_denom' may be used uninitialized in this function [-Wmaybe-uninitialized]
    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:334:33: warning: 'logP_numer' may be used uninitialized in this function [-Wmaybe-uninitialized]
    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
                      ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Gibbs_e_it_no_ann.cpp -o Gibbs_e_it_no_ann.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GGPA.dll tmp.def 1_Main.o 3_Param.o Gibbs_e_it_no_ann.o RcppExports.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GGPA.buildbin-libdir/GGPA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGPA' as GGPA_1.6.0.zip
* DONE (GGPA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GGPA' successfully unpacked and MD5 sums checked

Tests output


Example timings

GGPA.Rcheck/examples_i386/GGPA-Ex.timings

nameusersystemelapsed
GGPA-class35.95 2.2538.28
GGPA-internal37.25 1.1938.72
GGPA-package74.95 2.3177.34
GGPA35.97 1.2537.25
assoc36.05 1.0037.07
simulation0.410.060.47

GGPA.Rcheck/examples_x64/GGPA-Ex.timings

nameusersystemelapsed
GGPA-class33.32 1.1734.50
GGPA-internal34.33 0.6434.98
GGPA-package69.06 1.1170.18
GGPA35.48 0.4435.92
assoc37.04 0.5537.58
simulation0.310.120.44