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CHECK report for MIGSAdata on riesling1

This page was generated on 2021-01-18 15:58:48 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE MIGSAdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 223/385HostnameOS / ArchINSTALLBUILDCHECK
MIGSAdata 1.15.0
Juan C. Rodriguez
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/MIGSAdata
Branch: master
Last Commit: f10eae5
Last Changed Date: 2020-10-27 10:22:40 -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: MIGSAdata
Version: 1.15.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MIGSAdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MIGSAdata_1.15.0.tar.gz
StartedAt: 2021-01-18 11:32:15 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:35:47 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 212.3 seconds
RetCode: 0
Status:  OK  
CheckDir: MIGSAdata.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MIGSAdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MIGSAdata_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/MIGSAdata.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 'MIGSAdata/DESCRIPTION' ... OK
* this is package 'MIGSAdata' version '1.15.0'
* 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 'MIGSAdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 80.5Mb
  sub-directories of 1Mb or more:
    data  80.4Mb
* 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/MIGSAdata.Rcheck/00check.log'
for details.



Installation output

MIGSAdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/MIGSAdata_1.15.0.tar.gz && rm -rf MIGSAdata.buildbin-libdir && mkdir MIGSAdata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MIGSAdata.buildbin-libdir MIGSAdata_1.15.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MIGSAdata_1.15.0.zip && rm MIGSAdata_1.15.0.tar.gz MIGSAdata_1.15.0.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
  0 80.4M    0  7053    0     0  57811      0  0:24:18 --:--:--  0:24:18 57341
  1 80.4M    1  966k    0     0   865k      0  0:01:35  0:00:01  0:01:34  865k
  2 80.4M    2 2042k    0     0   921k      0  0:01:29  0:00:02  0:01:27  921k
 14 80.4M   14 11.5M    0     0  3713k      0  0:00:22  0:00:03  0:00:19 3712k
 46 80.4M   46 37.5M    0     0  9331k      0  0:00:08  0:00:04  0:00:04 9329k
 63 80.4M   63 51.1M    0     0  10.0M      0  0:00:07  0:00:05  0:00:02 10.3M
 65 80.4M   65 52.7M    0     0  8791k      0  0:00:09  0:00:06  0:00:03 10.3M
 96 80.4M   96 77.2M    0     0  10.3M      0  0:00:07  0:00:07 --:--:-- 14.2M
100 80.4M  100 80.4M    0     0  10.5M      0  0:00:07  0:00:07 --:--:-- 15.5M

install for i386

* installing *source* package 'MIGSAdata' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MIGSAdata'
    finding HTML links ... done
    MIGSAdata                               html  
REDIRECT:topic	 MIGSAdata -> MIGSAdata.html [ SUCCESS ]
    bcMigsaResAsList                        html  
REDIRECT:topic	 bcMigsaResAsList -> bcMigsaResAsList.html [ SUCCESS ]
    mGSZspeedup                             html  
REDIRECT:topic	 mGSZspeedup -> mGSZspeedup.html [ SUCCESS ]
    pbcmcData                               html  
REDIRECT:topic	 pbcmcData -> pbcmcData.html [ SUCCESS ]
    tcgaMAdata                              html  
REDIRECT:topic	 tcgaMAdata -> tcgaMAdata.html [ SUCCESS ]
    tcgaRNAseqData                          html  
REDIRECT:topic	 tcgaRNAseqData -> tcgaRNAseqData.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 'MIGSAdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIGSAdata' as MIGSAdata_1.15.0.zip
* DONE (MIGSAdata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'MIGSAdata' successfully unpacked and MD5 sums checked

Tests output

MIGSAdata.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("MIGSAdata")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Mon Jan 18 11:33:08 2021 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MIGSAdata RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   9.09    0.21    9.29 

MIGSAdata.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("MIGSAdata")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Mon Jan 18 11:33:16 2021 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MIGSAdata RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   7.40    0.20    7.62 

Example timings