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BioC 3.5: CHECK report for annotatr on tokay2

This page was generated on 2017-08-16 13:26:22 -0400 (Wed, 16 Aug 2017).

Package 55/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.2.1
Raymond G. Cavalcante
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/annotatr
Last Changed Rev: 130640 / Revision: 131943
Last Changed Date: 2017-06-23 13:26:50 -0400 (Fri, 23 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: annotatr
Version: 1.2.1
Command: rm -rf annotatr.buildbin-libdir annotatr.Rcheck && mkdir annotatr.buildbin-libdir annotatr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotatr.buildbin-libdir annotatr_1.2.1.tar.gz >annotatr.Rcheck\00install.out 2>&1 && cp annotatr.Rcheck\00install.out annotatr-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=annotatr.buildbin-libdir --install="check:annotatr-install.out" --force-multiarch --no-vignettes --timings annotatr_1.2.1.tar.gz
StartedAt: 2017-08-15 22:00:34 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:09:50 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 556.4 seconds
RetCode: 0
Status:  OK  
CheckDir: annotatr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf annotatr.buildbin-libdir annotatr.Rcheck && mkdir annotatr.buildbin-libdir annotatr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotatr.buildbin-libdir annotatr_1.2.1.tar.gz >annotatr.Rcheck\00install.out 2>&1 && cp annotatr.Rcheck\00install.out annotatr-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=annotatr.buildbin-libdir --install="check:annotatr-install.out" --force-multiarch --no-vignettes --timings annotatr_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/annotatr.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 'annotatr/DESCRIPTION' ... OK
* this is package 'annotatr' version '1.2.1'
* 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 'annotatr' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_coannotations: no visible binding for global variable '.'
plot_numerical_coannotations: no visible binding for global variable
  '.'
Undefined global functions or variables:
  .
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
build_ah_annots 3.34   0.49    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
build_ah_annots 3.44   0.41    5.36
* 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/annotatr.Rcheck/00check.log'
for details.


annotatr.Rcheck/00install.out:


install for i386

* installing *source* package 'annotatr' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'annotatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotatr' as annotatr_1.2.1.zip
* DONE (annotatr)

annotatr.Rcheck/examples_i386/annotatr-Ex.timings:

nameusersystemelapsed
annotate_regions0.890.020.90
annotatr_cache1.070.371.46
build_ah_annots3.340.495.16
build_annotations4.470.154.63
builtin_annotations000
builtin_genomes000
plot_annotation2.420.083.50
plot_categorical2.410.083.47
plot_coannotations1.560.001.56
plot_numerical0.50.00.5
plot_numerical_coannotations0.880.060.94
randomize_regions1.280.032.47
read_annotations0.420.020.44
read_regions0.420.000.42
summarize_annotations1.330.092.44
summarize_categorical0.340.030.38
summarize_numerical0.470.000.47

annotatr.Rcheck/examples_x64/annotatr-Ex.timings:

nameusersystemelapsed
annotate_regions1.220.041.27
annotatr_cache1.620.251.87
build_ah_annots3.440.415.36
build_annotations4.200.174.37
builtin_annotations000
builtin_genomes000
plot_annotation2.970.084.03
plot_categorical1.970.113.31
plot_coannotations2.360.002.36
plot_numerical0.50.00.5
plot_numerical_coannotations1.060.001.06
randomize_regions1.360.092.94
read_annotations0.390.020.40
read_regions0.330.050.38
summarize_annotations2.190.033.20
summarize_categorical0.470.060.53
summarize_numerical0.570.000.58