Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 792/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GDSArray 1.24.1  (landing page)
Qian Liu
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/GDSArray
git_branch: RELEASE_3_19
git_last_commit: f5c946e
git_last_commit_date: 2024-05-22 15:38:11 -0400 (Wed, 22 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for GDSArray on nebbiolo1

To the developers/maintainers of the GDSArray package:
- 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 Troubleshooting Build Report for more information.
- 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: GDSArray
Version: 1.24.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GDSArray.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GDSArray_1.24.1.tar.gz
StartedAt: 2024-06-19 23:24:40 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 23:26:47 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 127.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GDSArray.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GDSArray.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GDSArray_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GDSArray.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘GDSArray/DESCRIPTION’ ... OK
* this is package ‘GDSArray’ version ‘1.24.1’
* 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 for sufficient/correct file permissions ... 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 code 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘DelayedArray:::get_Nindex_lengths’
  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 ... WARNING
Undocumented S4 methods:
  generic 'gdsfile<-' and siglist 'GDSFile'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'acquireGDS.Rd'
  ‘...’
Documented arguments not in \usage in Rd file 'acquireGDS.Rd':
  ‘other’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::normalizePath(gdsfn(ga))
   5.   └─base::path.expand(path)
  ── Error ('test_GDSFile-class.R:13:5'): gdsfile getter and setter works ────────
  Error in `gdsfn(gf)`: could not find function "gdsfn"
  Backtrace:
      ▆
   1. └─testthat::expect_equal(gdsfn(gf), file) at test_GDSFile-class.R:13:5
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GDSArray.Rcheck/00check.log’
for details.


Installation output

GDSArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GDSArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘GDSArray’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (GDSArray)

Tests output

GDSArray.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, aperm, 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, 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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, 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 SNP GDS file
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 18 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_GDSArray-method.R:6:5'): filename getter and setter works ──────
Error in `gdsfn(ga)`: could not find function "gdsfn"
Backtrace:
    ▆
 1. ├─testthat::expect_equal(normalizePath(gdsfn(ga)), normalizePath(file)) at test_GDSArray-method.R:6:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─base::normalizePath(gdsfn(ga))
 5.   └─base::path.expand(path)
── Error ('test_GDSFile-class.R:13:5'): gdsfile getter and setter works ────────
Error in `gdsfn(gf)`: could not find function "gdsfn"
Backtrace:
    ▆
 1. └─testthat::expect_equal(gdsfn(gf), file) at test_GDSFile-class.R:13:5
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted

Example timings

GDSArray.Rcheck/GDSArray-Ex.timings

nameusersystemelapsed
GDSArray-classes1.6940.0441.740
GDSArray-methods0.0060.0000.005
GDSFile-class0.0170.0000.016
acquireGDS0.0830.0040.087