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This page was generated on 2024-02-14 13:20:58 -0500 (Wed, 14 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4644
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4384
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4413
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4351
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 1700/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
restfulSE 1.25.0  (landing page)
Shweta Gopaulakrishnan
Snapshot Date: 2024-02-13 14:10:17 -0500 (Tue, 13 Feb 2024)
git_url: https://git.bioconductor.org/packages/restfulSE
git_branch: devel
git_last_commit: 0505582
git_last_commit_date: 2023-10-24 10:59:57 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    NA  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    TIMEOUT  skipped

CHECK results for restfulSE on merida1


To the developers/maintainers of the restfulSE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/restfulSE.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: restfulSE
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings restfulSE_1.25.0.tar.gz
StartedAt: 2024-02-14 08:32:41 -0500 (Wed, 14 Feb 2024)
EndedAt: 2024-02-14 08:41:31 -0500 (Wed, 14 Feb 2024)
EllapsedTime: 529.6 seconds
RetCode: 0
Status:   OK  
CheckDir: restfulSE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings restfulSE_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/restfulSE.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘restfulSE/DESCRIPTION’ ... OK
* this is package ‘restfulSE’ version ‘1.25.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘restfulSE’ 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
* 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BQ3_ArraySeed: no visible global function definition for ‘is’
BQ3_ArraySeed: no visible global function definition for ‘new’
BQ3_Source: no visible global function definition for ‘slot’
BQ3_Source: no visible binding for global variable
  ‘SampleTypeLetterCode’
BQ3_Source: no visible global function definition for ‘new’
BQ3m2: no visible binding for global variable ‘SampleTypeLetterCode’
BQM_ArraySeed: no visible global function definition for ‘is’
BQM_ArraySeed: no visible global function definition for ‘new’
BQM_Source: no visible global function definition for ‘new’
TCGA_tablerefs: no visible global function definition for ‘new’
newDA: no visible global function definition for ‘new’
replaceSlots: no visible global function definition for ‘validObject’
seByTumor: no visible global function definition for ‘new’
unsafe_replaceSlots: no visible global function definition for ‘slot’
unsafe_replaceSlots: no visible global function definition for ‘slot<-’
coerce,BQ3_Array-BQ3_Matrix: no visible global function definition for
  ‘new’
coerce,BQM_Array-BQM_Matrix: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  SampleTypeLetterCode is new slot slot<- validObject
Consider adding
  importFrom("methods", "is", "new", "slot", "slot<-", "validObject")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
gtexTiss 7.963  1.458  12.932
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/restfulSE.Rcheck/00check.log’
for details.



Installation output

restfulSE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL restfulSE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘restfulSE’ ...
** 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 (restfulSE)

Tests output

restfulSE.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(restfulSE)
Loading required package: SummarizedExperiment
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: GenomicRanges
Loading required package: stats4
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: S4Vectors

Attaching package: 'S4Vectors'

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: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

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


> library(rhdf5client)
> 
> test_check("restfulSE")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 3 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• CGC_BILLING not set (1): 'testBQ.R:38:2'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 21.253   1.225  27.744 

Example timings

restfulSE.Rcheck/restfulSE-Ex.timings

nameusersystemelapsed
BQ3_Array0.0000.0010.002
BQ3_Source0.0000.0000.001
BQM_Array0.0010.0020.002
BQM_Source0.0010.0000.002
bqConn0.0000.0010.001
cgcConn0.0010.0010.001
goPatt2.3430.3783.588
gtexTiss 7.963 1.45812.932
isbCgcDatasets0.0010.0000.001
isbCgcTables0.0000.0000.001
pancan_SE0.0010.0010.001
seByTumor0.0020.0010.002
tasicCortex0.0020.0010.003