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This page was generated on 2024-05-15 13:46:32 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 735/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FRASER 2.1.0  (landing page)
Christian Mertes
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/FRASER
git_branch: devel
git_last_commit: 14fe09e
git_last_commit_date: 2024-04-30 11:23:25 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for FRASER on kunpeng2


To the developers/maintainers of the FRASER package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FRASER.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: FRASER
Version: 2.0.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FRASER.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FRASER_2.0.0.tar.gz
StartedAt: 2024-05-09 07:31:37 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 07:53:30 -0000 (Thu, 09 May 2024)
EllapsedTime: 1312.4 seconds
RetCode: 0
Status:   OK  
CheckDir: FRASER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FRASER.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FRASER_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FRASER.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FRASER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FRASER’ version ‘2.0.0’
* 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 ‘FRASER’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   6.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::selectSome' 'ggbio:::.buildFacetsFromArgs'
  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 ... NOTE
annotateRangesWithTxDb: no visible binding for global variable
  ‘include’
calculatePadjValuesOnSubset : <anonymous>: no visible binding for
  global variable ‘gene_rowIdx’
plotVolcano.FRASER: no visible binding for global variable
  ‘aberrantLabel’
plotVolcano,FraserDataSet: no visible binding for global variable
  ‘aberrantLabel’
results,FraserDataSet: no visible binding for global variable ‘padjust’
results,FraserDataSet: no visible binding for global variable
  ‘pValueGene’
results,FraserDataSet: no visible binding for global variable
  ‘padjustGene’
Undefined global functions or variables:
  aberrantLabel gene_rowIdx include pValueGene padjust padjustGene
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
plotFunctions              164.718  0.879 165.903
potentialImpactAnnotations  57.197  0.339  57.625
FRASER                      52.942  0.544  53.647
injectOutliers              36.572  0.136  36.732
results                     29.793  0.072  29.917
optimHyperParams            28.510  0.219  28.786
annotateRanges              27.647  0.127  65.947
mergeExternalData           27.541  0.072  27.667
calculatePSIValues          24.136  0.319  24.573
fds-methods                 22.346  0.103  22.487
filtering                   21.874  0.048  21.957
getter_setter_functions     20.920  0.048  21.007
createTestFraserDataSet     20.728  0.059  20.832
counts                      20.616  0.109  20.820
subset                      20.244  0.124  20.402
makeSimulatedFraserDataSet   5.537  0.008   5.555
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/FRASER.Rcheck/00check.log’
for details.


Installation output

FRASER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL FRASER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘FRASER’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o FRASER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-FRASER/00new/FRASER/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FRASER)

Tests output

FRASER.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(FRASER)
Loading required package: BiocParallel
Loading required package: data.table
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
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
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

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

Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

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: 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


Attaching package: 'FRASER'

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

    samples

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

    mapSeqlevels

> 
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+     register(SerialParam())
+ }
> 
> test_check("FRASER")
[ FAIL 0 | WARN 523 | SKIP 0 | PASS 97 ]

[ FAIL 0 | WARN 523 | SKIP 0 | PASS 97 ]
> 
> proc.time()
   user  system elapsed 
241.648  54.967 219.125 

Example timings

FRASER.Rcheck/FRASER-Ex.timings

nameusersystemelapsed
FRASER52.942 0.54453.647
FraserDataSet0.5230.0120.538
annotateRanges27.647 0.12765.947
calculatePSIValues24.136 0.31924.573
countRNA1.1480.0121.166
counts20.616 0.10920.820
createTestFraserDataSet20.728 0.05920.832
fds-methods22.346 0.10322.487
filtering21.874 0.04821.957
getter_setter_functions20.920 0.04821.007
injectOutliers36.572 0.13636.732
loadFraserDataSet0.4580.0000.458
makeSimulatedFraserDataSet5.5370.0085.555
mergeExternalData27.541 0.07227.667
optimHyperParams28.510 0.21928.786
plotFunctions164.718 0.879165.903
potentialImpactAnnotations57.197 0.33957.625
psiTypes000
results29.793 0.07229.917
subset20.244 0.12420.402