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CHECK report for GEOmetadb on tokay2

This page was generated on 2019-05-11 11:42:24 -0400 (Sat, 11 May 2019).

Package 668/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOmetadb 1.46.0
Jack Zhu
Snapshot Date: 2019-05-10 17:01:41 -0400 (Fri, 10 May 2019)
URL: https://git.bioconductor.org/packages/GEOmetadb
Branch: RELEASE_3_9
Last Commit: 27a3741
Last Changed Date: 2019-05-02 11:53:09 -0400 (Thu, 02 May 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: GEOmetadb
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEOmetadb.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GEOmetadb_1.46.0.tar.gz
StartedAt: 2019-05-11 03:42:12 -0400 (Sat, 11 May 2019)
EndedAt: 2019-05-11 03:53:45 -0400 (Sat, 11 May 2019)
EllapsedTime: 692.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GEOmetadb.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:GEOmetadb.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GEOmetadb_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEOmetadb.Rcheck'
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEOmetadb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOmetadb' version '1.46.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
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 'GEOmetadb' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEOmetadb.Rcheck/00install.out' for details.
* 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
getSQLiteFile: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
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-3.9-bioc/meat/GEOmetadb.Rcheck/00check.log'
for details.



Installation output

GEOmetadb.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/GEOmetadb_1.46.0.tar.gz && rm -rf GEOmetadb.buildbin-libdir && mkdir GEOmetadb.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GEOmetadb.buildbin-libdir GEOmetadb_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GEOmetadb_1.46.0.zip && rm GEOmetadb_1.46.0.tar.gz GEOmetadb_1.46.0.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  114k  100  114k    0     0  1710k      0 --:--:-- --:--:-- --:--:-- 1901k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'GEOmetadb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GEOmetadb'
    finding HTML links ... done
    GEOmetadb-package                       html  
    columnDescriptions                      html  
    geoConvert                              html  
    getBiocPlatformMap                      html  
    getSQLiteFile                           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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'GEOmetadb' ...
** using non-staged installation
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEOmetadb' as GEOmetadb_1.46.0.zip
* DONE (GEOmetadb)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GEOmetadb' successfully unpacked and MD5 sums checked

Tests output


Example timings

GEOmetadb.Rcheck/examples_i386/GEOmetadb-Ex.timings

nameusersystemelapsed
GEOmetadb-package000
columnDescriptions000
geoConvert000
getBiocPlatformMap000
getSQLiteFile000

GEOmetadb.Rcheck/examples_x64/GEOmetadb-Ex.timings

nameusersystemelapsed
GEOmetadb-package000
columnDescriptions000
geoConvert000
getBiocPlatformMap000
getSQLiteFile000