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This page was generated on 2024-06-20 14:51 -0400 (Thu, 20 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
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 52/425HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.37.0  (landing page)
Yuan Tian
Snapshot Date: 2024-06-20 07:30 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: devel
git_last_commit: 38aa067
git_last_commit_date: 2024-04-30 10:40:30 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for ChAMPdata on nebbiolo2

To the developers/maintainers of the ChAMPdata 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: ChAMPdata
Version: 2.37.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChAMPdata_2.37.0.tar.gz
StartedAt: 2024-06-20 11:05:06 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 11:09:36 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 270.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChAMPdata_2.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.37.0’
* 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 ‘ChAMPdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 730.0Mb
  sub-directories of 1Mb or more:
    data     606.3Mb
    extdata  123.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 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 ... WARNING
  Error loading dataset 'bloodCtl':
   Error in .requirePackage(package) : 
    unable to find required package 'minfi'
  
  Error loading dataset 'myLoad':
   Error in .requirePackage(package) : 
    unable to find required package 'minfi'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
ChAMPdata-package 31.782  0.736  32.519
testDataSet        9.181  0.188   9.369
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.


Installation output

ChAMPdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ChAMPdata’ ...
** using staged installation
** data
** inst
** 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 (ChAMPdata)

Tests output


Example timings

ChAMPdata.Rcheck/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K2.5740.0602.634
AnnoEPIC3.6930.0603.753
CellTypeMeans27K0.0010.0000.002
CellTypeMeans450K0.0010.0000.002
ChAMPdata-package31.782 0.73632.519
ControlProbes450K0.0010.0000.000
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.3990.1954.595
EPIC.manifest.pop.hg192.5880.0362.624
EPICSimData2.4590.0602.519
MatchGeneName0.0190.0000.019
PathwayList0.3910.0120.403
bloodCtl0.0010.0000.001
hm450.manifest.hg191.7470.0121.759
hm450.manifest.pop.hg191.8290.0451.873
hprdAsigH2.0890.2512.341
illumina450Gr2.9690.0242.993
illuminaEPICGr3.9840.0404.024
multi.hit1.1140.0481.163
probe.features0.6390.0080.647
probe.features.epic1.5200.0281.549
probeInfoALL.epic.lv0.610.000.61
probeInfoALL.lv0.4620.0080.470
snp.hit0.7860.0000.786
testDataSet9.1810.1889.369