BioC 3.2: CHECK report for Repitools on moscato1

Package: Repitools

Version: 1.16.0

Command: rm -rf Repitools.buildbin-libdir Repitools.Rcheck && mkdir Repitools.buildbin-libdir Repitools.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.16.0.tar.gz >Repitools.Rcheck\00install.out 2>&1 && cp Repitools.Rcheck\00install.out Repitools-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.16.0.tar.gz

StartedAt: 2016-04-23 06:40:36 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 07:04:13 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 1416.8 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf Repitools.buildbin-libdir Repitools.Rcheck && mkdir Repitools.buildbin-libdir Repitools.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.16.0.tar.gz >Repitools.Rcheck\00install.out 2>&1 && cp Repitools.Rcheck\00install.out Repitools-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.16.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/Repitools.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.16.0'
* 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 '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 ... NOTE
clusterPlots,ClusteredScoresList : .local : <anonymous>: warning in
  axis(2, at = c(y.min, (y.min + y.max)/2, y.max), label =
  score.labels): partial argument match of 'label' to 'labels'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for 'nbrOfArrays'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for 'extract'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible binding for
  global variable 'verbose'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for 'getCdf'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for 'extractMatrix'
.featureScores,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for 'getCdf'
.featureScores,AffymetrixCelSet-GRanges : .local: no visible binding
  for global variable 'verbose'
.featureScores,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for 'extractMatrix'
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
  variable 'Arguments'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'pushState'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'popState'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'nbrOfArrays'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'getCdf'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'getMainCdf'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'nbrOfUnits'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'indexOf'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'enter'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'getCellIndices'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'exit'
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
  variable 'AromaCellSequenceFile'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'getChipType'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'countBases'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'extract'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'getNames'
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for 'extractMatrix'
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
  variable 'AromaCellCpgFile'
cpgBoxplots,matrix : .local: no visible binding for global variable
  'Arguments'
cpgBoxplots,matrix : .local: no visible global function definition for
  'pushState'
cpgBoxplots,matrix : .local: no visible global function definition for
  'popState'
cpgBoxplots,matrix : .local: no visible global function definition for
  'enter'
cpgBoxplots,matrix : .local: no visible global function definition for
  'exit'
cpgDensityCalc,GRanges-BSgenome : .local: no visible global function
  definition for 'DNAString'
getProbePositionsDf,AffymetrixCdfFile : .local: no visible global
  function definition for 'getCellIndices'
getProbePositionsDf,AffymetrixCdfFile : .local: no visible binding for
  global variable 'AromaCellPositionFile'
getProbePositionsDf,AffymetrixCdfFile : .local: no visible global
  function definition for 'getChipType'
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for 'getCdf'
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for 'getCellIndices'
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for 'nbrOfArrays'
regionStats,AffymetrixCelSet : .local: no visible binding for global
  variable 'AromaCellPositionFile'
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for 'getChipType'
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for 'extract'
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for 'extractMatrix'
sequenceCalc,GRanges-BSgenome : .local : <anonymous>: no visible global
  function definition for 'matchPattern'
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for 'getNames'
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for 'extract'
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for 'getCdf'
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for 'extractMatrix'
* 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 'D:/biocbld/bbs-3.2-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386/Repitools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-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, 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' ... [325s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         143.09   0.03  143.12
empBayes           65.60   0.91   66.51
sequenceCalc       12.49   0.36   13.09
cpgDensityCalc     12.34   0.39   19.69
BayMethList-class  11.18   0.29   15.33
maskOut             9.08   0.11    9.19
determineOffset     8.67   0.36    9.03
gcContentCalc       5.79   0.30    6.09
cpgDensityPlot      5.29   0.17    5.46
** running examples for arch 'x64' ... [299s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         123.93   0.08  124.01
empBayes           56.32   1.39   57.70
BayMethList-class  15.27   0.35   15.64
cpgDensityCalc     14.65   0.69   15.33
sequenceCalc       12.85   0.70   13.56
determineOffset    11.28   0.36   11.64
maskOut             7.78   0.08    7.86
cpgDensityPlot      6.37   0.42    6.79
gcContentCalc       5.39   0.17    5.57
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'tests.R' [143s]
 [144s] OK
** running tests for arch 'x64' ...
  Running 'tests.R' [128s]
 [128s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/Repitools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Repitools' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -c const.c -o const.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -c hyp2f1.c -o hyp2f1.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/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:\rtools33\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:\rtools33\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:\rtools33\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:\rtools33\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:\rtools33\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:\rtools33\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/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-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"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -c const.c -o const.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -c hyp2f1.c -o hyp2f1.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/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:\rtools33\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:\rtools33\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:\rtools33\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:\rtools33\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:\rtools33\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:\rtools33\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/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.16.0.zip
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	0.28	0.00	0.37
BayMethList-class	11.18	0.29	15.33
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
QdnaData	0.14	0.02	0.31
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.03	0.00	0.03
annoGR2DF	0.17	0.00	0.17
annotationBlocksCounts	0.2	0.0	0.2
annotationBlocksLookup	0.14	0.00	0.14
annotationCounts	0.19	0.00	2.31
annotationLookup	0.06	0.00	0.07
binPlots	2.07	0.17	2.24
blocksStats	0.36	0.00	0.36
checkProbes	0.30	0.00	1.87
chromosomeCNplots	0	0	0
clusterPlots	1.50	0.06	1.56
cpgDensityCalc	12.34	0.39	19.69
cpgDensityPlot	5.29	0.17	5.46
determineOffset	8.67	0.36	9.03
empBayes	65.60	0.91	66.51
enrichmentCalc	2.76	0.03	2.79
enrichmentPlot	3.14	0.01	3.16
featureBlocks	0.03	0.00	0.03
featureScores	1.78	0.02	1.79
findClusters	3.01	0.00	3.01
gcContentCalc	5.79	0.30	6.09
genQC	0	0	0
genomeBlocks	0.07	0.00	0.06
getProbePositionsDf	0	0	0
getSampleOffsets	0	0	0
hyper	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0	0	0
makeWindowLookupTable	0.11	0.00	0.11
mappabilityCalc	0.00	0.01	0.01
maskOut	9.08	0.11	9.19
mergeReplicates	0.91	0.00	0.91
methylEst	143.09	0.03	143.12
multiHeatmap	0.08	0.00	0.08
plotClusters	0.23	0.00	0.70
plotQdnaByCN	0	0	0
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.08	0.00	0.08
sequenceCalc	12.49	0.36	13.09
setCNVOffsets	0.02	0.00	0.01
summarizeScores	1.60	0.05	1.66
writeWig	0	0	0

name	user	system	elapsed
BAM2GRanges	0.92	0.00	0.92
BayMethList-class	15.27	0.35	15.64
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
QdnaData	0.26	0.02	0.39
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.03	0.00	0.03
annoGR2DF	0.25	0.00	0.25
annotationBlocksCounts	0.28	0.02	0.30
annotationBlocksLookup	0.11	0.00	0.11
annotationCounts	0.29	0.04	0.34
annotationLookup	0.16	0.00	0.16
binPlots	3.28	0.13	3.40
blocksStats	0.32	0.01	0.34
checkProbes	0.35	0.00	0.36
chromosomeCNplots	0	0	0
clusterPlots	2.90	0.19	3.09
cpgDensityCalc	14.65	0.69	15.33
cpgDensityPlot	6.37	0.42	6.79
determineOffset	11.28	0.36	11.64
empBayes	56.32	1.39	57.70
enrichmentCalc	2.01	0.03	2.04
enrichmentPlot	2.17	0.03	2.22
featureBlocks	0.03	0.00	0.03
featureScores	1.23	0.01	1.24
findClusters	2.69	0.00	2.69
gcContentCalc	5.39	0.17	5.57
genQC	0	0	0
genomeBlocks	0.05	0.00	0.04
getProbePositionsDf	0	0	0
getSampleOffsets	0	0	0
hyper	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0	0	0
makeWindowLookupTable	0.06	0.00	0.06
mappabilityCalc	0	0	0
maskOut	7.78	0.08	7.86
mergeReplicates	1.23	0.00	1.23
methylEst	123.93	0.08	124.01
multiHeatmap	0.09	0.00	0.09
plotClusters	0.27	0.00	0.27
plotQdnaByCN	0	0	0
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.07	0.00	0.06
sequenceCalc	12.85	0.70	13.56
setCNVOffsets	0	0	0
summarizeScores	1.80	0.00	1.81
writeWig	0.02	0.00	0.01