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CHECK report for pd.atdschip.tiling on riesling1

This page was generated on 2021-01-14 15:59:10 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE pd.atdschip.tiling PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 262/385HostnameOS / ArchINSTALLBUILDCHECK
pd.atdschip.tiling 0.29.0
Kristof De Beuf
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/pd.atdschip.tiling
Branch: master
Last Commit: c41aa07
Last Changed Date: 2020-10-27 09:56:59 -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: pd.atdschip.tiling
Version: 0.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pd.atdschip.tiling.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pd.atdschip.tiling_0.29.0.tar.gz
StartedAt: 2021-01-14 11:33:36 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:35:56 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 140.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: pd.atdschip.tiling.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pd.atdschip.tiling.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pd.atdschip.tiling_0.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/pd.atdschip.tiling.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 'pd.atdschip.tiling/DESCRIPTION' ... OK
* this is package 'pd.atdschip.tiling' version '0.29.0'
* 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 '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
* 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' 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.13-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:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/pd.atdschip.tiling_0.29.0.tar.gz && rm -rf pd.atdschip.tiling.buildbin-libdir && mkdir pd.atdschip.tiling.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling_0.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pd.atdschip.tiling_0.29.0.zip && rm pd.atdschip.tiling_0.29.0.tar.gz pd.atdschip.tiling_0.29.0.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  135M    0  1212    0     0   6965      0  5:40:12 --:--:--  5:40:12  6925
 52  135M   52 70.9M    0     0  68.2M      0  0:00:01  0:00:01 --:--:-- 68.2M
100  135M  100  135M    0     0  84.2M      0  0:00:01  0:00:01 --:--:-- 84.1M

install for i386

* installing *source* package 'pd.atdschip.tiling' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pd.atdschip.tiling'
    finding HTML links ... done
    pkg                                     html  
REDIRECT:topic	 pd.atdschip.tiling -> pkg.html [ SUCCESS ]
REDIRECT:file	 pkg.html -> pkg.html [ SUCCESS ]
    probeSequences                          html  
REDIRECT:topic	 pmSequence -> probeSequences.html [ SUCCESS ]
REDIRECT:topic	 data:pmSequence -> probeSequences.html [ FAIL ]
REDIRECT:topic	 bgSequence -> probeSequences.html [ SUCCESS ]
REDIRECT:topic	 data:bgSequence -> probeSequences.html [ FAIL ]
REDIRECT:topic	 mmSequence -> probeSequences.html [ SUCCESS ]
REDIRECT:topic	 data:mmSequence -> probeSequences.html [ FAIL ]
REDIRECT:file	 probeSequences.html -> probeSequences.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'pd.atdschip.tiling' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pd.atdschip.tiling' as pd.atdschip.tiling_0.29.0.zip
* DONE (pd.atdschip.tiling)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'pd.atdschip.tiling' successfully unpacked and MD5 sums checked

Tests output


Example timings

pd.atdschip.tiling.Rcheck/examples_i386/pd.atdschip.tiling-Ex.timings

nameusersystemelapsed
probeSequences4.860.114.97

pd.atdschip.tiling.Rcheck/examples_x64/pd.atdschip.tiling-Ex.timings

nameusersystemelapsed
probeSequences4.330.104.42