Package: regionReport

Version: 1.18.2

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regionReport.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings regionReport_1.18.2.tar.gz

StartedAt: 2019-10-16 06:25:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:47:23 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 1299.3 seconds

RetCode: 0

Status:  OK

CheckDir: regionReport.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regionReport.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings regionReport_1.18.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/regionReport.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.18.2'
* 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 '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    92.52   5.14  104.29
DESeq2Report    35.45   3.31  551.16
derfinderReport 29.97   4.51   37.25
edgeReport      18.80   2.68   22.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
renderReport    85.98   4.72   94.25
DESeq2Report    34.11   1.94   38.25
derfinderReport 31.09   4.33   39.64
edgeReport      23.82   1.87   28.28
* 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-3.9-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/3.9/bioc/src/contrib/regionReport_1.18.2.tar.gz && rm -rf regionReport.buildbin-libdir && mkdir regionReport.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regionReport.buildbin-libdir regionReport_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL regionReport_1.18.2.zip && rm regionReport_1.18.2.tar.gz regionReport_1.18.2.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 46666  100 46666    0     0   573k      0 --:--:-- --:--:-- --:--:--  624k

install for i386

* installing *source* package 'regionReport' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'regionReport'
    finding HTML links ... done
    DESeq2Report                            html  
    derfinderReport                         html  
    edgeReport                              html  
    load_check                              html  
    regionReport-package                    html  
    renderReport                            html  
    with_wd                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'regionReport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regionReport' as regionReport_1.18.2.zip
* DONE (regionReport)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'regionReport' successfully unpacked and MD5 sums checked