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This page was generated on 2021-11-26 15:05:18 -0500 (Fri, 26 Nov 2021).

CHECK results for GDSArray on tokay2

To the developers/maintainers of the GDSArray package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GDSArray.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 710/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GDSArray 1.14.0  (landing page)
Qian Liu
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/GDSArray
git_branch: RELEASE_3_14
git_last_commit: 26fa732
git_last_commit_date: 2021-10-26 12:43:25 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GDSArray
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GDSArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GDSArray_1.14.0.tar.gz
StartedAt: 2021-11-25 22:46:09 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 22:48:52 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 163.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GDSArray.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GDSArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GDSArray_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GDSArray.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GDSArray/DESCRIPTION' ... OK
* this is package 'GDSArray' version '1.14.0'
* package encoding: UTF-8
* 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 'GDSArray' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'DelayedArray:::get_Nindex_lengths'
  'gdsfmt:::.reopen'
  See the note in ?`:::` about the use of this operator.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
GDSArray-classes 2.22   0.09     9.5
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  This is a SeqArray GDS file
  This is a SeqArray GDS file
  This is a SNP GDS file
  == Failed tests ================================================================
  -- Failure (test_GDSArray-method.R:4:5): gdsfile getter and setter works -------
  gdsfile(ga) not equal to `file`.
  1/1 mismatches
  x[1]: "C:\\Users\\biocbuild\\bbs-3.14-bioc\\R\\library\\SNPRelate\\extdata\\hapm
  x[1]: ap_geno.gds"
  y[1]: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/hapmap_geno.
  y[1]: gds"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  This is a SeqArray GDS file
  This is a SeqArray GDS file
  This is a SNP GDS file
  == Failed tests ================================================================
  -- Failure (test_GDSArray-method.R:4:5): gdsfile getter and setter works -------
  gdsfile(ga) not equal to `file`.
  1/1 mismatches
  x[1]: "C:\\Users\\biocbuild\\bbs-3.14-bioc\\R\\library\\SNPRelate\\extdata\\hapm
  x[1]: ap_geno.gds"
  y[1]: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/hapmap_geno.
  y[1]: gds"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GDSArray.Rcheck/00check.log'
for details.


Installation output

GDSArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GDSArray_1.14.0.tar.gz && rm -rf GDSArray.buildbin-libdir && mkdir GDSArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GDSArray.buildbin-libdir GDSArray_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GDSArray_1.14.0.zip && rm GDSArray_1.14.0.tar.gz GDSArray_1.14.0.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
100 11897  100 11897    0     0   144k      0 --:--:-- --:--:-- --:--:--  147k

install for i386

* installing *source* package 'GDSArray' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GDSArray'
    finding HTML links ... done
    GDSArray-classes                        html  
    GDSArray-methods                        html  
    GDSFile-class                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GDSArray.buildbin-libdir/00LOCK-GDSArray/00new/GDSArray/help/GDSFile.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GDSArray.buildbin-libdir/00LOCK-GDSArray/00new/GDSArray/help/GDSFile+2Cgdsfile-method.html
** building package indices
** installing vignettes
** 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 'GDSArray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GDSArray' as GDSArray_1.14.0.zip
* DONE (GDSArray)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GDSArray' successfully unpacked and MD5 sums checked

Tests output

GDSArray.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> library(testthat)
> library(GDSArray)
Loading required package: gdsfmt
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

> 
> test_check("GDSArray")
This is a SNP GDS file
This is a SNP GDS file
This is a SeqArray GDS file
This is a SeqArray GDS file
This is a SNP GDS file
== Failed tests ================================================================
-- Failure (test_GDSArray-method.R:4:5): gdsfile getter and setter works -------
gdsfile(ga) not equal to `file`.
1/1 mismatches
x[1]: "C:\\Users\\biocbuild\\bbs-3.14-bioc\\R\\library\\SNPRelate\\extdata\\hapm
x[1]: ap_geno.gds"
y[1]: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/hapmap_geno.
y[1]: gds"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted

GDSArray.Rcheck/tests_x64/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> library(testthat)
> library(GDSArray)
Loading required package: gdsfmt
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

> 
> test_check("GDSArray")
This is a SNP GDS file
This is a SNP GDS file
This is a SeqArray GDS file
This is a SeqArray GDS file
This is a SNP GDS file
== Failed tests ================================================================
-- Failure (test_GDSArray-method.R:4:5): gdsfile getter and setter works -------
gdsfile(ga) not equal to `file`.
1/1 mismatches
x[1]: "C:\\Users\\biocbuild\\bbs-3.14-bioc\\R\\library\\SNPRelate\\extdata\\hapm
x[1]: ap_geno.gds"
y[1]: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/hapmap_geno.
y[1]: gds"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted

Example timings

GDSArray.Rcheck/examples_i386/GDSArray-Ex.timings

nameusersystemelapsed
GDSArray-classes2.220.099.50
GDSArray-methods0.010.000.02
GDSFile-class0.010.020.04

GDSArray.Rcheck/examples_x64/GDSArray-Ex.timings

nameusersystemelapsed
GDSArray-classes2.770.163.76
GDSArray-methods0.010.000.02
GDSFile-class0.010.030.04