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BioC 3.4: CHECK report for R3CPET on tokay1

This page was generated on 2017-04-15 16:19:55 -0400 (Sat, 15 Apr 2017).

Package 989/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R3CPET 1.6.0
Mohamed Nadhir Djekidel
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/R3CPET
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: R3CPET
Version: 1.6.0
Command: rm -rf R3CPET.buildbin-libdir R3CPET.Rcheck && mkdir R3CPET.buildbin-libdir R3CPET.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R3CPET.buildbin-libdir R3CPET_1.6.0.tar.gz >R3CPET.Rcheck\00install.out 2>&1 && cp R3CPET.Rcheck\00install.out R3CPET-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=R3CPET.buildbin-libdir --install="check:R3CPET-install.out" --force-multiarch --no-vignettes --timings R3CPET_1.6.0.tar.gz
StartedAt: 2017-04-15 00:18:45 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:25:31 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 406.6 seconds
RetCode: 0
Status:  OK  
CheckDir: R3CPET.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf R3CPET.buildbin-libdir R3CPET.Rcheck && mkdir R3CPET.buildbin-libdir R3CPET.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R3CPET.buildbin-libdir R3CPET_1.6.0.tar.gz >R3CPET.Rcheck\00install.out 2>&1 && cp R3CPET.Rcheck\00install.out R3CPET-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=R3CPET.buildbin-libdir --install="check:R3CPET-install.out" --force-multiarch --no-vignettes --timings R3CPET_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/R3CPET.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R3CPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R3CPET' 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 'R3CPET' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
    libs      1.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GetClusterInfo: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
.GetClusterInfo: no visible global function definition for 'toTable'
.GetClusterInfo: no visible binding for global variable
  'org.Hs.egUCSCKG'
.GetClusterInfo: no visible global function definition for 'select'
.GetClusterInfo: no visible binding for global variable 'org.Hs.eg.db'
.formatDAVIDResult: no visible global function definition for
  'formatGeneReportFull'
.formatDAVIDResult: no visible global function definition for
  'formatGeneReport'
.formatDAVIDResult: no visible global function definition for
  'formatList'
.formatDAVIDResult: no visible global function definition for
  'formatGene2Gene'
.formatDAVIDResult: no visible global function definition for
  'formatAnnotationReport'
.get.NetworksGenes: no visible global function definition for
  'annotatePeakInBatch'
EnsemblToHGNC: no visible global function definition for 'useMart'
EnsemblToHGNC: no visible global function definition for 'useDataset'
EnsemblToHGNC: no visible global function definition for 'getBM'
EntrezToHGNC: no visible global function definition for 'useMart'
EntrezToHGNC: no visible global function definition for 'useDataset'
EntrezToHGNC: no visible global function definition for 'getBM'
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
  no visible global function definition for 'runApp'
Undefined global functions or variables:
  TxDb.Hsapiens.UCSC.hg19.knownGene annotatePeakInBatch
  formatAnnotationReport formatGene2Gene formatGeneReport
  formatGeneReportFull formatList getBM org.Hs.eg.db org.Hs.egUCSCKG
  runApp select toTable useDataset useMart
* 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-3.4-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/i386/R3CPET.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'tests.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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/R3CPET.Rcheck/00check.log'
for details.


R3CPET.Rcheck/00install.out:


install for i386

* installing *source* package 'R3CPET' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R3CPET_init.c -o R3CPET_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c corpus.cpp -o corpus.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:20: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c stirln.cpp -o stirln.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/i386
** R
** data
** inst
** preparing package for lazy loading
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'R3CPET' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R3CPET_init.c -o R3CPET_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c corpus.cpp -o corpus.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c main.cpp -o main.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:20: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
                    ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c stirln.cpp -o stirln.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R3CPET' as R3CPET_1.6.0.zip
* DONE (R3CPET)

R3CPET.Rcheck/examples_i386/R3CPET-Ex.timings:

nameusersystemelapsed
Biogrid1.210.001.20
ChiapetExperimentData-class000
ChromMaintainers-class000
CreateCenteredBED-methods0.010.000.02
EnsemblToHGNC000
EntrezToHGNC000
GOEnrich-methods000
GenerateNetworks-methods000
HLDAResult-class000
HPRD0.100.000.09
InferNetworks-methods000
NetworkCollection-class000
PrepareData-methods0.010.000.02
RPKMS0.060.000.06
annotateExpression-methods000
buildNetworks-methods000
chromosoms000
cluesOrSota-class000
clusterInteractions-methods0.060.000.07
createIndexes-methods000
createServer-methods0.000.020.01
geneLocations0.110.000.11
getRegionsInNetwork-methods000
getRegionsIncluster-methods000
loadPETs-methods0.190.060.25
loadPPI-methods1.030.051.08
loadTFBS-methods0.500.030.53
outputGenesPerClusterToDir-methods000
outputGenesPerNetworkToDir-methods000
plotRes-methods0.020.000.02
plotTrack000
updateResults-methods000
visualizeCircos-methods000
visualizeInteractions-methods000

R3CPET.Rcheck/examples_x64/R3CPET-Ex.timings:

nameusersystemelapsed
Biogrid1.550.051.59
ChiapetExperimentData-class000
ChromMaintainers-class000
CreateCenteredBED-methods0.020.000.01
EnsemblToHGNC000
EntrezToHGNC000
GOEnrich-methods000
GenerateNetworks-methods000
HLDAResult-class000
HPRD0.070.000.08
InferNetworks-methods000
NetworkCollection-class000
PrepareData-methods000
RPKMS0.050.010.07
annotateExpression-methods000
buildNetworks-methods0.020.000.01
chromosoms000
cluesOrSota-class000
clusterInteractions-methods0.060.000.06
createIndexes-methods000
createServer-methods000
geneLocations0.090.000.10
getRegionsInNetwork-methods000
getRegionsIncluster-methods000
loadPETs-methods0.210.020.22
loadPPI-methods0.500.050.54
loadTFBS-methods1.200.011.22
outputGenesPerClusterToDir-methods000
outputGenesPerNetworkToDir-methods000
plotRes-methods0.010.000.02
plotTrack000
updateResults-methods000
visualizeCircos-methods000
visualizeInteractions-methods000