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CHECK report for KEGGREST on tokay2

This page was generated on 2019-10-16 12:27:24 -0400 (Wed, 16 Oct 2019).

Package 858/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGREST 1.24.1
Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/KEGGREST
Branch: RELEASE_3_9
Last Commit: bbc3ef4
Last Changed Date: 2019-10-08 11:43:04 -0400 (Tue, 08 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: KEGGREST
Version: 1.24.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGREST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings KEGGREST_1.24.1.tar.gz
StartedAt: 2019-10-16 04:44:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:51:20 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 400.4 seconds
RetCode: 0
Status:  OK  
CheckDir: KEGGREST.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGREST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings KEGGREST_1.24.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/KEGGREST.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 'KEGGREST/DESCRIPTION' ... OK
* this is package 'KEGGREST' version '1.24.1'
* 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 '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
* 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: '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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
listDatabases           2.82   0.55   11.87
keggList                2.84   0.51   15.27
keggLink                0.94   0.02    7.00
mark.pathway.by.objects 0.22   0.03   12.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
listDatabases           2.28   0.75   10.00
keggList                2.34   0.63   14.68
keggLink                0.69   0.03    6.70
mark.pathway.by.objects 0.16   0.04   18.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'KEGGREST_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/KEGGREST.Rcheck/00check.log'
for details.



Installation output

KEGGREST.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/KEGGREST_1.24.1.tar.gz && rm -rf KEGGREST.buildbin-libdir && mkdir KEGGREST.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGREST.buildbin-libdir KEGGREST_1.24.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL KEGGREST_1.24.1.zip && rm KEGGREST_1.24.1.tar.gz KEGGREST_1.24.1.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 14174  100 14174    0     0   226k      0 --:--:-- --:--:-- --:--:--  256k

install for i386

* installing *source* package 'KEGGREST' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KEGGREST'
    finding HTML links ... done
    keggConv                                html  
    keggFind                                html  
    keggGet                                 html  
    keggInfo                                html  
    keggLink                                html  
    keggList                                html  
    listDatabases                           html  
    mark.pathway.by.objects                 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 'KEGGREST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGREST' as KEGGREST_1.24.1.zip
* DONE (KEGGREST)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'KEGGREST' successfully unpacked and MD5 sums checked

Tests output

KEGGREST.Rcheck/tests_i386/KEGGREST_unit_tests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Wed Oct 16 04:49:43 2019 
*********************************************** 
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 
  17.82    1.76   89.48 

KEGGREST.Rcheck/tests_x64/KEGGREST_unit_tests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Wed Oct 16 04:51:14 2019 
*********************************************** 
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 
  18.03    1.81   90.23 

Example timings

KEGGREST.Rcheck/examples_i386/KEGGREST-Ex.timings

nameusersystemelapsed
keggConv0.230.003.09
keggFind0.050.002.86
keggGet2.140.033.93
keggInfo0.030.004.25
keggLink0.940.027.00
keggList 2.84 0.5115.27
listDatabases 2.82 0.5511.87
mark.pathway.by.objects 0.22 0.0312.45

KEGGREST.Rcheck/examples_x64/KEGGREST-Ex.timings

nameusersystemelapsed
keggConv0.170.002.58
keggFind0.030.003.03
keggGet2.270.104.08
keggInfo0.020.004.30
keggLink0.690.036.70
keggList 2.34 0.6314.68
listDatabases 2.28 0.7510.00
mark.pathway.by.objects 0.16 0.0418.14