##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf genoset.buildbin-libdir genoset.Rcheck && mkdir genoset.buildbin-libdir genoset.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genoset.buildbin-libdir genoset_1.28.2.tar.gz >genoset.Rcheck\00install.out 2>&1 && cp genoset.Rcheck\00install.out genoset-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=genoset.buildbin-libdir --install="check:genoset-install.out" --force-multiarch --no-vignettes --timings genoset_1.28.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/genoset.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.28.2'
* 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: multiple methods tables found for 'colMeans'
Warning: multiple methods tables found for 'colSums'
Warning: multiple methods tables found for 'rowMeans'
Warning: multiple methods tables found for 'rowSums'
See 'E:/biocbld/bbs-3.3-bioc/meat/genoset.Rcheck/00install.out' for details.
* 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 ... NOTE
Warning: multiple methods tables found for 'colMeans'
Warning: multiple methods tables found for 'colSums'
Warning: multiple methods tables found for 'rowMeans'
Warning: multiple methods tables found for 'rowSums'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: multiple methods tables found for 'colMeans'
Warning: multiple methods tables found for 'colSums'
Warning: multiple methods tables found for 'rowMeans'
Warning: multiple methods tables found for 'rowSums'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... WARNING
Undocumented code objects:
'colMeans' 'colSums' 'rowMeans' 'rowSums'
Undocumented S4 methods:
generic 'locData' and siglist 'GenoSet'
generic 'locData<-' and siglist 'GenoSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'GenoSet'
'object' '...' 'value'
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 'E:/biocbld/bbs-3.3-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'prove.R'
Comparing 'prove.Rout' to 'prove.Rout.save' ...20,31c20,24
< as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
< get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
< match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
< rbind, rownames, sapply, setdiff, sort, table, tapply, union,
< unique, unsplit
<
<
< Attaching package: 'S4Vectors'
<
< The following objects are masked from 'package:base':
<
< colMeans, colSums, expand.grid, rowMeans, rowSums
---
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> 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
41,57c34,37
< The genoset class has transitioned to the
< RangedSummarizedExperiment API from the eSet API (e.g. use colnames instead of sampleNames). ***
<
< Attaching package: 'genoset'
<
< The following object is masked from 'package:GenomicRanges':
<
< pos
<
< The following objects are masked from 'package:S4Vectors':
<
< colMeans, colSums, rowMeans, rowSums
<
< The following objects are masked from 'package:base':
<
< colMeans, colSums, rowMeans, rowSums
<
---
> The genoset class is transitioning to extending
> RangedSummarizedExperiment rather than eSet. For this release,
> please use the RSE API as the eSet API has been deprecated
> (e.g. colnames instead of sampleNames). ***
59,63d38
< Warning messages:
< 1: multiple methods tables found for 'colMeans'
< 2: multiple methods tables found for 'colSums'
< 3: multiple methods tables found for 'rowMeans'
< 4: multiple methods tables found for 'rowSums'
64a40
> Using mclapply for segmentation ...
66a43
> Using mclapply for segmentation ...
68a46
> Using mclapply for segmentation ...
70a49
> Using mclapply for segmentation ...
72a52
> Using mclapply for segmentation ...
77c57
< RUNIT TEST PROTOCOL -- Thu Oct 13 04:19:31 2016
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
79c59
< Number of test functions: 32
---
> Number of test functions: 36
85,86c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36
88a69
> There were 19 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "E:\biocbld\bbs-3.3-bioc\tmpdir\RtmpGkoue4\Rdiffa216443681634" "E:\biocbld\bbs-3.3-bioc\tmpdir\RtmpGkoue4\Rdiffb216431a74021"' had status 1
OK
** running tests for arch 'x64' ...
Running 'prove.R'
Comparing 'prove.Rout' to 'prove.Rout.save' ...20,31c20,24
< as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
< get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
< match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
< rbind, rownames, sapply, setdiff, sort, table, tapply, union,
< unique, unsplit
<
<
< Attaching package: 'S4Vectors'
<
< The following objects are masked from 'package:base':
<
< colMeans, colSums, expand.grid, rowMeans, rowSums
---
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> 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
41,57c34,37
< The genoset class has transitioned to the
< RangedSummarizedExperiment API from the eSet API (e.g. use colnames instead of sampleNames). ***
<
< Attaching package: 'genoset'
<
< The following object is masked from 'package:GenomicRanges':
<
< pos
<
< The following objects are masked from 'package:S4Vectors':
<
< colMeans, colSums, rowMeans, rowSums
<
< The following objects are masked from 'package:base':
<
< colMeans, colSums, rowMeans, rowSums
<
---
> The genoset class is transitioning to extending
> RangedSummarizedExperiment rather than eSet. For this release,
> please use the RSE API as the eSet API has been deprecated
> (e.g. colnames instead of sampleNames). ***
59,63d38
< Warning messages:
< 1: multiple methods tables found for 'colMeans'
< 2: multiple methods tables found for 'colSums'
< 3: multiple methods tables found for 'rowMeans'
< 4: multiple methods tables found for 'rowSums'
64a40
> Using mclapply for segmentation ...
66a43
> Using mclapply for segmentation ...
68a46
> Using mclapply for segmentation ...
70a49
> Using mclapply for segmentation ...
72a52
> Using mclapply for segmentation ...
77c57
< RUNIT TEST PROTOCOL -- Thu Oct 13 04:19:55 2016
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
79c59
< Number of test functions: 32
---
> Number of test functions: 36
85,86c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36
88a69
> There were 19 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "E:\biocbld\bbs-3.3-bioc\tmpdir\RtmpUfnCJ5\Rdiffa1c888652a64" "E:\biocbld\bbs-3.3-bioc\tmpdir\RtmpUfnCJ5\Rdiffb1c881c885365"' had status 1
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: 3 WARNINGs, 5 NOTEs
See
'E:/biocbld/bbs-3.3-bioc/meat/genoset.Rcheck/00check.log'
for details.
