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CHECK report for brendaDb on tokay1

This page was generated on 2020-09-28 11:20:58 -0400 (Mon, 28 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE brendaDb PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 199/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
brendaDb 1.3.0
Yi Zhou
Snapshot Date: 2020-09-27 14:41:58 -0400 (Sun, 27 Sep 2020)
URL: https://git.bioconductor.org/packages/brendaDb
Branch: master
Last Commit: b348776
Last Changed Date: 2020-04-27 15:29:29 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: brendaDb
Version: 1.3.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brendaDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings brendaDb_1.3.0.tar.gz
StartedAt: 2020-09-28 06:12:48 -0400 (Mon, 28 Sep 2020)
EndedAt: 2020-09-28 06:15:52 -0400 (Mon, 28 Sep 2020)
EllapsedTime: 184.1 seconds
RetCode: 0
Status:  OK  
CheckDir: brendaDb.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brendaDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings brendaDb_1.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/brendaDb.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'brendaDb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'brendaDb' version '1.3.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'brendaDb' 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/brendaDb/libs/i386/brendaDb.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/brendaDb/libs/x64/brendaDb.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ExtractField         0.43   0.03    7.89
BiocycPathwayEnzymes 0.23   0.00    5.09
QueryBrenda          0.19   0.00    8.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ExtractField         0.59   0.00    5.78
BiocycPathwayEnzymes 0.27   0.03    5.06
QueryBrenda          0.29   0.01   10.82
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/brendaDb.Rcheck/00check.log'
for details.



Installation output

brendaDb.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/brendaDb_1.3.0.tar.gz && rm -rf brendaDb.buildbin-libdir && mkdir brendaDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=brendaDb.buildbin-libdir brendaDb_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL brendaDb_1.3.0.zip && rm brendaDb_1.3.0.tar.gz brendaDb_1.3.0.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  363k  100  363k    0     0  7575k      0 --:--:-- --:--:-- --:--:-- 8261k

install for i386

* installing *source* package 'brendaDb' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c read_brenda.cpp -o read_brenda.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o brendaDb.dll tmp.def RcppExports.o read_brenda.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/brendaDb.buildbin-libdir/00LOCK-brendaDb/00new/brendaDb/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'brendaDb'
    finding HTML links ... done
    BiocycPathwayEnzymes                    html  
    BiocycPathwayGenes                      html  
    CleanECNumber                           html  
    ConfigBPCores                           html  
    DownloadBrenda                          html  
    ExtractField                            html  
    ID2Enzyme                               html  
    InitBrendaDeprecatedEntry               html  
    InitBrendaEntry                         html  
    ParseGeneric                            html  
    ParseNoDescription                      html  
    ParseProtein                            html  
    ParseProteinNum                         html  
    ParseReaction                           html  
    ParseRecommendedName                    html  
    ParseReference                          html  
    ParseSystematicName                     html  
    PrettyPrintBrendaEntry                  html  
    PrintTreeHelper                         html  
    QueryBrenda                             html  
    QueryBrendaBase                         html  
    ReadBrenda                              html  
    ReadBrendaFile                          html  
    SelectOrganism                          html  
    SeparateEntries                         html  
    SeparateSubentries                      html  
    ShowFields                              html  
    acronyms                                html  
    brendaDb-package                        html  
    print.brenda.entries                    html  
    print.brenda.entry                      html  
*** copying figures
** 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 'brendaDb' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c read_brenda.cpp -o read_brenda.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o brendaDb.dll tmp.def RcppExports.o read_brenda.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/brendaDb.buildbin-libdir/brendaDb/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'brendaDb' as brendaDb_1.3.0.zip
* DONE (brendaDb)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'brendaDb' successfully unpacked and MD5 sums checked

Tests output

brendaDb.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

> library(testthat)
> library(brendaDb)
> 
> test_check("brendaDb")
There were 42 warnings (use warnings() to see them)
== testthat results  ===========================================================
[ OK: 116 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.92    1.20   28.51 

brendaDb.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

> library(testthat)
> library(brendaDb)
> 
> test_check("brendaDb")
There were 42 warnings (use warnings() to see them)
== testthat results  ===========================================================
[ OK: 116 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.35    0.70   20.48 

Example timings

brendaDb.Rcheck/examples_i386/brendaDb-Ex.timings

nameusersystemelapsed
BiocycPathwayEnzymes0.230.005.09
BiocycPathwayGenes0.070.021.25
CleanECNumber0.220.010.32
ConfigBPCores0.020.000.02
DownloadBrenda000
ExtractField0.430.037.89
ID2Enzyme0.140.000.14
InitBrendaDeprecatedEntry0.210.000.20
InitBrendaEntry0.080.000.08
ParseProtein0.030.000.03
ParseProteinNum000
ParseRecommendedName000
ParseReference0.010.000.02
ParseSystematicName000
QueryBrenda0.190.008.61
QueryBrendaBase2.280.222.71
ReadBrenda0.080.000.07
SeparateSubentries000
ShowFields0.090.000.10

brendaDb.Rcheck/examples_x64/brendaDb-Ex.timings

nameusersystemelapsed
BiocycPathwayEnzymes0.270.035.06
BiocycPathwayGenes0.120.001.36
CleanECNumber0.250.000.40
ConfigBPCores0.020.000.02
DownloadBrenda000
ExtractField0.590.005.78
ID2Enzyme0.120.020.14
InitBrendaDeprecatedEntry0.240.000.24
InitBrendaEntry0.080.000.07
ParseProtein0.040.000.05
ParseProteinNum000
ParseRecommendedName000
ParseReference0.020.000.02
ParseSystematicName000
QueryBrenda 0.29 0.0110.82
QueryBrendaBase2.530.212.73
ReadBrenda0.080.000.08
SeparateSubentries000
ShowFields0.100.000.09