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BioC 3.5: CHECK report for Organism.dplyr on tokay2

This page was generated on 2017-08-16 13:26:43 -0400 (Wed, 16 Aug 2017).

Package 931/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Organism.dplyr 1.2.1
Martin Morgan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Organism.dplyr
Last Changed Rev: 130625 / Revision: 131943
Last Changed Date: 2017-06-22 17:17:51 -0400 (Thu, 22 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Organism.dplyr
Version: 1.2.1
Command: rm -rf Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && mkdir Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Organism.dplyr.buildbin-libdir Organism.dplyr_1.2.1.tar.gz >Organism.dplyr.Rcheck\00install.out 2>&1 && cp Organism.dplyr.Rcheck\00install.out Organism.dplyr-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Organism.dplyr.buildbin-libdir --install="check:Organism.dplyr-install.out" --force-multiarch --no-vignettes --timings Organism.dplyr_1.2.1.tar.gz
StartedAt: 2017-08-16 01:44:03 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:52:37 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 514.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Organism.dplyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && mkdir Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Organism.dplyr.buildbin-libdir Organism.dplyr_1.2.1.tar.gz >Organism.dplyr.Rcheck\00install.out 2>&1 && cp Organism.dplyr.Rcheck\00install.out Organism.dplyr-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Organism.dplyr.buildbin-libdir --install="check:Organism.dplyr-install.out" --force-multiarch --no-vignettes --timings Organism.dplyr_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Organism.dplyr.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Organism.dplyr/DESCRIPTION' ... OK
* this is package 'Organism.dplyr' version '1.2.1'
* package encoding: UTF-8
* 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 'Organism.dplyr' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::smartKeys' 'GenomicFeatures:::.exons_with_3utr'
  'GenomicFeatures:::.exons_with_5utr'
  'GenomicFeatures:::get_TxDb_seqinfo0'
  'S4Vectors:::extract_data_frame_rows'
  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 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
Examples with CPU or elapsed time > 5s
           user system elapsed
extractors 4.75   0.08    7.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/Organism.dplyr.Rcheck/00check.log'
for details.


Organism.dplyr.Rcheck/00install.out:


install for i386

* installing *source* package 'Organism.dplyr' ...
** R
** inst
** preparing 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 'Organism.dplyr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Organism.dplyr' as Organism.dplyr_1.2.1.zip
* DONE (Organism.dplyr)

Organism.dplyr.Rcheck/examples_i386/Organism.dplyr-Ex.timings:

nameusersystemelapsed
extractors4.200.114.31
filter0.240.060.30
select1.300.031.33
src0.100.000.09
utils0.010.000.02

Organism.dplyr.Rcheck/examples_x64/Organism.dplyr-Ex.timings:

nameusersystemelapsed
extractors4.750.087.03
filter0.670.000.67
select2.720.012.74
src0.160.000.16
utils000