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CHECK report for vtpnet on tokay1

This page was generated on 2019-04-13 11:22:55 -0400 (Sat, 13 Apr 2019).

Package 1626/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vtpnet 0.22.0
VJ Carey
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/vtpnet
Branch: RELEASE_3_8
Last Commit: f45d71c
Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: vtpnet
Version: 0.22.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vtpnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings vtpnet_0.22.0.tar.gz
StartedAt: 2019-04-13 06:10:27 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:18:45 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 498.3 seconds
RetCode: 0
Status:  OK  
CheckDir: vtpnet.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vtpnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings vtpnet_0.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/vtpnet.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'vtpnet/DESCRIPTION' ... OK
* this is package 'vtpnet' version '0.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'vtpnet' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data  20.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls to packages already attached by Depends:
  'doParallel' 'foreach'
  Please remove these calls from your code.
'library' or 'require' call to 'MotifDb' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'doParallel' 'foreach'
  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
rng2facHits: warning in dir(patt = "rda$"): partial argument match of
  'patt' to 'pattern'
runfimo: warning in dir(patt = "_out"): partial argument match of
  'patt' to 'pattern'
filterGWASbyMap: no visible global function definition for 'as'
getMtags: no visible global function definition for 'is'
getOneHits: no visible global function definition for 'queryHits'
getOneHits: no visible global function definition for 'subjectHits'
getOneHits: no visible global function definition for 'metadata<-'
gwMatchPWM: no visible binding for global variable 'Hsapiens'
gwMatchPWM: no visible global function definition for 'is'
gwMatchPWM: no visible global function definition for '%dopar%'
gwMatchPWM: no visible global function definition for 'foreach'
gwMatchPWM: no visible binding for global variable 'i'
gwMatchPWM: no visible global function definition for 'matchPWM'
gwMatchPWM: no visible global function definition for
  'PWMscoreStartingAt'
gwMatchPWM: no visible global function definition for 'subject'
gwMatchPWM: no visible global function definition for 'as'
rng2facHits: no visible global function definition for 'as'
rng2facHits: no visible global function definition for
  'registerDoParallel'
rng2facHits: no visible global function definition for '%dopar%'
rng2facHits: no visible global function definition for 'foreach'
rng2facHits: no visible binding for global variable 'i'
runfimo: no visible global function definition for '%dopar%'
runfimo: no visible global function definition for 'foreach'
runfimo: no visible binding for global variable 'i'
setupGWPM: no visible global function definition for
  'registerDoParallel'
Undefined global functions or variables:
  %dopar% Hsapiens PWMscoreStartingAt as foreach i is matchPWM
  metadata<- queryHits registerDoParallel subject subjectHits
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: vtpnet-package.Rd:48-50: Dropping empty section \references
prepare_Rd: vtpnet-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: vtpnet-package.Rd:55-56: Dropping empty section \examples
* 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 ... NONE
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/vtpnet.Rcheck/00check.log'
for details.



Installation output

vtpnet.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/vtpnet_0.22.0.tar.gz && rm -rf vtpnet.buildbin-libdir && mkdir vtpnet.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vtpnet.buildbin-libdir vtpnet_0.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL vtpnet_0.22.0.zip && rm vtpnet_0.22.0.tar.gz vtpnet_0.22.0.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 19.9M  100 19.9M    0     0  76.5M      0 --:--:-- --:--:-- --:--:-- 77.7M

install for i386

* installing *source* package 'vtpnet' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'vtpnet'
    finding HTML links ... done
    vtpnet-package                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'vtpnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vtpnet' as vtpnet_0.22.0.zip
* DONE (vtpnet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'vtpnet' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings