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CHECK report for ChAMPdata on riesling1

This page was generated on 2021-01-14 15:59:07 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ChAMPdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 56/385HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.23.0
Yuan Tian
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: master
Last Commit: 9095bbe
Last Changed Date: 2020-10-27 10:05:58 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: ChAMPdata
Version: 2.23.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMPdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChAMPdata_2.23.0.tar.gz
StartedAt: 2021-01-14 11:09:49 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:14:45 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 295.9 seconds
RetCode: 0
Status:  OK  
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMPdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChAMPdata_2.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.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 'ChAMPdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChAMPdata' version '2.23.0'
* 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 'ChAMPdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 743.1Mb
  sub-directories of 1Mb or more:
    data     619.2Mb
    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
* 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 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 ... NOTE
  Error loading dataset 'bloodCtl':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "elementMetadata" for this object of class "RGChannelSetExtended"
  
  Error loading dataset 'myLoad':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "elementMetadata" for this object of class "MethylSet"
  
* checking data for ASCII and uncompressed saves ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
ChAMPdata-package 23.19   0.56   23.75
testDataSet        8.17   0.31    8.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
ChAMPdata-package 21.38   0.53   21.91
testDataSet        6.81   0.29    7.10
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.Rcheck/00check.log'
for details.



Installation output

ChAMPdata.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/ChAMPdata_2.23.0.tar.gz && rm -rf ChAMPdata.buildbin-libdir && mkdir ChAMPdata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChAMPdata.buildbin-libdir ChAMPdata_2.23.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChAMPdata_2.23.0.zip && rm ChAMPdata_2.23.0.tar.gz ChAMPdata_2.23.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  6  679M    6 46.4M    0     0  76.1M      0  0:00:08 --:--:--  0:00:08 75.9M
 22  679M   22  154M    0     0  95.8M      0  0:00:07  0:00:01  0:00:06 95.7M
 39  679M   39  265M    0     0   101M      0  0:00:06  0:00:02  0:00:04  101M
 52  679M   52  354M    0     0  98.0M      0  0:00:06  0:00:03  0:00:03 98.0M
 66  679M   66  454M    0     0  98.5M      0  0:00:06  0:00:04  0:00:02 98.5M
 83  679M   83  567M    0     0   101M      0  0:00:06  0:00:05  0:00:01  104M
 97  679M   97  665M    0     0   100M      0  0:00:06  0:00:06 --:--:--  101M
100  679M  100  679M    0     0  99.3M      0  0:00:06  0:00:06 --:--:-- 97.8M

install for i386

* installing *source* package 'ChAMPdata' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'ChAMPdata'
    finding HTML links ... done
    Anno450K                                html  
REDIRECT:topic	 Anno450K -> Anno450K.html [ SUCCESS ]
    AnnoEPIC                                html  
REDIRECT:topic	 AnnoEPIC -> AnnoEPIC.html [ SUCCESS ]
    CellTypeMeans27K                        html  
REDIRECT:topic	 CellTypeMeans27K -> CellTypeMeans27K.html [ SUCCESS ]
    CellTypeMeans450K                       html  
REDIRECT:topic	 CellTypeMeans450K -> CellTypeMeans450K.html [ SUCCESS ]
    ChAMPdata-package                       html  
REDIRECT:topic	 ChAMPdata-package -> ChAMPdata-package.html [ SUCCESS ]
REDIRECT:topic	 ChAMPdata -> ChAMPdata-package.html [ SUCCESS ]
    ControlProbes450K                       html  
REDIRECT:topic	 ControlProbes450K -> ControlProbes450K.html [ SUCCESS ]
    ControlProbesEPIC                       html  
REDIRECT:topic	 ControlProbesEPIC -> ControlProbesEPIC.html [ SUCCESS ]
    EPIC.manifest.hg19                      html  
REDIRECT:topic	 EPIC.manifest.hg19 -> EPIC.manifest.hg19.html [ SUCCESS ]
    EPIC.manifest.pop.hg19                  html  
REDIRECT:topic	 EPIC.manifest.pop.hg19 -> EPIC.manifest.pop.hg19.html [ SUCCESS ]
    EPICSimData                             html  
REDIRECT:topic	 EPICSimData -> EPICSimData.html [ SUCCESS ]
    MatchGeneName                           html  
REDIRECT:topic	 MatchGeneName -> MatchGeneName.html [ SUCCESS ]
    PathwayList                             html  
REDIRECT:topic	 PathwayList -> PathwayList.html [ SUCCESS ]
    bloodCtl                                html  
REDIRECT:topic	 bloodCtl -> bloodCtl.html [ SUCCESS ]
    hm450.manifest.hg19                     html  
REDIRECT:topic	 hm450.manifest.hg19 -> hm450.manifest.hg19.html [ SUCCESS ]
    hm450.manifest.pop.hg19                 html  
REDIRECT:topic	 hm450.manifest.pop.hg19 -> hm450.manifest.pop.hg19.html [ SUCCESS ]
    hprdAsigH                               html  
REDIRECT:topic	 hprdAsigH -> hprdAsigH.html [ SUCCESS ]
    illumina450Gr                           html  
REDIRECT:topic	 illumina450Gr -> illumina450Gr.html [ SUCCESS ]
    illuminaEPICGr                          html  
REDIRECT:topic	 illuminaEPICGr -> illuminaEPICGr.html [ SUCCESS ]
    multi.hit                               html  
REDIRECT:topic	 multi.hit -> multi.hit.html [ SUCCESS ]
    probe.features                          html  
REDIRECT:topic	 probe.features -> probe.features.html [ SUCCESS ]
    probe.features.epic                     html  
REDIRECT:topic	 probe.features.epic -> probe.features.epic.html [ SUCCESS ]
    probeInfoALL.epic.lv                    html  
REDIRECT:topic	 probeInfoALL.epic.lv -> probeInfoALL.epic.lv.html [ SUCCESS ]
    probeInfoALL.lv                         html  
REDIRECT:topic	 probeInfoALL.lv -> probeInfoALL.lv.html [ SUCCESS ]
    snp.hit                                 html  
REDIRECT:topic	 snp.hit -> snp.hit.html [ SUCCESS ]
    testDataSet                             html  
REDIRECT:topic	 testDataSet -> testDataSet.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 'ChAMPdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChAMPdata' as ChAMPdata_2.23.0.zip
* DONE (ChAMPdata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'ChAMPdata' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChAMPdata.Rcheck/examples_i386/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K1.400.051.44
AnnoEPIC3.730.003.73
CellTypeMeans27K0.000.020.02
CellTypeMeans450K000
ChAMPdata-package23.19 0.5623.75
ControlProbes450K000
ControlProbesEPIC000
EPIC.manifest.hg193.500.083.58
EPIC.manifest.pop.hg192.260.192.45
EPICSimData1.670.011.69
MatchGeneName0.020.000.01
PathwayList0.280.020.29
bloodCtl000
hm450.manifest.hg191.330.041.38
hm450.manifest.pop.hg190.780.030.81
hprdAsigH2.060.182.23
illumina450Gr1.300.011.31
illuminaEPICGr2.020.002.02
multi.hit0.590.000.59
probe.features0.470.030.50
probe.features.epic1.470.021.48
probeInfoALL.epic.lv0.540.000.55
probeInfoALL.lv0.410.010.42
snp.hit0.610.020.63
testDataSet8.170.318.48

ChAMPdata.Rcheck/examples_x64/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K1.700.061.76
AnnoEPIC4.310.024.32
CellTypeMeans27K0.000.010.02
CellTypeMeans450K000
ChAMPdata-package21.38 0.5321.91
ControlProbes450K000
ControlProbesEPIC000
EPIC.manifest.hg193.330.133.46
EPIC.manifest.pop.hg191.950.031.98
EPICSimData1.890.132.02
MatchGeneName0.020.000.01
PathwayList0.250.030.28
bloodCtl0.010.000.02
hm450.manifest.hg192.140.202.34
hm450.manifest.pop.hg190.690.020.71
hprdAsigH1.410.061.47
illumina450Gr1.280.111.39
illuminaEPICGr1.730.011.75
multi.hit0.590.000.60
probe.features0.470.020.48
probe.features.epic1.100.051.14
probeInfoALL.epic.lv0.470.010.49
probeInfoALL.lv0.310.060.37
snp.hit0.550.030.58
testDataSet6.810.297.10