Jianhong Ou
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneNetworkBuilder |
| Branch: RELEASE_3_8 |
| Last Commit: c100f80 |
| Last Changed Date: 2019-04-08 18:41:34 -0400 (Mon, 08 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:19 -0400 (Sat, 13 Apr 2019).
| Package 600/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneNetworkBuilder 1.24.1 Jianhong Ou
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GeneNetworkBuilder |
| Version: 1.24.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneNetworkBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneNetworkBuilder_1.24.1.tar.gz |
| StartedAt: 2019-04-13 02:28:16 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:30:43 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 146.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneNetworkBuilder.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneNetworkBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneNetworkBuilder_1.24.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneNetworkBuilder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneNetworkBuilder' version '1.24.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'GeneNetworkBuilder' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 2.8Mb
htmlwidgets 1.8Mb
libs 1.5Mb
* 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 ... 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
browseNetwork 2.3 0.14 5.13
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log'
for details.
GeneNetworkBuilder.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GeneNetworkBuilder_1.24.1.tar.gz && rm -rf GeneNetworkBuilder.buildbin-libdir && mkdir GeneNetworkBuilder.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneNetworkBuilder.buildbin-libdir GeneNetworkBuilder_1.24.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GeneNetworkBuilder_1.24.1.zip && rm GeneNetworkBuilder_1.24.1.tar.gz GeneNetworkBuilder_1.24.1.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 4145k 100 4145k 0 0 47.4M 0 --:--:-- --:--:-- --:--:-- 49.9M
install for i386
* installing *source* package 'GeneNetworkBuilder' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c geneTree.cpp -o geneTree.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c nodefilter.cpp -o nodefilter.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GeneNetworkBuilder.dll tmp.def geneTree.o nodefilter.o registerDynamicSymbol.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneNetworkBuilder'
finding HTML links ... done
GeneNetworkBuilder-package html
browseNetwork-shiny html
browseNetwork html
buildNetwork html
ce.IDsMap html
ce.interactionmap html
ce.mapIDs html
ce.miRNA.map html
convertID html
example.data html
exportNetwork html
filterNetwork html
hs.IDsMap html
hs.interactionmap html
hs.mapIDs html
hs.miRNA.map html
networkFromGenes html
polishNetwork html
saveXGMML html
uniqueExprsData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GeneNetworkBuilder' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c geneTree.cpp -o geneTree.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c nodefilter.cpp -o nodefilter.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GeneNetworkBuilder.dll tmp.def geneTree.o nodefilter.o registerDynamicSymbol.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneNetworkBuilder' as GeneNetworkBuilder_1.24.1.zip
* DONE (GeneNetworkBuilder)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GeneNetworkBuilder' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GeneNetworkBuilder.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GeneNetworkBuilder") || stop("unable to load Package:GeneNetworkBuilder")
Loading required package: GeneNetworkBuilder
Loading required package: Rcpp
[1] TRUE
> BiocGenerics:::testPackage("GeneNetworkBuilder")
RUNIT TEST PROTOCOL -- Sat Apr 13 02:30:38 2019
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
GeneNetworkBuilder RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.39 0.14 1.53
|
GeneNetworkBuilder.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GeneNetworkBuilder") || stop("unable to load Package:GeneNetworkBuilder")
Loading required package: GeneNetworkBuilder
Loading required package: Rcpp
[1] TRUE
> BiocGenerics:::testPackage("GeneNetworkBuilder")
RUNIT TEST PROTOCOL -- Sat Apr 13 02:30:39 2019
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
GeneNetworkBuilder RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.00 0.07 1.07
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GeneNetworkBuilder.Rcheck/examples_i386/GeneNetworkBuilder-Ex.timings
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GeneNetworkBuilder.Rcheck/examples_x64/GeneNetworkBuilder-Ex.timings
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