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CHECK report for MeSHDbi on tokay2

This page was generated on 2018-10-17 08:38:34 -0400 (Wed, 17 Oct 2018).

Package 861/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MeSHDbi 1.16.0
Koki Tsuyuzaki
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/MeSHDbi
Branch: RELEASE_3_7
Last Commit: 78dd065
Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MeSHDbi
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MeSHDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MeSHDbi_1.16.0.tar.gz
StartedAt: 2018-10-17 03:09:51 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:11:32 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 100.6 seconds
RetCode: 0
Status:  OK  
CheckDir: MeSHDbi.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MeSHDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MeSHDbi_1.16.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MeSHDbi.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MeSHDbi/DESCRIPTION' ... OK
* this is package 'MeSHDbi' version '1.16.0'
* 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 'MeSHDbi' 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 ... NOTE
.div: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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-3.7-bioc/meat/MeSHDbi.Rcheck/00check.log'
for details.

Installation output

MeSHDbi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/MeSHDbi_1.16.0.tar.gz && rm -rf MeSHDbi.buildbin-libdir && mkdir MeSHDbi.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MeSHDbi.buildbin-libdir MeSHDbi_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL MeSHDbi_1.16.0.zip && rm MeSHDbi_1.16.0.tar.gz MeSHDbi_1.16.0.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 19456  100 19456    0     0   289k      0 --:--:-- --:--:-- --:--:--  327k

install for i386

* installing *source* package 'MeSHDbi' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'packageName' in package 'MeSHDbi'
** help
*** installing help indices
  converting help for package 'MeSHDbi'
    finding HTML links ... done
    MeSHDb                                  html  
    PAO1                                    html  
    listDatabases                           html  
    makeMeSHPackage                         html  
    meshVersion                             html  
    metaPAO1                                html  
    nomenclature                            html  
    packageName                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MeSHDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MeSHDbi' as MeSHDbi_1.16.0.zip
* DONE (MeSHDbi)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'MeSHDbi' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MeSHDbi.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("MeSHDbi")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'MeSHDbi'

The following object is masked from 'package:utils':

    packageName

Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:24'
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:24'
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:24'
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:24'


RUNIT TEST PROTOCOL -- Wed Oct 17 03:11:24 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MeSHDbi RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
In getPackageName(where) :
  Created a package name, '2018-10-17 03:11:24', when none found
> 
> proc.time()
   user  system elapsed 
   2.60    0.21    2.81 
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:24'

MeSHDbi.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("MeSHDbi")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'MeSHDbi'

The following object is masked from 'package:utils':

    packageName

Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:27'
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:27'
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:27'
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:27'


RUNIT TEST PROTOCOL -- Wed Oct 17 03:11:27 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MeSHDbi RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
In getPackageName(where) :
  Created a package name, '2018-10-17 03:11:27', when none found
> 
> proc.time()
   user  system elapsed 
   2.82    0.12    2.95 
Found more than one class "MeSHDb" in cache; using the first, from namespace 'MeSHDbi'
Also defined by '2018-10-17 03:11:27'

Example timings

MeSHDbi.Rcheck/examples_i386/MeSHDbi-Ex.timings

nameusersystemelapsed
MeSHDb000
PAO10.030.000.03
listDatabases000
makeMeSHPackage0.050.030.19
meshVersion000
metaPAO10.000.020.01
nomenclature000
packageName000

MeSHDbi.Rcheck/examples_x64/MeSHDbi-Ex.timings

nameusersystemelapsed
MeSHDb000
PAO10.030.000.03
listDatabases000
makeMeSHPackage0.030.030.11
meshVersion000
metaPAO10.000.010.02
nomenclature000
packageName000