Christian Mertes
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: master |
| git_last_commit: 82ab04c |
| git_last_commit_date: 2021-10-26 12:45:42 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:14 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1364/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.13.0 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OUTRIDER |
| Version: 1.13.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OUTRIDER_1.13.0.tar.gz |
| StartedAt: 2022-03-17 19:48:06 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:55:50 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 464.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OUTRIDER_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/OUTRIDER.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OUTRIDER' version '1.13.0'
* 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
* 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 'D:/biocbuild/bbs-3.15-bioc/R/library/OUTRIDER/libs/x64/OUTRIDER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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. 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEncodingDim 6.93 0.00 6.93
plotFunctions 5.78 0.30 6.08
OUTRIDER 3.75 0.17 32.33
aberrant 2.23 0.02 30.05
computePvalues 2.00 0.01 30.09
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.
OUTRIDER.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'OUTRIDER' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OUTRIDER/00new/OUTRIDER/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'OUTRIDER'
finding HTML links ... done
OUTRIDER html
OutriderDataSet-class html
aberrant html
computeGeneLength html
computeLatentSpace html
computePvalues html
computeZscores html
controlForConfounders html
counts html
estimateBestQ html
filterExpression html
findEncodingDim html
fit html
fpkm html
getter_setter_functions html
makeExampleOutriderDataSet html
normalizationFactors html
plotFunctions html
results html
sampleExclusionMask html
sizeFactors html
** 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)
Making 'packages.html' ... done
OUTRIDER.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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, 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 Mar 17 19:54:48 2022: Initial PCA loss: 6.09730784164367"
[1] "Thu Mar 17 19:54:50 2022: Iteration: 1 loss: 4.37096108448462"
[1] "Thu Mar 17 19:54:50 2022: Iteration: 2 loss: 4.32007481757969"
[1] "Thu Mar 17 19:54:51 2022: Iteration: 3 loss: 4.29865666344361"
[1] "Thu Mar 17 19:54:51 2022: Iteration: 4 loss: 4.27985282810642"
[1] "Thu Mar 17 19:54:52 2022: Iteration: 5 loss: 4.25095384272757"
[1] "Thu Mar 17 19:54:52 2022: Iteration: 6 loss: 4.22505335378728"
Time difference of 3.077628 secs
[1] "Thu Mar 17 19:54:52 2022: 6 Final nb-AE loss: 4.22505335378728"
[1] "Thu Mar 17 19:54:53 2022: Initial PCA loss: 6.09730784164367"
[1] "Thu Mar 17 19:54:54 2022: Iteration: 1 loss: 4.37096108448462"
[1] "Thu Mar 17 19:54:55 2022: Iteration: 2 loss: 4.32007481757969"
[1] "Thu Mar 17 19:54:55 2022: Iteration: 3 loss: 4.29865666344361"
[1] "Thu Mar 17 19:54:56 2022: Iteration: 4 loss: 4.27985282810642"
[1] "Thu Mar 17 19:54:56 2022: Iteration: 5 loss: 4.25095384272757"
[1] "Thu Mar 17 19:54:56 2022: Iteration: 6 loss: 4.22505335378728"
Time difference of 2.999518 secs
[1] "Thu Mar 17 19:54:56 2022: 6 Final nb-AE loss: 4.22505335378728"
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 17 19:55:10 2022: Initial PCA loss: 4.47577617680092"
[1] "Thu Mar 17 19:55:11 2022: Iteration: 1 loss: 4.13719508882248"
[1] "Thu Mar 17 19:55:11 2022: Iteration: 2 loss: 4.13052842172437"
Time difference of 1.296665 secs
[1] "Thu Mar 17 19:55:11 2022: 2 Final nb-AE loss: 4.13052842172437"
[1] "Evaluation loss: 0.541017268060457 for q=3"
[1] "Thu Mar 17 19:55:12 2022: Initial PCA loss: 4.45451397869572"
[1] "Thu Mar 17 19:55:14 2022: Iteration: 1 loss: 4.07317977087015"
[1] "Thu Mar 17 19:55:14 2022: Iteration: 2 loss: 4.05790304644131"
Time difference of 1.421646 secs
[1] "Thu Mar 17 19:55:14 2022: 2 Final nb-AE loss: 4.05790304644131"
[1] "Evaluation loss: 0.582404530773154 for q=4"
[1] "Thu Mar 17 19:55:15 2022: Initial PCA loss: 4.42786275045834"
[1] "Thu Mar 17 19:55:16 2022: Iteration: 1 loss: 3.9847527061761"
[1] "Thu Mar 17 19:55:17 2022: Iteration: 2 loss: 3.96556032716693"
Time difference of 1.296668 secs
[1] "Thu Mar 17 19:55:17 2022: 2 Final nb-AE loss: 3.96556032716693"
[1] "Evaluation loss: 0.505113628716774 for q=5"
[1] "Thu Mar 17 19:55:26 2022: Initial PCA loss: 6.46616282459584"
[1] "Thu Mar 17 19:55:28 2022: Iteration: 1 loss: 4.81544153905003"
[1] "Thu Mar 17 19:55:28 2022: Iteration: 2 loss: 4.78966886254391"
Time difference of 1.624735 secs
[1] "Thu Mar 17 19:55:28 2022: 2 Final nb-AE loss: 4.78966886254391"
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
62.29 1.43 63.70
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 3.75 | 0.17 | 32.33 | |
| OutriderDataSet-class | 0.56 | 0.00 | 0.56 | |
| aberrant | 2.23 | 0.02 | 30.05 | |
| computeGeneLength | 0.94 | 0.00 | 0.94 | |
| computeLatentSpace | 0.49 | 0.00 | 0.48 | |
| computePvalues | 2.00 | 0.01 | 30.09 | |
| computeZscores | 0.60 | 0.05 | 0.66 | |
| controlForConfounders | 0.82 | 0.09 | 0.91 | |
| counts | 0.37 | 0.00 | 0.37 | |
| estimateBestQ | 0.28 | 0.00 | 0.28 | |
| filterExpression | 1.03 | 0.00 | 1.03 | |
| findEncodingDim | 6.93 | 0.00 | 6.93 | |
| fit | 0.59 | 0.00 | 0.59 | |
| fpkm | 0.47 | 0.02 | 0.48 | |
| getter_setter_functions | 1.91 | 0.00 | 1.91 | |
| makeExampleOutriderDataSet | 0.7 | 0.0 | 0.7 | |
| normalizationFactors | 0.47 | 0.00 | 0.47 | |
| plotFunctions | 5.78 | 0.30 | 6.08 | |
| results | 1.69 | 0.00 | 1.68 | |
| sampleExclusionMask | 0.28 | 0.00 | 0.29 | |
| sizeFactors | 0.42 | 0.00 | 0.42 | |