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This page was generated on 2024-02-22 11:37:04 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1480/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.20.0  (landing page)
Christian Mertes
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/OUTRIDER
git_branch: RELEASE_3_18
git_last_commit: 0528b44
git_last_commit_date: 2023-10-24 11:06:34 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for OUTRIDER on palomino4


To the developers/maintainers of the OUTRIDER package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.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: OUTRIDER
Version: 1.20.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings OUTRIDER_1.20.0.tar.gz
StartedAt: 2024-02-22 04:43:13 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 04:54:21 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 668.0 seconds
RetCode: 0
Status:   OK  
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings OUTRIDER_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/OUTRIDER.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OUTRIDER' version '1.20.0'
* 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 'OUTRIDER' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
padjOnSubset: no visible global function definition for 'bpmapply'
Undefined global functions or variables:
  bpmapply
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/OUTRIDER/libs/x64/OUTRIDER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
OUTRIDER        12.11   0.38  110.89
findEncodingDim 10.28   0.05   10.35
plotFunctions    7.77   0.23    8.00
computePvalues   7.05   0.09  105.61
aberrant         3.14   0.07   38.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.



Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'OUTRIDER' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-OUTRIDER/00new/OUTRIDER/libs/x64
** 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 (OUTRIDER)

Tests output

OUTRIDER.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 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(OUTRIDER)
Loading required package: BiocParallel
Loading required package: GenomicFeatures
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: data.table

Attaching package: 'data.table'

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

    shift

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

    shift

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

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

> 
> register(SerialParam())
> 
> test_check("OUTRIDER")
[1] "Thu Feb 22 04:53:20 2024: Initial PCA loss: 6.36735577297173"
[1] "Thu Feb 22 04:53:21 2024: Iteration: 1 loss: 4.58323084080103"
[1] "Thu Feb 22 04:53:22 2024: Iteration: 2 loss: 4.49921854582372"
[1] "Thu Feb 22 04:53:22 2024: Iteration: 3 loss: 4.46193062532251"
[1] "Thu Feb 22 04:53:23 2024: Iteration: 4 loss: 4.45457134500562"
[1] "Thu Feb 22 04:53:23 2024: Iteration: 5 loss: 4.45311932646774"
[1] "Thu Feb 22 04:53:24 2024: Iteration: 6 loss: 4.45221290094061"
Time difference of 3.86748 secs
[1] "Thu Feb 22 04:53:24 2024: 6 Final nb-AE loss: 4.45221290094061"
[1] "Thu Feb 22 04:53:25 2024: Initial PCA loss: 6.36735577297173"
[1] "Thu Feb 22 04:53:26 2024: Iteration: 1 loss: 4.58323084080103"
[1] "Thu Feb 22 04:53:27 2024: Iteration: 2 loss: 4.49921854582372"
[1] "Thu Feb 22 04:53:27 2024: Iteration: 3 loss: 4.46193062532251"
[1] "Thu Feb 22 04:53:28 2024: Iteration: 4 loss: 4.45457134500562"
[1] "Thu Feb 22 04:53:29 2024: Iteration: 5 loss: 4.45311932646774"
[1] "Thu Feb 22 04:53:29 2024: Iteration: 6 loss: 4.45221290094061"
Time difference of 3.517657 secs
[1] "Thu Feb 22 04:53:29 2024: 6 Final nb-AE loss: 4.45221290094061"
class: OutriderDataSet
class: RangedSummarizedExperiment 
dim: 100 50 
metadata(1): version
assays(1): counts
rownames(100): ENSG00000223972.4 ENSG00000227232.4 ...
  ENSG00000107404.13 ENSG00000162576.12
rowData names(0):
colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ...
  GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D
colData names(1): sampleID
[1] "Thu Feb 22 04:53:42 2024: Initial PCA loss: 4.48452494271901"
[1] "Thu Feb 22 04:53:43 2024: Iteration: 1 loss: 4.09275252278402"
[1] "Thu Feb 22 04:53:44 2024: Iteration: 2 loss: 4.0732098689548"
Time difference of 1.232087 secs
[1] "Thu Feb 22 04:53:44 2024: 2 Final nb-AE loss: 4.0732098689548"
[1] "Evaluation loss: 0.406601763753087 for q=3"
[1] "Thu Feb 22 04:53:45 2024: Initial PCA loss: 4.43978912938032"
[1] "Thu Feb 22 04:53:46 2024: Iteration: 1 loss: 4.01428258788813"
[1] "Thu Feb 22 04:53:47 2024: Iteration: 2 loss: 3.99582433921213"
Time difference of 1.260727 secs
[1] "Thu Feb 22 04:53:47 2024: 2 Final nb-AE loss: 3.99582433921213"
[1] "Evaluation loss: 0.15292141502564 for q=4"
[1] "Thu Feb 22 04:53:47 2024: Initial PCA loss: 4.41573713043904"
[1] "Thu Feb 22 04:53:48 2024: Iteration: 1 loss: 3.9359129391748"
[1] "Thu Feb 22 04:53:49 2024: Iteration: 2 loss: 3.90916916865603"
Time difference of 1.191118 secs
[1] "Thu Feb 22 04:53:49 2024: 2 Final nb-AE loss: 3.90916916865603"
[1] "Evaluation loss: 0.403731333142172 for q=5"
[1] "Thu Feb 22 04:53:58 2024: Initial PCA loss: 6.46616282459584"
[1] "Thu Feb 22 04:54:00 2024: Iteration: 1 loss: 4.81533525649303"
[1] "Thu Feb 22 04:54:01 2024: Iteration: 2 loss: 4.78969612137411"
Time difference of 2.05435 secs
[1] "Thu Feb 22 04:54:01 2024: 2 Final nb-AE loss: 4.78969612137411"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 103 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
  67.07    1.57   68.67 

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER 12.11 0.38110.89
OutriderDataSet-class0.810.040.86
aberrant 3.14 0.0738.78
computeGeneLength1.380.011.39
computeLatentSpace0.670.020.72
computePvalues 7.05 0.09105.61
computeZscores0.810.000.81
controlForConfounders1.180.001.19
counts0.540.000.53
estimateBestQ0.350.020.38
filterExpression1.410.011.43
findEncodingDim10.28 0.0510.35
fit0.880.010.89
fpkm0.810.000.82
getter_setter_functions3.090.003.09
makeExampleOutriderDataSet1.080.021.09
normalizationFactors0.670.000.68
plotFunctions7.770.238.00
results2.920.022.93
sampleExclusionMask0.440.000.44
sizeFactors0.550.030.58