| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:42 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the OUTRIDER package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1405/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.17.0 (landing page) Christian Mertes
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: OUTRIDER |
| Version: 1.17.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings OUTRIDER_1.17.0.tar.gz |
| StartedAt: 2022-12-29 02:05:55 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 02:13:23 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 448.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings OUTRIDER_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/OUTRIDER.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.17.0'
* 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) 12.2.0'
* 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: 'Rcpp'
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 ... OK
* 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-3.17-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
findEncodingDim 8.44 0.08 8.54
plotFunctions 7.13 0.29 7.46
OUTRIDER 5.43 0.28 33.63
aberrant 2.67 0.04 31.43
computePvalues 2.13 0.00 25.84
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/OUTRIDER.Rcheck/00check.log'
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'OUTRIDER' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/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-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/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-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 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 Dec 29 02:12:31 2022: Initial PCA loss: 6.10461182956774"
[1] "Thu Dec 29 02:12:32 2022: Iteration: 1 loss: 4.36098404230226"
[1] "Thu Dec 29 02:12:33 2022: Iteration: 2 loss: 4.30410232019229"
[1] "Thu Dec 29 02:12:33 2022: Iteration: 3 loss: 4.28198727027249"
[1] "Thu Dec 29 02:12:33 2022: Iteration: 4 loss: 4.26568339294486"
[1] "Thu Dec 29 02:12:34 2022: Iteration: 5 loss: 4.26367985976514"
[1] "Thu Dec 29 02:12:34 2022: Iteration: 6 loss: 4.26362042355757"
Time difference of 3.250414 secs
[1] "Thu Dec 29 02:12:35 2022: 6 Final nb-AE loss: 4.26362042355757"
[1] "Thu Dec 29 02:12:35 2022: Initial PCA loss: 6.10461182956774"
[1] "Thu Dec 29 02:12:36 2022: Iteration: 1 loss: 4.36098404230226"
[1] "Thu Dec 29 02:12:37 2022: Iteration: 2 loss: 4.30410232019229"
[1] "Thu Dec 29 02:12:37 2022: Iteration: 3 loss: 4.28198727027249"
[1] "Thu Dec 29 02:12:38 2022: Iteration: 4 loss: 4.26568339294486"
[1] "Thu Dec 29 02:12:38 2022: Iteration: 5 loss: 4.26367985976514"
[1] "Thu Dec 29 02:12:39 2022: Iteration: 6 loss: 4.26362042355757"
Time difference of 3.130731 secs
[1] "Thu Dec 29 02:12:39 2022: 6 Final nb-AE loss: 4.26362042355757"
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 Dec 29 02:12:50 2022: Initial PCA loss: 4.69775531874642"
[1] "Thu Dec 29 02:12:51 2022: Iteration: 1 loss: 4.2119028742619"
[1] "Thu Dec 29 02:12:51 2022: Iteration: 2 loss: 4.19704054397676"
Time difference of 1.066286 secs
[1] "Thu Dec 29 02:12:51 2022: 2 Final nb-AE loss: 4.19704054397676"
[1] "Evaluation loss: 0.447150066806835 for q=3"
[1] "Thu Dec 29 02:12:52 2022: Initial PCA loss: 4.57818860947212"
[1] "Thu Dec 29 02:12:53 2022: Iteration: 1 loss: 4.12077907323777"
[1] "Thu Dec 29 02:12:53 2022: Iteration: 2 loss: 4.09889607748919"
Time difference of 1.108061 secs
[1] "Thu Dec 29 02:12:53 2022: 2 Final nb-AE loss: 4.09889607748919"
[1] "Evaluation loss: 0.417868905793121 for q=4"
[1] "Thu Dec 29 02:12:54 2022: Initial PCA loss: 4.52813306014329"
[1] "Thu Dec 29 02:12:55 2022: Iteration: 1 loss: 4.04092327161567"
[1] "Thu Dec 29 02:12:55 2022: Iteration: 2 loss: 4.02200031451921"
Time difference of 1.135013 secs
[1] "Thu Dec 29 02:12:55 2022: 2 Final nb-AE loss: 4.02200031451921"
[1] "Evaluation loss: 0.380780898431292 for q=5"
[1] "Thu Dec 29 02:13:03 2022: Initial PCA loss: 6.46616282459584"
[1] "Thu Dec 29 02:13:04 2022: Iteration: 1 loss: 4.81533525649303"
[1] "Thu Dec 29 02:13:05 2022: Iteration: 2 loss: 4.78969612137411"
Time difference of 1.422627 secs
[1] "Thu Dec 29 02:13:05 2022: 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
52.92 1.31 54.29
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 5.43 | 0.28 | 33.63 | |
| OutriderDataSet-class | 0.69 | 0.05 | 0.75 | |
| aberrant | 2.67 | 0.04 | 31.43 | |
| computeGeneLength | 1.31 | 0.02 | 1.35 | |
| computeLatentSpace | 0.59 | 0.00 | 0.60 | |
| computePvalues | 2.13 | 0.00 | 25.84 | |
| computeZscores | 0.64 | 0.00 | 0.64 | |
| controlForConfounders | 0.95 | 0.03 | 1.00 | |
| counts | 0.45 | 0.00 | 0.45 | |
| estimateBestQ | 0.31 | 0.00 | 0.31 | |
| filterExpression | 1.25 | 0.00 | 1.25 | |
| findEncodingDim | 8.44 | 0.08 | 8.54 | |
| fit | 0.92 | 0.00 | 0.92 | |
| fpkm | 0.55 | 0.02 | 0.56 | |
| getter_setter_functions | 2.19 | 0.00 | 2.19 | |
| makeExampleOutriderDataSet | 0.83 | 0.00 | 0.83 | |
| normalizationFactors | 0.54 | 0.00 | 0.54 | |
| plotFunctions | 7.13 | 0.29 | 7.46 | |
| results | 2.39 | 0.00 | 2.39 | |
| sampleExclusionMask | 0.30 | 0.03 | 0.32 | |
| sizeFactors | 0.54 | 0.00 | 0.55 | |