Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.13: CHECK report for GeneNetworkBuilder on moscato1

This page was generated on 2014-04-05 09:50:58 -0700 (Sat, 05 Apr 2014).

Package 286/750HostnameOS / ArchBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.4.1
Jianhong Ou
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GeneNetworkBuilder
Last Changed Rev: 86057 / Revision: 88450
Last Changed Date: 2014-02-04 10:03:14 -0800 (Tue, 04 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GeneNetworkBuilder
Version: 1.4.1
Command: rm -rf GeneNetworkBuilder.buildbin-libdir && mkdir GeneNetworkBuilder.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneNetworkBuilder.buildbin-libdir GeneNetworkBuilder_1.4.1.tar.gz >GeneNetworkBuilder-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GeneNetworkBuilder.buildbin-libdir --install="check:GeneNetworkBuilder-install.out" --force-multiarch --no-vignettes --timings GeneNetworkBuilder_1.4.1.tar.gz && mv GeneNetworkBuilder.buildbin-libdir/* GeneNetworkBuilder.Rcheck/ && rmdir GeneNetworkBuilder.buildbin-libdir
StartedAt: 2014-04-05 04:04:53 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:06:58 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 124.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneNetworkBuilder.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GeneNetworkBuilder.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.4.1'
* 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 'GeneNetworkBuilder' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'graph'
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'checkCName' 'checkMCName' 'checkMap' 'getMax' 'getMedian' 'getMin'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 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 'D:/biocbld/bbs-2.13-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x64/GeneNetworkBuilder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [14s] OK
** running examples for arch 'x64' ... [19s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
filterNetwork 6.77   0.06    6.83
polishNetwork 5.30   0.00    5.30
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [1s]
 [2s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [2s]
 [2s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RBGL'
* 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log'
for details.

GeneNetworkBuilder.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneNetworkBuilder' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c geneTree.cpp -o geneTree.o
geneTree.cpp: In member function 'void GTree::ChangeTolerance(node*)':
geneTree.cpp:112:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
geneTree.cpp: In member function 'std::vector<node*> GTree::Travel()':
geneTree.cpp:207:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
geneTree.cpp: In member function 'void GTree::verifyFilter(int)':
geneTree.cpp:275:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c nodefilter.cpp -o nodefilter.o
nodefilter.cpp: In function 'SEXPREC* filterNodes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
nodefilter.cpp:76:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
nodefilter.cpp:86:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
nodefilter.cpp:94:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -shared -s -static-libgcc -o GeneNetworkBuilder.dll tmp.def geneTree.o nodefilter.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GeneNetworkBuilder' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c geneTree.cpp -o geneTree.o
geneTree.cpp: In member function 'void GTree::ChangeTolerance(node*)':
geneTree.cpp:112:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
geneTree.cpp: In member function 'std::vector<node*> GTree::Travel()':
geneTree.cpp:207:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
geneTree.cpp: In member function 'void GTree::verifyFilter(int)':
geneTree.cpp:275:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c nodefilter.cpp -o nodefilter.o
nodefilter.cpp: In function 'SEXPREC* filterNodes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
nodefilter.cpp:76:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
nodefilter.cpp:86:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
nodefilter.cpp:94:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -shared -s -static-libgcc -o GeneNetworkBuilder.dll tmp.def geneTree.o nodefilter.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneNetworkBuilder' as GeneNetworkBuilder_1.4.1.zip
* DONE (GeneNetworkBuilder)

GeneNetworkBuilder.Rcheck/examples_i386/GeneNetworkBuilder-Ex.timings:

nameusersystemelapsed
buildNetwork0.690.000.68
ce.IDsMap0.920.000.92
ce.interactionmap0.080.000.08
ce.mapIDs0.430.010.45
ce.miRNA.map0.040.000.04
convertID0.780.020.80
example.data0.200.000.21
filterNetwork4.120.004.12
hs.IDsMap0.250.030.28
hs.interactionmap0.280.000.29
hs.mapIDs0.050.000.05
hs.miRNA.map0.010.000.02
polishNetwork3.510.023.54
uniqueExprsData0.570.000.58

GeneNetworkBuilder.Rcheck/examples_x64/GeneNetworkBuilder-Ex.timings:

nameusersystemelapsed
buildNetwork1.170.021.18
ce.IDsMap0.770.000.86
ce.interactionmap0.050.000.05
ce.mapIDs0.670.000.67
ce.miRNA.map0.040.000.04
convertID1.280.001.28
example.data0.130.000.13
filterNetwork6.770.066.83
hs.IDsMap0.190.000.18
hs.interactionmap0.110.000.11
hs.mapIDs0.110.000.11
hs.miRNA.map0.010.000.02
polishNetwork5.30.05.3
uniqueExprsData0.590.000.60