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BioC 3.2: CHECK report for GeneNetworkBuilder on zin1

This page was generated on 2015-08-24 10:48:53 -0700 (Mon, 24 Aug 2015).

Package 391/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.11.0
Jianhong Ou
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneNetworkBuilder
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneNetworkBuilder
Version: 1.11.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GeneNetworkBuilder_1.11.0.tar.gz
StartedAt: 2015-08-24 00:04:26 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:05:07 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 41.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneNetworkBuilder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GeneNetworkBuilder_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GeneNetworkBuilder.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneNetworkBuilder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneNetworkBuilder’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GeneNetworkBuilder’ can be installed ... [8s/8s] 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
* 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 loading without being on the library search path ... 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’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log’
for details.


GeneNetworkBuilder.Rcheck/00install.out:

* installing *source* package ‘GeneNetworkBuilder’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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]
   for (int i=0; i<n->chd->size(); i++) {
                                ^
geneTree.cpp: In member function ‘std::vector<node*> GTree::Travel()’:
geneTree.cpp:207:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<(*cur->chd).size(); i++) {
                                     ^
geneTree.cpp: In member function ‘void GTree::verifyFilter(int)’:
geneTree.cpp:275:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<(*cur->chd).size(); i++) {
                                      ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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]
    for (int i=0; i<(*(*nit)->par).size(); i++) {
                                        ^
nodefilter.cpp:86:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<parents.size(); i++) {
                                  ^
nodefilter.cpp:94:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int i=0; i<(*(*nit)->chd).size(); i++) {
                                            ^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o GeneNetworkBuilder.so geneTree.o nodefilter.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/GeneNetworkBuilder.Rcheck/GeneNetworkBuilder/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneNetworkBuilder)

GeneNetworkBuilder.Rcheck/GeneNetworkBuilder-Ex.timings:

nameusersystemelapsed
buildNetwork0.6210.0160.637
ce.IDsMap0.5540.0040.558
ce.interactionmap0.040.000.04
ce.mapIDs0.4000.0000.399
ce.miRNA.map0.0040.0000.004
convertID0.7380.0000.738
example.data0.0460.0000.049
filterNetwork2.5370.0162.551
hs.IDsMap0.2270.0000.227
hs.interactionmap0.0970.0000.097
hs.mapIDs0.0580.0000.058
hs.miRNA.map0.0040.0000.004
polishNetwork1.9960.0082.005
uniqueExprsData0.4320.0040.436