Package: regionReport

Version: 1.14.3

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regionReport.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings regionReport_1.14.3.tar.gz

StartedAt: 2018-10-17 04:20:43 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:33:35 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 772.0 seconds

RetCode: 0

Status:  OK

CheckDir: regionReport.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regionReport.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings regionReport_1.14.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/regionReport.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'regionReport/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'regionReport' version '1.14.3'
* 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 'regionReport' 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
* 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: 'DESeq2:::pvalueAdjustment'
  See the note in ?`:::` about the use of this operator.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
renderReport    94.00   4.95  100.78
DESeq2Report    35.11   3.17   40.43
derfinderReport 32.78   3.89   38.50
edgeReport      21.40   1.55   24.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
renderReport    96.72   4.61  104.12
derfinderReport 32.34   4.37   38.25
DESeq2Report    33.76   1.94   37.43
edgeReport      19.17   1.47   22.17
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/regionReport.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/regionReport_1.14.3.tar.gz && rm -rf regionReport.buildbin-libdir && mkdir regionReport.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regionReport.buildbin-libdir regionReport_1.14.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL regionReport_1.14.3.zip && rm regionReport_1.14.3.tar.gz regionReport_1.14.3.zip
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100 46112  100 46112    0     0   864k      0 --:--:-- --:--:-- --:--:--  978k

install for i386

* installing *source* package 'regionReport' ...
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
** help
*** installing help indices
  converting help for package 'regionReport'
    finding HTML links ... done
    DESeq2Report                            html  
    derfinderReport                         html  
    edgeReport                              html  
    load_install                            html  
    regionReport-package                    html  
    renderReport                            html  
    with_wd                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
In R CMD INSTALL

install for x64

* installing *source* package 'regionReport' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
* MD5 sums
packaged installation of 'regionReport' as regionReport_1.14.3.zip
* DONE (regionReport)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'regionReport' successfully unpacked and MD5 sums checked
In R CMD INSTALL