BioC 3.2: CHECK report for genoset on moscato1

Package: genoset

Version: 1.24.0

Command: rm -rf genoset.buildbin-libdir genoset.Rcheck && mkdir genoset.buildbin-libdir genoset.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genoset.buildbin-libdir genoset_1.24.0.tar.gz >genoset.Rcheck\00install.out 2>&1 && cp genoset.Rcheck\00install.out genoset-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genoset.buildbin-libdir --install="check:genoset-install.out" --force-multiarch --no-vignettes --timings genoset_1.24.0.tar.gz

StartedAt: 2016-04-23 02:47:45 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:53:21 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 336.1 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf genoset.buildbin-libdir genoset.Rcheck && mkdir genoset.buildbin-libdir genoset.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genoset.buildbin-libdir genoset_1.24.0.tar.gz >genoset.Rcheck\00install.out 2>&1 && cp genoset.Rcheck\00install.out genoset-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genoset.buildbin-libdir --install="check:genoset-install.out" --force-multiarch --no-vignettes --timings genoset_1.24.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/genoset.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 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.24.0'
* 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 'genoset' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 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/genoset.buildbin-libdir/genoset/libs/i386/genoset.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64/genoset.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [21s] OK
** running examples for arch 'x64' ... [22s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'prove.R' [27s]
  Comparing 'prove.Rout' to 'prove.Rout.save' ...22,23c22,23
<     lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
---
>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
39a40
> Using mclapply for segmentation ...
41a43
> Using mclapply for segmentation ...
43a46
> Using mclapply for segmentation ...
45a49
> Using mclapply for segmentation ...
47a52
> Using mclapply for segmentation ...
52c57
< RUNIT TEST PROTOCOL -- Sat Apr 23 02:52:36 2016 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
64c69
< There were 16 warnings (use warnings() to see them)
---
> There were 19 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpaE43KY\Rdiffa23ac664e6d9e" "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpaE43KY\Rdiffb23ac54485475"' had status 1 
 [30s] OK
** running tests for arch 'x64' ...
  Running 'prove.R' [23s]
  Comparing 'prove.Rout' to 'prove.Rout.save' ...22,23c22,23
<     lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
---
>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
39a40
> Using mclapply for segmentation ...
41a43
> Using mclapply for segmentation ...
43a46
> Using mclapply for segmentation ...
45a49
> Using mclapply for segmentation ...
47a52
> Using mclapply for segmentation ...
52c57
< RUNIT TEST PROTOCOL -- Sat Apr 23 02:53:04 2016 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
64c69
< There were 16 warnings (use warnings() to see them)
---
> There were 19 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.2-bioc\tmpdir\Rtmp0okJmP\Rdiffa30829862b4f" "D:\biocbld\bbs-3.2-bioc\tmpdir\Rtmp0okJmP\Rdiffb3083a1e7f4e"' had status 1 
 [28s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/genoset.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genoset' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bounds.c -o bounds.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rangeSummaries.c -o rangeSummaries.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
gcc -m32 -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.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/genoset.buildbin-libdir/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare 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 'genoset' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bounds.c -o bounds.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rangeSummaries.c -o rangeSummaries.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
gcc -m64 -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.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/genoset.buildbin-libdir/genoset/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoset' as genoset_1.24.0.zip
* DONE (genoset)

name	user	system	elapsed
GenoSet-class	0.36	0.00	0.36
GenoSet	0.05	0.00	0.04
RleDataFrame-class	0.22	0.00	0.22
RleDataFrame-views	0.05	0.00	0.04
baf2mbaf	0.03	0.00	0.03
boundingIndices	0	0	0
calcGC	0	0	0
calcGC2	0.01	0.00	0.00
chr-methods	0.02	0.00	0.01
chrIndices-methods	0.01	0.00	0.02
chrInfo-methods	0.02	0.02	0.03
chrNames-methods	0.01	0.00	0.01
chrOrder	0	0	0
colnames	0.00	0.01	0.02
gcCorrect	0	0	0
genoPlot-methods	0.05	0.00	0.05
genoPos-methods	0.03	0.00	0.03
genome-methods	0.00	0.02	0.02
genome	0.00	0.02	0.01
genomeAxis	0.03	0.01	0.05
genoset-subset	0.23	0.00	0.23
initGenoSet	0.07	0.00	0.46
isGenomeOrder-methods	0.01	0.00	0.01
locData-methods	0.03	0.00	0.03
modeCenter	0	0	0
pos-methods	0.03	0.00	0.03
rangeSampleMeans	0.05	0.00	0.05
readGenoSet	0	0	0
rownames-methods	0.01	0.00	0.01
runCBS	3.98	0.00	3.98
segPairTable-methods	0.02	0.00	0.02
segTable-methods	3.07	0.00	3.07
segs2Rle	3.12	0.02	3.14
segs2RleDataFrame	3.18	0.01	3.19
toGenomeOrder-methods	0.09	0.00	0.09

name	user	system	elapsed
GenoSet-class	0.44	0.00	0.43
GenoSet	0.06	0.00	0.07
RleDataFrame-class	0.41	0.01	0.42
RleDataFrame-views	0.11	0.00	0.11
baf2mbaf	0.06	0.00	0.06
boundingIndices	0	0	0
calcGC	0	0	0
calcGC2	0	0	0
chr-methods	0.02	0.00	0.01
chrIndices-methods	0.02	0.00	0.02
chrInfo-methods	0.03	0.00	0.03
chrNames-methods	0.01	0.00	0.02
chrOrder	0	0	0
colnames	0.00	0.02	0.01
gcCorrect	0.02	0.00	0.02
genoPlot-methods	0.06	0.00	0.09
genoPos-methods	0.03	0.00	0.03
genome-methods	0.02	0.01	0.03
genome	0.01	0.02	0.03
genomeAxis	0.06	0.00	0.07
genoset-subset	0.33	0.01	0.34
initGenoSet	0.08	0.02	3.91
isGenomeOrder-methods	0.03	0.00	0.04
locData-methods	0.02	0.00	0.01
modeCenter	0.01	0.00	0.02
pos-methods	0.02	0.02	0.03
rangeSampleMeans	0.04	0.00	0.04
readGenoSet	0	0	0
rownames-methods	0.03	0.00	0.04
runCBS	3.45	0.00	3.44
segPairTable-methods	0.02	0.00	0.02
segTable-methods	2.32	0.01	2.34
segs2Rle	2.01	0.00	2.01
segs2RleDataFrame	2.14	0.00	2.14
toGenomeOrder-methods	0.13	0.02	0.14