BioC 2.14: CHECK report for Repitools on moscato2

Package: Repitools

Version: 1.10.1

Command: rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.10.1.tar.gz >Repitools-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.10.1.tar.gz

StartedAt: 2014-10-08 04:27:48 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 04:49:15 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 1286.8 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.10.1.tar.gz >Repitools-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.10.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/Repitools.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.10.1'
* 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 'Repitools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 'E:/biocbld/bbs-2.14-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386/Repitools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.14-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64/Repitools.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' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [306s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         126.75   0.47  127.24
empBayes           62.25   0.80   63.04
BayMethList-class  16.64   0.30   16.96
cpgDensityCalc     12.84   0.26   13.11
sequenceCalc       11.64   0.26   11.91
determineOffset    10.22   0.52   10.73
maskOut             9.58   0.27    9.85
cpgDensityPlot      8.41   0.39    8.80
gcContentCalc       4.91   0.22    5.13
** running examples for arch 'x64' ... [282s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         111.70   0.28  112.00
empBayes           51.23   0.77   51.99
BayMethList-class  19.87   0.36   20.24
cpgDensityCalc     11.82   0.35   12.17
sequenceCalc       11.82   0.25   12.08
determineOffset    10.41   0.37   10.78
maskOut             9.47   0.24    9.70
cpgDensityPlot      8.82   0.42    9.23
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'tests.R' [128s]
 [128s] OK
** running tests for arch 'x64' ...
  Running 'tests.R' [125s]
 [125s] 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/Repitools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Repitools' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -c const.c -o const.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -c hyp2f1.c -o hyp2f1.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
./mconf.h:101:0: warning: "SING" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
./mconf.h:102:0: warning: "OVERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
./mconf.h:103:0: warning: "UNDERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
./mconf.h:104:0: warning: "TLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
./mconf.h:105:0: warning: "PLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
gcc -m32 -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'windows' in package 'Repitools'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Repitools' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -c const.c -o const.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -c hyp2f1.c -o hyp2f1.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
./mconf.h:101:0: warning: "SING" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
./mconf.h:102:0: warning: "OVERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
./mconf.h:103:0: warning: "UNDERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
./mconf.h:104:0: warning: "TLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
./mconf.h:105:0: warning: "PLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
gcc -m64 -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.10.1.zip
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	0.66	0.00	0.66
BayMethList-class	16.64	0.30	16.96
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
GDL2GRL	0.46	0.01	0.50
QdnaData	0.14	0.00	0.14
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.04	0.00	0.03
annoGR2DF	0.11	0.02	0.13
annotationBlocksCounts	0.16	0.01	0.17
annotationBlocksLookup	0.10	0.00	0.09
annotationCounts	0.20	0.00	0.21
annotationLookup	0.11	0.00	0.10
binPlots	2.67	0.08	2.75
blocksStats	0.30	0.03	0.32
checkProbes	0.40	0.00	0.42
chromosomeCNplots	0.02	0.00	0.02
clusterPlots	2.49	0.05	2.54
cpgDensityCalc	12.84	0.26	13.11
cpgDensityPlot	8.41	0.39	8.80
determineOffset	10.22	0.52	10.73
empBayes	62.25	0.80	63.04
enrichmentCalc	2.98	0.00	2.98
enrichmentPlot	2.20	0.06	2.26
featureBlocks	0.04	0.00	0.05
featureScores	1.61	0.03	1.64
findClusters	4.43	0.01	4.44
gcContentCalc	4.91	0.22	5.13
genQC	0	0	0
genomeBlocks	0.06	0.00	0.06
getProbePositionsDf	0.02	0.00	0.02
getSampleOffsets	0	0	0
hyper	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0	0	0
makeWindowLookupTable	0.12	0.00	0.12
mappabilityCalc	0	0	0
maskOut	9.58	0.27	9.85
mergeReplicates	1	0	1
methylEst	126.75	0.47	127.24
multiHeatmap	0.08	0.00	0.07
plotClusters	0.24	0.03	0.27
plotQdnaByCN	0	0	0
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.14	0.00	0.14
sequenceCalc	11.64	0.26	11.91
setCNVOffsets	0	0	0
summarizeScores	1.76	0.03	1.80
writeWig	0	0	0

name	user	system	elapsed
BAM2GRanges	0.72	0.02	0.73
BayMethList-class	19.87	0.36	20.24
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
GDL2GRL	0.92	0.05	0.97
QdnaData	0.11	0.01	0.12
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.03	0.00	0.03
annoGR2DF	0.11	0.00	0.11
annotationBlocksCounts	0.19	0.00	0.19
annotationBlocksLookup	0.10	0.02	0.13
annotationCounts	0.22	0.01	0.23
annotationLookup	0.13	0.00	0.13
binPlots	2.59	0.10	2.68
blocksStats	0.32	0.00	0.33
checkProbes	0.36	0.00	0.39
chromosomeCNplots	0.02	0.00	0.01
clusterPlots	1.81	0.04	1.86
cpgDensityCalc	11.82	0.35	12.17
cpgDensityPlot	8.82	0.42	9.23
determineOffset	10.41	0.37	10.78
empBayes	51.23	0.77	51.99
enrichmentCalc	2.21	0.00	2.21
enrichmentPlot	2.34	0.00	2.34
featureBlocks	0.05	0.00	0.05
featureScores	1.67	0.00	1.67
findClusters	4.86	0.01	4.88
gcContentCalc	4.52	0.20	4.72
genQC	0	0	0
genomeBlocks	0.08	0.00	0.08
getProbePositionsDf	0	0	0
getSampleOffsets	0	0	0
hyper	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0	0	0
makeWindowLookupTable	0.14	0.00	0.14
mappabilityCalc	0	0	0
maskOut	9.47	0.24	9.70
mergeReplicates	0.99	0.01	1.02
methylEst	111.70	0.28	112.00
multiHeatmap	0.06	0.00	0.06
plotClusters	0.17	0.02	0.19
plotQdnaByCN	0.00	0.00	0.01
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.09	0.00	0.10
sequenceCalc	11.82	0.25	12.08
setCNVOffsets	0	0	0
summarizeScores	1.81	0.02	1.81
writeWig	0	0	0