Back to Build/check report for BioC 3.17 experimental data
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 283/421HostnameOS / ArchINSTALLBUILDCHECK
pd.atdschip.tiling 0.38.0  (landing page)
Kristof De Beuf
Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling
git_branch: RELEASE_3_17
git_last_commit: 178a74d
git_last_commit_date: 2023-04-25 09:54:58 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

CHECK results for pd.atdschip.tiling on nebbiolo1


To the developers/maintainers of the pd.atdschip.tiling package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: pd.atdschip.tiling
Version: 0.38.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pd.atdschip.tiling.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pd.atdschip.tiling_0.38.0.tar.gz
StartedAt: 2023-10-12 11:50:19 -0400 (Thu, 12 Oct 2023)
EndedAt: 2023-10-12 11:52:42 -0400 (Thu, 12 Oct 2023)
EllapsedTime: 143.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pd.atdschip.tiling.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pd.atdschip.tiling.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pd.atdschip.tiling_0.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/pd.atdschip.tiling.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘pd.atdschip.tiling/DESCRIPTION’ ... OK
* this is package ‘pd.atdschip.tiling’ version ‘0.38.0’
* 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 183.5Mb
  sub-directories of 1Mb or more:
    data      43.2Mb
    extdata  140.2Mb
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 6.32  0.219    6.54
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-data-experiment/meat/pd.atdschip.tiling.Rcheck/00check.log’
for details.



Installation output

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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pd.atdschip.tiling
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
probeSequences6.3200.2196.540