Dongjun Chung
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GGPA |
| Branch: RELEASE_3_11 |
| Last Commit: 7ceda35 |
| Last Changed Date: 2020-04-27 15:35:52 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:41 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GGPA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 730/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GGPA 1.0.0 Dongjun Chung
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: GGPA |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GGPA_1.0.0.tar.gz |
| StartedAt: 2020-10-17 04:30:52 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:40:29 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 576.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GGPA.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GGPA_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GGPA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.0'
* 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 77.31 3.13 80.45
GGPA-internal 42.58 1.22 43.80
assoc 40.78 1.81 42.59
GGPA-class 39.00 1.97 40.97
GGPA 36.45 1.48 37.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GGPA-package 66.98 1.83 68.83
GGPA-class 39.00 1.67 40.74
GGPA 39.22 1.22 40.44
assoc 37.23 0.97 38.25
GGPA-internal 34.30 0.83 35.15
* 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-3.11-bioc/meat/GGPA.Rcheck/00check.log'
for details.
GGPA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GGPA_1.0.0.tar.gz && rm -rf GGPA.buildbin-libdir && mkdir GGPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GGPA.buildbin-libdir GGPA_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GGPA_1.0.0.zip && rm GGPA_1.0.0.tar.gz GGPA_1.0.0.zip
###
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% 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 36.2M 0 --:--:-- --:--:-- --:--:-- 39.0M
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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/GGPA.buildbin-libdir/GGPA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGPA' as GGPA_1.0.0.zip
* DONE (GGPA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GGPA' successfully unpacked and MD5 sums checked
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GGPA.Rcheck/examples_i386/GGPA-Ex.timings
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GGPA.Rcheck/examples_x64/GGPA-Ex.timings
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