Package: KEGGREST

Version: 1.20.2

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:KEGGREST.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings KEGGREST_1.20.2.tar.gz

StartedAt: 2018-10-16 01:28:50 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:33:24 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 273.6 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGREST.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:KEGGREST.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings KEGGREST_1.20.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/KEGGREST.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.20.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGREST’ 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
* 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: ‘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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
listDatabases           2.288  0.588  29.449
keggList                2.308  0.488  52.285
keggLink                0.940  0.224  15.854
mark.pathway.by.objects 0.528  0.032   8.771
keggFind                0.092  0.004   5.496
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL KEGGREST
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘KEGGREST’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KEGGREST)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("KEGGREST")
No encoding supplied: defaulting to UTF-8.


RUNIT TEST PROTOCOL -- Tue Oct 16 01:33:21 2018 
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Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
KEGGREST RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 10.324   0.224  93.068 

name	user	system	elapsed
keggConv	0.528	0.008	3.705
keggFind	0.092	0.004	5.496
keggGet	0.876	0.064	4.842
keggInfo	0.044	0.000	4.383
keggLink	0.940	0.224	15.854
keggList	2.308	0.488	52.285
listDatabases	2.288	0.588	29.449
mark.pathway.by.objects	0.528	0.032	8.771