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CHECK results for vtpnet on riesling1

This page was generated on 2021-06-12 12:05:23 -0400 (Sat, 12 Jun 2021).

Package 1966/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vtpnet 0.33.0  (landing page)
VJ Carey
Snapshot Date: 2021-06-11 14:50:09 -0400 (Fri, 11 Jun 2021)
URL: https://git.bioconductor.org/packages/vtpnet
Branch: master
Last Commit: 9ed355f
Last Changed Date: 2021-05-19 11:59:05 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'gwascat' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
To the developers/maintainers of the vtpnet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vtpnet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

Summary

Package: vtpnet
Version: 0.33.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vtpnet.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings vtpnet_0.33.0.tar.gz
StartedAt: 2021-06-12 02:32:05 -0400 (Sat, 12 Jun 2021)
EndedAt: 2021-06-12 02:36:46 -0400 (Sat, 12 Jun 2021)
EllapsedTime: 281.3 seconds
RetCode: 0
Status:   OK   
CheckDir: vtpnet.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vtpnet.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings vtpnet_0.33.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/vtpnet.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '0.33.0'
* 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 'vtpnet' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.1Mb
  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'
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
  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
  'D:/biocbuild/bbs-3.14-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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/vtpnet_0.33.0.tar.gz && rm -rf vtpnet.buildbin-libdir && mkdir vtpnet.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vtpnet.buildbin-libdir vtpnet_0.33.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL vtpnet_0.33.0.zip && rm vtpnet_0.33.0.tar.gz vtpnet_0.33.0.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
  0 19.9M    0  195k    0     0  1212k      0  0:00:16 --:--:--  0:00:16 1204k
 36 19.9M   36 7434k    0     0  6354k      0  0:00:03  0:00:01  0:00:02 6348k
 81 19.9M   81 16.2M    0     0  7678k      0  0:00:02  0:00:02 --:--:-- 7675k
100 19.9M  100 19.9M    0     0  7983k      0  0:00:02  0:00:02 --:--:-- 7980k

install for i386

* installing *source* package 'vtpnet' ...
** using staged installation
** 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 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 'vtpnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vtpnet' as vtpnet_0.33.0.zip
* DONE (vtpnet)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'vtpnet' successfully unpacked and MD5 sums checked

Tests output


Example timings