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CHECK report for VariantToolsData on riesling1

This page was generated on 2021-01-14 15:59:12 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE VariantToolsData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 374/385HostnameOS / ArchINSTALLBUILDCHECK
VariantToolsData 1.15.0
Michael Lawrence
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/VariantToolsData
Branch: master
Last Commit: b62c1ca
Last Changed Date: 2020-10-27 10:22:22 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: VariantToolsData
Version: 1.15.0
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantToolsData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VariantToolsData_1.15.0.tar.gz
StartedAt: 2021-01-14 11:46:39 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:51:03 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 264.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: VariantToolsData.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantToolsData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VariantToolsData_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/VariantToolsData.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VariantToolsData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantToolsData' version '1.15.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'gmapR'
* 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:
  .BBSoptions
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 'VariantToolsData' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 201.6Mb
  sub-directories of 1Mb or more:
    data       2.2Mb
    extdata  199.2Mb
* 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
TP53Region: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  geno.rda        24Kb     14Kb       xz
  tallies.rda    2.2Mb    1.3Mb       xz
* 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: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/VariantToolsData.Rcheck/00check.log'
for details.



Installation output

VariantToolsData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/VariantToolsData_1.15.0.tar.gz && rm -rf VariantToolsData.buildbin-libdir && mkdir VariantToolsData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantToolsData.buildbin-libdir VariantToolsData_1.15.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL VariantToolsData_1.15.0.zip && rm VariantToolsData_1.15.0.tar.gz VariantToolsData_1.15.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  201M    0  724k    0     0  3602k      0  0:00:57 --:--:--  0:00:57 3584k
 16  201M   16 33.1M    0     0  29.0M      0  0:00:06  0:00:01  0:00:05 29.0M
 46  201M   46 93.1M    0     0  43.4M      0  0:00:04  0:00:02  0:00:02 43.4M
 67  201M   67  136M    0     0  43.5M      0  0:00:04  0:00:03  0:00:01 43.4M
100  201M  100  201M    0     0  53.0M      0  0:00:03  0:00:03 --:--:-- 53.0M

install for i386

* installing *source* package 'VariantToolsData' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'VariantToolsData'
    finding HTML links ... done
    TP53Region                              html  
REDIRECT:topic	 TP53Region -> TP53Region.html [ SUCCESS ]
    geno                                    html  
REDIRECT:topic	 geno -> geno.html [ SUCCESS ]
    repeats                                 html  
REDIRECT:topic	 repeats -> repeats.html [ SUCCESS ]
    sumDepths                               html  
REDIRECT:topic	 sumDepths -> sumDepths.html [ SUCCESS ]
    tallies                                 html  
REDIRECT:topic	 tallies -> tallies.html [ SUCCESS ]
** 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 'VariantToolsData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantToolsData' as VariantToolsData_1.15.0.zip
* DONE (VariantToolsData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'VariantToolsData' successfully unpacked and MD5 sums checked

Tests output


Example timings

VariantToolsData.Rcheck/examples_i386/VariantToolsData-Ex.timings

nameusersystemelapsed
TP53Region0.080.000.08
geno0.000.010.02
repeats0.010.000.02
sumDepths0.880.000.87
tallies0.260.020.30

VariantToolsData.Rcheck/examples_x64/VariantToolsData-Ex.timings

nameusersystemelapsed
TP53Region0.080.010.09
geno0.020.000.02
repeats0.020.000.02
sumDepths0.920.000.92
tallies0.250.020.26