Christian Mertes
| Snapshot Date: 2024-05-26 14:00:09 -0400 (Sun, 26 May 2024) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_19 |
| git_last_commit: 7b58f60 |
| git_last_commit_date: 2024-04-30 11:07:46 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-27 11:35:28 -0400 (Mon, 27 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4752 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4517 |
| 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 1495/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.22.0 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.22.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OUTRIDER_1.22.0.tar.gz |
| StartedAt: 2024-05-27 01:24:05 -0400 (Mon, 27 May 2024) |
| EndedAt: 2024-05-27 01:44:45 -0400 (Mon, 27 May 2024) |
| EllapsedTime: 1240.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OUTRIDER_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.22.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs'
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
checkRd: (-1) results.Rd:48-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:68-71: Lost braces in \itemize; \value handles \item{}{} directly
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotFunctions 28.085 1.465 34.807
OUTRIDER 19.911 6.437 25.370
findEncodingDim 22.947 1.354 27.054
results 8.328 0.691 12.092
getter_setter_functions 6.699 0.194 10.049
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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, 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
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] "Mon May 27 01:39:01 2024: Initial PCA loss: 6.29483479009807"
[1] "Mon May 27 01:39:03 2024: Iteration: 1 loss: 4.54698521658257"
[1] "Mon May 27 01:39:04 2024: Iteration: 2 loss: 4.51734621569786"
[1] "Mon May 27 01:39:04 2024: Iteration: 3 loss: 4.49749046224733"
[1] "Mon May 27 01:39:05 2024: Iteration: 4 loss: 4.48444280964306"
[1] "Mon May 27 01:39:06 2024: Iteration: 5 loss: 4.48098405476996"
[1] "Mon May 27 01:39:08 2024: Iteration: 6 loss: 4.47282997240024"
Time difference of 6.51598 secs
[1] "Mon May 27 01:39:08 2024: 6 Final nb-AE loss: 4.47282997240024"
[1] "Mon May 27 01:39:10 2024: Initial PCA loss: 6.29483479009807"
[1] "Mon May 27 01:39:11 2024: Iteration: 1 loss: 4.54698521658257"
[1] "Mon May 27 01:39:12 2024: Iteration: 2 loss: 4.51734621569786"
[1] "Mon May 27 01:39:13 2024: Iteration: 3 loss: 4.49749046224733"
[1] "Mon May 27 01:39:14 2024: Iteration: 4 loss: 4.48444280964306"
[1] "Mon May 27 01:39:15 2024: Iteration: 5 loss: 4.48098405476996"
[1] "Mon May 27 01:39:17 2024: Iteration: 6 loss: 4.47282997240024"
Time difference of 6.533143 secs
[1] "Mon May 27 01:39:17 2024: 6 Final nb-AE loss: 4.47282997240024"
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] "Mon May 27 01:39:40 2024: Initial PCA loss: 4.49361823217909"
[1] "Mon May 27 01:39:41 2024: Iteration: 1 loss: 4.12697193165039"
[1] "Mon May 27 01:39:42 2024: Iteration: 2 loss: 4.10102137426779"
Time difference of 1.269604 secs
[1] "Mon May 27 01:39:42 2024: 2 Final nb-AE loss: 4.10102137426779"
[1] "Evaluation loss: 0.53076026217341 for q=3"
[1] "Mon May 27 01:39:43 2024: Initial PCA loss: 4.44927082730532"
[1] "Mon May 27 01:39:44 2024: Iteration: 1 loss: 4.04883444240869"
[1] "Mon May 27 01:39:45 2024: Iteration: 2 loss: 4.02765888764537"
Time difference of 1.336457 secs
[1] "Mon May 27 01:39:45 2024: 2 Final nb-AE loss: 4.02765888764537"
[1] "Evaluation loss: 0.437262502777447 for q=4"
[1] "Mon May 27 01:39:45 2024: Initial PCA loss: 4.42397861754504"
[1] "Mon May 27 01:39:47 2024: Iteration: 1 loss: 3.97754859600435"
[1] "Mon May 27 01:39:47 2024: Iteration: 2 loss: 3.95952694176135"
Time difference of 1.24229 secs
[1] "Mon May 27 01:39:47 2024: 2 Final nb-AE loss: 3.95952694176135"
[1] "Evaluation loss: 0.410521072759809 for q=5"
[1] "Mon May 27 01:39:55 2024: Initial PCA loss: 7.16457134714849"
[1] "Mon May 27 01:39:56 2024: Iteration: 1 loss: 6.82915165643358"
[1] "Mon May 27 01:39:57 2024: Iteration: 2 loss: 6.82749554346071"
Time difference of 1.443922 secs
[1] "Mon May 27 01:39:57 2024: 2 Final nb-AE loss: 6.82749554346071"
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
>
> proc.time()
user system elapsed
100.857 5.536 111.019
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 19.911 | 6.437 | 25.370 | |
| OutriderDataSet-class | 1.085 | 0.140 | 1.227 | |
| aberrant | 2.135 | 1.156 | 2.235 | |
| computeGeneLength | 1.495 | 0.148 | 1.643 | |
| computeLatentSpace | 0.725 | 0.044 | 0.769 | |
| computePvalues | 2.056 | 2.232 | 2.451 | |
| computeZscores | 0.761 | 0.160 | 0.920 | |
| controlForConfounders | 1.066 | 0.104 | 1.170 | |
| counts | 0.549 | 0.036 | 0.585 | |
| estimateBestQ | 0.406 | 0.048 | 0.454 | |
| filterExpression | 1.412 | 0.108 | 1.521 | |
| findEncodingDim | 22.947 | 1.354 | 27.054 | |
| fit | 1.973 | 0.051 | 2.065 | |
| fpkm | 1.785 | 0.049 | 1.839 | |
| getter_setter_functions | 6.699 | 0.194 | 10.049 | |
| makeExampleOutriderDataSet | 2.487 | 0.080 | 3.834 | |
| normalizationFactors | 1.747 | 0.019 | 2.489 | |
| plotFunctions | 28.085 | 1.465 | 34.807 | |
| results | 8.328 | 0.691 | 12.092 | |
| sampleExclusionMask | 0.757 | 0.036 | 0.792 | |
| sizeFactors | 0.859 | 0.032 | 0.891 | |