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This page was generated on 2021-10-23 15:51:47 -0400 (Sat, 23 Oct 2021).

CHECK results for pd.atdschip.tiling on nebbiolo2

To the developers/maintainers of the pd.atdschip.tiling package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 272/408HostnameOS / ArchINSTALLBUILDCHECK
pd.atdschip.tiling 0.31.0  (landing page)
Kristof De Beuf
Snapshot Date: 2021-10-23 09:30:01 -0400 (Sat, 23 Oct 2021)
git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling
git_branch: master
git_last_commit: 5e1cb43
git_last_commit_date: 2021-05-19 11:35:26 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: pd.atdschip.tiling
Version: 0.31.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:pd.atdschip.tiling.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings pd.atdschip.tiling_0.31.0.tar.gz
StartedAt: 2021-10-23 12:34:25 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 12:36:39 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 133.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pd.atdschip.tiling.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:pd.atdschip.tiling.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings pd.atdschip.tiling_0.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/pd.atdschip.tiling.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pd.atdschip.tiling/DESCRIPTION’ ... OK
* this is package ‘pd.atdschip.tiling’ version ‘0.31.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pd.atdschip.tiling’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 256.4Mb
  sub-directories of 1Mb or more:
    data      43.3Mb
    extdata  213.0Mb
* checking package 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
* 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' call to ‘RSQLite’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘IRanges’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘methods’ ‘oligo’ ‘oligoClasses’
  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
File ‘pd.atdschip.tiling/R/all.R’:
  .onLoad calls:
    require(RSQLite, quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* 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 ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  inst/UnitTests/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking include directives in Makefiles ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
probeSequences 5.268  0.196   5.464
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/pd.atdschip.tiling.Rcheck/00check.log’
for details.



Installation output

pd.atdschip.tiling.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL pd.atdschip.tiling
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘pd.atdschip.tiling’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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
* DONE (pd.atdschip.tiling)

Tests output


Example timings

pd.atdschip.tiling.Rcheck/pd.atdschip.tiling-Ex.timings

nameusersystemelapsed
probeSequences5.2680.1965.464