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### Running command:
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### 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_1.23.5.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_1.23.5.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/genoset.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.23.5'
* 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 ... WARNING
Found the following significant warnings:
Warning: subclass "GNCList" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "GIntervalTree" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: bad markup (extra space?) at GenoSet.Rd:15:56
Warning: bad markup (extra space?) at baf2mbaf.Rd:10:61
Warning: bad markup (extra space?) at calcGC.Rd:10:58
Warning: bad markup (extra space?) at calcGC.Rd:13:59
Warning: bad markup (extra space?) at do_rledf_views.Rd:17:56
Warning: bad markup (extra space?) at gcCorrect.Rd:12:60
Warning: bad markup (extra space?) at genoPlot-methods.Rd:23:56
Warning: bad markup (extra space?) at genoPlot-methods.Rd:56:56
Warning: bad markup (extra space?) at genomeAxis.Rd:13:59
Warning: bad markup (extra space?) at runCBS.Rd:17:63
Warning: bad markup (extra space?) at segs2Rle.Rd:11:56
See 'D:/biocbld/bbs-3.2-bioc/meat/genoset.Rcheck/00install.out' for details.
* 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 ... WARNING
Found .Internal calls in methods for the following S4 generics:
'rowMeans' 'rowSums'
Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
In addition to the above warning(s), found the following notes:
calcGC : <anonymous>: no visible global function definition for 'Views'
calcGC : <anonymous>: no visible global function definition for
'alphabetFrequency'
calcGC2: no visible binding for global variable 'gmapGenome'
calcGC2: no visible global function definition for 'RleList'
calcGC2 : <anonymous>: no visible global function definition for
'letterFrequencyInSlidingView'
initGenoSet: no visible global function definition for 'universe<-'
initGenoSet: no visible global function definition for
'assayDataValidMembers'
[<-,GenoSet-ANY-ANY-ANY : .local: no visible global function definition
for 'assayDataElement<-'
colnames,GenoSet : .local: no visible global function definition for
'pData'
colnames<-,GenoSet: no visible global function definition for 'pData'
colnames<-,GenoSet: no visible global function definition for 'pData<-'
colnames<-,GenoSet: no visible global function definition for
'assayData'
colnames<-,GenoSet: no visible global function definition for
'assayData<-'
dim,GenoSet: no visible global function definition for 'featureData'
rownames,GenoSet : .local: no visible global function definition for
'featureData'
rownames<-,GenoSet: no visible global function definition for 'fData<-'
rownames<-,GenoSet: no visible global function definition for
'assayData'
rownames<-,GenoSet: no visible global function definition for
'assayData<-'
* checking Rd files ... WARNING
prepare_Rd: bad markup (extra space?) at GenoSet.Rd:15:56
prepare_Rd: bad markup (extra space?) at baf2mbaf.Rd:10:61
prepare_Rd: bad markup (extra space?) at calcGC.Rd:10:58
prepare_Rd: bad markup (extra space?) at calcGC.Rd:13:59
prepare_Rd: bad markup (extra space?) at do_rledf_views.Rd:17:56
prepare_Rd: bad markup (extra space?) at gcCorrect.Rd:12:60
prepare_Rd: bad markup (extra space?) at genoPlot-methods.Rd:23:56
prepare_Rd: bad markup (extra space?) at genoPlot-methods.Rd:56:56
prepare_Rd: bad markup (extra space?) at genomeAxis.Rd:13:59
prepare_Rd: bad markup (extra space?) at runCBS.Rd:17:63
prepare_Rd: bad markup (extra space?) at segs2Rle.Rd:11:56
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'bounds2Rle.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
'segPairTable,DataFrame,DataFrame- ' 'segTable,DataFrame- '
Missing link or links in documentation object 'chrOrder.Rd':
'isGenomeOrder,GRanges- ' 'isGenomeOrder,GenoSet- '
Missing link or links in documentation object 'genomeAxis.Rd':
'genoPlot,GenoSetOrGenomicRanges,ANY- '
Missing link or links in documentation object 'rangeSegMeanLength-methods.Rd':
'segPairTable,DataFrame,DataFrame- ' 'segTable,DataFrame- '
Missing link or links in documentation object 'runCBS.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
'segPairTable,DataFrame,DataFrame- ' 'segTable,DataFrame- '
Missing link or links in documentation object 'segPairTable-methods.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
Missing link or links in documentation object 'segTable-methods.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
'segPairTable,DataFrame,DataFrame- '
Missing link or links in documentation object 'segs2Granges.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
'segPairTable,DataFrame,DataFrame- ' 'segTable,DataFrame- '
Missing link or links in documentation object 'segs2Rle.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
'segPairTable,DataFrame,DataFrame- ' 'segTable,DataFrame- '
Missing link or links in documentation object 'segs2RleDataFrame.Rd':
'rangeSegMeanLength,GRanges,data.frame- '
'rangeSegMeanLength,GRanges,list- '
'segPairTable,DataFrame,DataFrame- ' 'segTable,DataFrame- '
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'calcGC2':
'window'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [20s] OK
** running examples for arch 'x64' ... [17s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'prove.R' [23s]
Comparing 'prove.Rout' to 'prove.Rout.save' ...13c13
< The following objects are masked from 'package:stats':
---
> The following object is masked from 'package:stats':
15c15
< IQR, mad, xtabs
---
> xtabs
21,24c21,24
< eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
< mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
< rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
< tapply, union, unique, unlist, unsplit
---
> eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
> mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
> rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unlist, unsplit
33a34
> Using mclapply for segmentation ...
35a37
> Using mclapply for segmentation ...
37a40
> Using mclapply for segmentation ...
39a43
> Using mclapply for segmentation ...
41a46
> Using mclapply for segmentation ...
46c51
< RUNIT TEST PROTOCOL -- Thu Aug 20 05:05:54 2015
---
> RUNIT TEST PROTOCOL -- Tue Mar 17 12:16:04 2015
48c53
< Number of test functions: 36
---
> Number of test functions: 33
54,55c59,60
< genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
< Number of test functions: 36
---
> genoset RUnit Tests - 33 test functions, 0 errors, 0 failures
> Number of test functions: 33
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpYdzXa2\Rdiffa3688504134b7" "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpYdzXa2\Rdiffb36887e9c7580"' had status 1
[24s] OK
** running tests for arch 'x64' ...
Running 'prove.R' [23s]
Comparing 'prove.Rout' to 'prove.Rout.save' ...13c13
< The following objects are masked from 'package:stats':
---
> The following object is masked from 'package:stats':
15c15
< IQR, mad, xtabs
---
> xtabs
21,24c21,24
< eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
< mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
< rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
< tapply, union, unique, unlist, unsplit
---
> eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
> mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
> rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unlist, unsplit
33a34
> Using mclapply for segmentation ...
35a37
> Using mclapply for segmentation ...
37a40
> Using mclapply for segmentation ...
39a43
> Using mclapply for segmentation ...
41a46
> Using mclapply for segmentation ...
46c51
< RUNIT TEST PROTOCOL -- Thu Aug 20 05:06:17 2015
---
> RUNIT TEST PROTOCOL -- Tue Mar 17 12:16:04 2015
48c53
< Number of test functions: 36
---
> Number of test functions: 33
54,55c59,60
< genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
< Number of test functions: 36
---
> genoset RUnit Tests - 33 test functions, 0 errors, 0 failures
> Number of test functions: 33
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpMjYc6I\Rdiffa10ec5d221c80" "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpMjYc6I\Rdiffb10ec7b379ab"' had status 1
[24s] OK
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/genoset.Rcheck/00check.log'
for details.