Christian Mertes
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 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 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:05 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1480/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.20.0 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| 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: 2024-03-28 03:33:46 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:46:41 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 775.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.3.3 (2024-02-29 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 14.13 0.28 110.80
findEncodingDim 12.18 0.14 12.32
plotFunctions 8.88 0.33 9.34
computePvalues 7.58 0.11 119.69
aberrant 3.69 0.00 43.58
* 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.
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)
OUTRIDER.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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 Mar 28 03:45:26 2024: Initial PCA loss: 6.39459542176222"
[1] "Thu Mar 28 03:45:28 2024: Iteration: 1 loss: 4.59078693370444"
[1] "Thu Mar 28 03:45:29 2024: Iteration: 2 loss: 4.52484768606024"
[1] "Thu Mar 28 03:45:30 2024: Iteration: 3 loss: 4.50447410187358"
[1] "Thu Mar 28 03:45:30 2024: Iteration: 4 loss: 4.49096780759337"
[1] "Thu Mar 28 03:45:31 2024: Iteration: 5 loss: 4.48482376388475"
[1] "Thu Mar 28 03:45:31 2024: Iteration: 6 loss: 4.48380774776591"
Time difference of 4.245446 secs
[1] "Thu Mar 28 03:45:31 2024: 6 Final nb-AE loss: 4.48380774776591"
[1] "Thu Mar 28 03:45:33 2024: Initial PCA loss: 6.39459542176222"
[1] "Thu Mar 28 03:45:35 2024: Iteration: 1 loss: 4.59078693370444"
[1] "Thu Mar 28 03:45:35 2024: Iteration: 2 loss: 4.52484768606024"
[1] "Thu Mar 28 03:45:36 2024: Iteration: 3 loss: 4.50447410187358"
[1] "Thu Mar 28 03:45:37 2024: Iteration: 4 loss: 4.49096780759337"
[1] "Thu Mar 28 03:45:38 2024: Iteration: 5 loss: 4.48482376388475"
[1] "Thu Mar 28 03:45:39 2024: Iteration: 6 loss: 4.48380774776591"
Time difference of 4.955799 secs
[1] "Thu Mar 28 03:45:39 2024: 6 Final nb-AE loss: 4.48380774776591"
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 Mar 28 03:45:55 2024: Initial PCA loss: 4.48392584970722"
[1] "Thu Mar 28 03:45:57 2024: Iteration: 1 loss: 4.14935622855858"
[1] "Thu Mar 28 03:45:57 2024: Iteration: 2 loss: 4.12433833116038"
Time difference of 1.555526 secs
[1] "Thu Mar 28 03:45:57 2024: 2 Final nb-AE loss: 4.12433833116038"
[1] "Evaluation loss: 0.837914418052908 for q=3"
[1] "Thu Mar 28 03:45:59 2024: Initial PCA loss: 4.45990787796558"
[1] "Thu Mar 28 03:46:00 2024: Iteration: 1 loss: 4.08542697621589"
[1] "Thu Mar 28 03:46:00 2024: Iteration: 2 loss: 4.05804417209767"
Time difference of 1.300325 secs
[1] "Thu Mar 28 03:46:00 2024: 2 Final nb-AE loss: 4.05804417209767"
[1] "Evaluation loss: 0.853187661469115 for q=4"
[1] "Thu Mar 28 03:46:01 2024: Initial PCA loss: 4.43284824710771"
[1] "Thu Mar 28 03:46:03 2024: Iteration: 1 loss: 4.01879343061641"
[1] "Thu Mar 28 03:46:04 2024: Iteration: 2 loss: 3.98203968276417"
Time difference of 1.80847 secs
[1] "Thu Mar 28 03:46:04 2024: 2 Final nb-AE loss: 3.98203968276417"
[1] "Evaluation loss: 0.785071073194197 for q=5"
Error in x$.self$finalize() : attempt to apply non-function
[1] "Thu Mar 28 03:46:14 2024: Initial PCA loss: 6.46616282459584"
[1] "Thu Mar 28 03:46:16 2024: Iteration: 1 loss: 4.81533525649303"
[1] "Thu Mar 28 03:46:17 2024: Iteration: 2 loss: 4.78969612137411"
Time difference of 1.906115 secs
[1] "Thu Mar 28 03:46:17 2024: 2 Final nb-AE loss: 4.78969612137411"
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
82.60 1.87 84.64
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 14.13 | 0.28 | 110.80 | |
| OutriderDataSet-class | 1.00 | 0.01 | 1.02 | |
| aberrant | 3.69 | 0.00 | 43.58 | |
| computeGeneLength | 1.53 | 0.03 | 1.58 | |
| computeLatentSpace | 0.75 | 0.00 | 0.75 | |
| computePvalues | 7.58 | 0.11 | 119.69 | |
| computeZscores | 1.30 | 0.00 | 1.29 | |
| controlForConfounders | 1.62 | 0.02 | 1.64 | |
| counts | 0.80 | 0.02 | 0.81 | |
| estimateBestQ | 0.56 | 0.02 | 0.58 | |
| filterExpression | 1.62 | 0.03 | 1.66 | |
| findEncodingDim | 12.18 | 0.14 | 12.32 | |
| fit | 0.90 | 0.00 | 0.91 | |
| fpkm | 1.10 | 0.00 | 1.09 | |
| getter_setter_functions | 3.12 | 0.01 | 3.14 | |
| makeExampleOutriderDataSet | 1.03 | 0.00 | 1.04 | |
| normalizationFactors | 0.75 | 0.03 | 0.78 | |
| plotFunctions | 8.88 | 0.33 | 9.34 | |
| results | 3.83 | 0.03 | 3.86 | |
| sampleExclusionMask | 0.40 | 0.02 | 0.42 | |
| sizeFactors | 0.64 | 0.02 | 0.66 | |