BicARE 1.34.0
Pierre Gestraud
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/BicARE | | Branch: RELEASE_3_5 | | Last Commit: 2cc62dd | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf BicARE.buildbin-libdir BicARE.Rcheck && mkdir BicARE.buildbin-libdir BicARE.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BicARE.buildbin-libdir BicARE_1.34.0.tar.gz >BicARE.Rcheck\00install.out 2>&1 && cp BicARE.Rcheck\00install.out BicARE-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BicARE.buildbin-libdir --install="check:BicARE-install.out" --force-multiarch --no-vignettes --timings BicARE_1.34.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BicARE.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.34.0'
* 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 'C:/Users/biocbuild/bbs-3.5-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 255.22 0.21 255.44
FLOC 24.33 0.00 24.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
testSet 339.79 0.22 340.01
FLOC 24.25 0.03 24.28
* 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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/BicARE.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'BicARE' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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 -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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"C:/Users/BIOCBU˜1/BBS-3˜1.5-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 -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/BicARE.buildbin-libdir/BicARE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BicARE' as BicARE_1.34.0.zip
* DONE (BicARE)