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CHECK report for AnnotationFuncs on tokay1

This page was generated on 2021-02-22 12:36:57 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the AnnotationFuncs package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 65/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationFuncs 1.40.0
Stefan McKinnon Edwards
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/AnnotationFuncs
Branch: RELEASE_3_12
Last Commit: 90cc52b
Last Changed Date: 2020-10-27 10:40:41 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationFuncs
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationFuncs.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationFuncs_1.40.0.tar.gz
StartedAt: 2021-02-22 00:21:59 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 00:23:29 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 90.4 seconds
RetCode: 0
Status:   OK   
CheckDir: AnnotationFuncs.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:AnnotationFuncs.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationFuncs_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationFuncs.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationFuncs/DESCRIPTION' ... OK
* this is package 'AnnotationFuncs' version '1.40.0'
* 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 'AnnotationFuncs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field should not be empty
* 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
Package in Depends field not imported from: 'AnnotationDbi'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getOrthologs: no visible global function definition for 'dbmeta'
getOrthologs: no visible global function definition for 'dbconn'
getOrthologs: no visible global function definition for 'dbfile'
getOrthologs: no visible global function definition for 'direction'
translate: no visible global function definition for 'dbmeta'
translate: no visible global function definition for 'dbconn'
translate: no visible global function definition for 'stack'
Undefined global functions or variables:
  dbconn dbfile dbmeta direction stack
Consider adding
  importFrom("utils", "stack")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationFuncs.Rcheck/00check.log'
for details.



Installation output

AnnotationFuncs.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/AnnotationFuncs_1.40.0.tar.gz && rm -rf AnnotationFuncs.buildbin-libdir && mkdir AnnotationFuncs.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationFuncs.buildbin-libdir AnnotationFuncs_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AnnotationFuncs_1.40.0.zip && rm AnnotationFuncs_1.40.0.tar.gz AnnotationFuncs_1.40.0.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 22566  100 22566    0     0   593k      0 --:--:-- --:--:-- --:--:--  667k

install for i386

* installing *source* package 'AnnotationFuncs' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AnnotationFuncs'
    finding HTML links ... done
    AnnotationFuncs-package                 html  
    dbEscapeString2                         html  
    getEvidenceCodes                        html  
    getOrthologs                            html  
    getTableName2                           html  
    mapLists                                html  
    pickGO                                  html  
    pickRef2                                html  
    pickRefSeq                              html  
    removeNAs                               html  
    translate                               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 'AnnotationFuncs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationFuncs' as AnnotationFuncs_1.40.0.zip
* DONE (AnnotationFuncs)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AnnotationFuncs' successfully unpacked and MD5 sums checked

Tests output


Example timings

AnnotationFuncs.Rcheck/examples_i386/AnnotationFuncs-Ex.timings

nameusersystemelapsed
AnnotationFuncs-package0.500.031.12
getEvidenceCodes000
getOrthologs1.000.011.72
mapLists000
pickGO0.040.000.11
pickRefSeq0.030.000.03
removeNAs000
translate0.130.020.14

AnnotationFuncs.Rcheck/examples_x64/AnnotationFuncs-Ex.timings

nameusersystemelapsed
AnnotationFuncs-package0.360.000.35
getEvidenceCodes000
getOrthologs0.780.010.79
mapLists000
pickGO0.030.000.03
pickRefSeq0.030.000.03
removeNAs000
translate0.110.020.13