Christian Mertes
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_13 |
| git_last_commit: c9c57ae |
| git_last_commit_date: 2021-05-19 12:36:45 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
|
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 1330/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.10.0 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OUTRIDER |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OUTRIDER_1.10.0.tar.gz |
| StartedAt: 2021-10-14 22:01:58 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:14:42 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 763.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OUTRIDER_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.10.0’
* 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 ‘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 is not available
* 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 45.792 0.264 46.106
plotFunctions 25.280 0.422 25.744
aberrant 9.698 2.282 6.260
getter_setter_functions 11.571 0.035 11.632
OUTRIDER 8.735 1.119 9.025
results 9.427 0.069 9.505
fit 6.078 0.106 6.188
* 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
‘/Users/biocbuild/bbs-3.13-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-OUTRIDER/00new/OUTRIDER/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 (OUTRIDER)
OUTRIDER.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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 Oct 14 22:11:31 2021: Initial PCA loss: 6.52820461605301"
[1] "Thu Oct 14 22:11:36 2021: Iteration: 1 loss: 4.63297178626901"
[1] "Thu Oct 14 22:11:39 2021: Iteration: 2 loss: 4.55234173455206"
[1] "Thu Oct 14 22:11:42 2021: Iteration: 3 loss: 4.51899616672322"
[1] "Thu Oct 14 22:11:45 2021: Iteration: 4 loss: 4.49726795737891"
[1] "Thu Oct 14 22:11:48 2021: Iteration: 5 loss: 4.48712179628123"
[1] "Thu Oct 14 22:11:51 2021: Iteration: 6 loss: 4.4855176435821"
Time difference of 17.62503 secs
[1] "Thu Oct 14 22:11:51 2021: 6 Final nb-AE loss: 4.4855176435821"
[1] "Thu Oct 14 22:11:54 2021: Initial PCA loss: 6.52820461605301"
[1] "Thu Oct 14 22:12:00 2021: Iteration: 1 loss: 4.63297178626901"
[1] "Thu Oct 14 22:12:03 2021: Iteration: 2 loss: 4.55234173455206"
[1] "Thu Oct 14 22:12:06 2021: Iteration: 3 loss: 4.51899616672322"
[1] "Thu Oct 14 22:12:09 2021: Iteration: 4 loss: 4.49726795737891"
[1] "Thu Oct 14 22:12:12 2021: Iteration: 5 loss: 4.48712179628123"
[1] "Thu Oct 14 22:12:15 2021: Iteration: 6 loss: 4.4855176435821"
Time difference of 17.77195 secs
[1] "Thu Oct 14 22:12:15 2021: 6 Final nb-AE loss: 4.4855176435821"
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 Oct 14 22:12:45 2021: Initial PCA loss: 4.44901974982455"
[1] "Thu Oct 14 22:12:52 2021: Iteration: 1 loss: 4.13588958470146"
[1] "Thu Oct 14 22:12:55 2021: Iteration: 2 loss: 4.12842508846871"
Time difference of 6.781232 secs
[1] "Thu Oct 14 22:12:55 2021: 2 Final nb-AE loss: 4.12842508846871"
[1] "Evaluation loss: 0.349664859208444 for q=3"
[1] "Thu Oct 14 22:12:58 2021: Initial PCA loss: 4.42436019015585"
[1] "Thu Oct 14 22:13:05 2021: Iteration: 1 loss: 4.05226640142655"
[1] "Thu Oct 14 22:13:08 2021: Iteration: 2 loss: 4.0402760863617"
Time difference of 7.203056 secs
[1] "Thu Oct 14 22:13:08 2021: 2 Final nb-AE loss: 4.0402760863617"
[1] "Evaluation loss: 0.334758330229599 for q=4"
[1] "Thu Oct 14 22:13:11 2021: Initial PCA loss: 4.40145640895893"
[1] "Thu Oct 14 22:13:17 2021: Iteration: 1 loss: 3.9744594315801"
[1] "Thu Oct 14 22:13:21 2021: Iteration: 2 loss: 3.96167869389219"
Time difference of 6.591168 secs
[1] "Thu Oct 14 22:13:21 2021: 2 Final nb-AE loss: 3.96167869389219"
[1] "Evaluation loss: 0.382425131359587 for q=5"
[1] "Thu Oct 14 22:13:44 2021: Initial PCA loss: 6.46616282459588"
[1] "Thu Oct 14 22:13:57 2021: Iteration: 1 loss: 4.81534335542007"
[1] "Thu Oct 14 22:14:04 2021: Iteration: 2 loss: 4.78989160274581"
Time difference of 13.39809 secs
[1] "Thu Oct 14 22:14:04 2021: 2 Final nb-AE loss: 4.78989160274581"
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
202.097 1.728 204.030
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 8.735 | 1.119 | 9.025 | |
| OutriderDataSet-class | 2.471 | 0.023 | 2.496 | |
| aberrant | 9.698 | 2.282 | 6.260 | |
| computeGeneLength | 2.984 | 0.074 | 3.083 | |
| computeLatentSpace | 2.148 | 0.007 | 2.155 | |
| computePvalues | 3.022 | 0.906 | 2.923 | |
| computeZscores | 2.234 | 0.082 | 2.320 | |
| controlForConfounders | 2.982 | 0.026 | 3.011 | |
| counts | 1.624 | 0.010 | 1.638 | |
| estimateBestQ | 0.931 | 0.003 | 0.937 | |
| filterExpression | 3.514 | 0.023 | 3.541 | |
| findEncodingDim | 45.792 | 0.264 | 46.106 | |
| fit | 6.078 | 0.106 | 6.188 | |
| fpkm | 2.221 | 0.033 | 2.256 | |
| getter_setter_functions | 11.571 | 0.035 | 11.632 | |
| makeExampleOutriderDataSet | 3.383 | 0.040 | 3.431 | |
| normalizationFactors | 2.048 | 0.005 | 2.055 | |
| plotFunctions | 25.280 | 0.422 | 25.744 | |
| results | 9.427 | 0.069 | 9.505 | |
| sampleExclusionMask | 1.296 | 0.018 | 1.317 | |
| sizeFactors | 1.755 | 0.017 | 1.776 | |