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BioC 3.4: CHECK report for BicARE on moscato1

This page was generated on 2016-09-21 03:42:39 -0700 (Wed, 21 Sep 2016).

Package 100/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BicARE 1.31.0
Pierre Gestraud
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BicARE
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: BicARE
Version: 1.31.0
Command: rm -rf BicARE.buildbin-libdir BicARE.Rcheck && mkdir BicARE.buildbin-libdir BicARE.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BicARE.buildbin-libdir BicARE_1.31.0.tar.gz >BicARE.Rcheck\00install.out 2>&1 && cp BicARE.Rcheck\00install.out BicARE-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BicARE.buildbin-libdir --install="check:BicARE-install.out" --force-multiarch --no-vignettes --timings BicARE_1.31.0.tar.gz
StartedAt: 2016-09-20 04:32:53 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:50:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1081.8 seconds
RetCode: 0
Status:  OK  
CheckDir: BicARE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BicARE.buildbin-libdir BicARE.Rcheck && mkdir BicARE.buildbin-libdir BicARE.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BicARE.buildbin-libdir BicARE_1.31.0.tar.gz >BicARE.Rcheck\00install.out 2>&1 && cp BicARE.Rcheck\00install.out BicARE-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BicARE.buildbin-libdir --install="check:BicARE-install.out" --force-multiarch --no-vignettes --timings BicARE_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/BicARE.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BicARE/DESCRIPTION' ... OK
* this is package 'BicARE' version '1.31.0'
* 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 'BicARE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  'Biobase' 'GSEABase' 'multtest'
  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 ... NOTE
FLOC: no visible global function definition for 'new'
FLOC: no visible global function definition for 'exprs'
FLOC: no visible global function definition for 'runif'
FLOC: no visible binding for global variable 'var'
bicluster: no visible global function definition for 'exprs'
bicluster: no visible global function definition for 'featureNames'
bicluster: no visible global function definition for 'sampleNames'
bicluster: no visible global function definition for 'plot'
makeReport: no visible global function definition for 'annotation'
makeReport: no visible global function definition for 'png'
makeReport: no visible global function definition for 'dev.off'
makeReport: no visible global function definition for 'getSYMBOL'
makeReport: no visible global function definition for 'setName'
makeReport: no visible global function definition for 'browseURL'
plot.bicluster: no visible global function definition for 'par'
plot.bicluster: no visible global function definition for 'matplot'
plot.bicluster: no visible global function definition for 'axis'
residue: no visible global function definition for 'new'
residue: no visible global function definition for 'exprs'
testAnnot: no visible global function definition for 'pData'
testAnnot: no visible global function definition for 'phenoData'
testAnnot: no visible global function definition for 'chisq.test'
testAnnot: no visible global function definition for 'mt.rawp2adjp'
testSet: no visible global function definition for 'exprs'
testSet: no visible global function definition for 'GeneSet'
testSet: no visible global function definition for 'geneIdType'
testSet: no visible global function definition for 'geneIds'
testSet: no visible global function definition for 'mapIdentifiers'
testSet: no visible global function definition for 'phyper'
testSet: no visible global function definition for 'mt.rawp2adjp'
Undefined global functions or variables:
  GeneSet annotation axis browseURL chisq.test dev.off exprs
  featureNames geneIdType geneIds getSYMBOL mapIdentifiers matplot
  mt.rawp2adjp new pData par phenoData phyper plot png runif
  sampleNames setName var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "matplot", "par", "plot")
  importFrom("methods", "new")
  importFrom("stats", "chisq.test", "phyper", "runif", "var")
  importFrom("utils", "browseURL")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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-3.4-bioc/meat/BicARE.buildbin-libdir/BicARE/libs/i386/BicARE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 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
Examples with CPU or elapsed time > 5s
             user system elapsed
testSet    380.07   0.22  384.46
FLOC        36.19   0.00   36.19
makeReport   3.23   0.37    7.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
testSet 467.16   0.16  467.32
FLOC     38.02   0.01   38.03
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/BicARE.Rcheck/00check.log'
for details.


BicARE.Rcheck/00install.out:


install for i386

* installing *source* package 'BicARE' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BicARE.c -o BicARE.o
BicARE.c: In function 'floc':
BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable]
     double invk = 1/(double)*k;
            ^
BicARE.c: In function 'action':
BicARE.c:391:29: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
        bicCol2[ncolData * z + j] = bicCol[ncolData * z +j];
                             ^
BicARE.c:380:29: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
        bicRow2[nrowData * z + i] = bicRow[nrowData * z + i];
                             ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o BicARE.dll tmp.def BicARE.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/BicARE.buildbin-libdir/BicARE/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 'BicARE' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BicARE.c -o BicARE.o
BicARE.c: In function 'floc':
BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable]
     double invk = 1/(double)*k;
            ^
BicARE.c: In function 'action':
BicARE.c:391:29: warning: 'j' may be used uninitialized in this function [-Wmaybe-uninitialized]
        bicCol2[ncolData * z + j] = bicCol[ncolData * z +j];
                             ^
BicARE.c:380:29: warning: 'i' may be used uninitialized in this function [-Wmaybe-uninitialized]
        bicRow2[nrowData * z + i] = bicRow[nrowData * z + i];
                             ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o BicARE.dll tmp.def BicARE.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/BicARE.buildbin-libdir/BicARE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BicARE' as BicARE_1.31.0.zip
* DONE (BicARE)

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

nameusersystemelapsed
FLOC36.19 0.0036.19
bicluster0.230.000.24
makeReport3.230.377.99
residue0.020.000.01
testAnnot0.010.000.02
testSet380.07 0.22384.46

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

nameusersystemelapsed
FLOC38.02 0.0138.03
bicluster0.280.020.30
makeReport3.090.233.41
residue000
testAnnot0.030.000.03
testSet467.16 0.16467.32