| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1440/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.17.1 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: OUTRIDER |
| Version: 1.17.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OUTRIDER_1.17.1.tar.gz |
| StartedAt: 2023-04-12 08:03:55 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 08:25:14 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 1278.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OUTRIDER_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.17.1’
* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* 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 ... 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEncodingDim 19.380 0.971 25.104
OUTRIDER 11.826 2.759 13.093
plotFunctions 11.897 0.406 13.681
results 6.984 0.132 9.329
computePvalues 2.589 2.884 3.683
filterExpression 4.052 0.196 9.313
controlForConfounders 2.543 0.194 7.680
computeZscores 1.747 0.202 5.114
* 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 ...
‘OUTRIDER.Rnw’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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] "Wed Apr 12 08:16:35 2023: Initial PCA loss: 6.35746495816198"
[1] "Wed Apr 12 08:16:39 2023: Iteration: 1 loss: 4.56299830883623"
[1] "Wed Apr 12 08:16:41 2023: Iteration: 2 loss: 4.50310875177656"
[1] "Wed Apr 12 08:16:43 2023: Iteration: 3 loss: 4.47075768980257"
[1] "Wed Apr 12 08:16:44 2023: Iteration: 4 loss: 4.45868512188815"
[1] "Wed Apr 12 08:16:46 2023: Iteration: 5 loss: 4.4512379294941"
[1] "Wed Apr 12 08:16:48 2023: Iteration: 6 loss: 4.44580062426305"
Time difference of 11.79662 secs
[1] "Wed Apr 12 08:16:48 2023: 6 Final nb-AE loss: 4.44580062426305"
[1] "Wed Apr 12 08:16:51 2023: Initial PCA loss: 6.35746495816198"
[1] "Wed Apr 12 08:16:53 2023: Iteration: 1 loss: 4.56299830883623"
[1] "Wed Apr 12 08:16:54 2023: Iteration: 2 loss: 4.50310875177656"
[1] "Wed Apr 12 08:16:55 2023: Iteration: 3 loss: 4.47075768980257"
[1] "Wed Apr 12 08:16:57 2023: Iteration: 4 loss: 4.45868512188815"
[1] "Wed Apr 12 08:16:58 2023: Iteration: 5 loss: 4.4512379294941"
[1] "Wed Apr 12 08:17:00 2023: Iteration: 6 loss: 4.44580062426305"
Time difference of 7.879888 secs
[1] "Wed Apr 12 08:17:00 2023: 6 Final nb-AE loss: 4.44580062426305"
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] "Wed Apr 12 08:17:31 2023: Initial PCA loss: 4.52239778298709"
[1] "Wed Apr 12 08:17:37 2023: Iteration: 1 loss: 4.17181507470827"
[1] "Wed Apr 12 08:17:41 2023: Iteration: 2 loss: 4.15368393818793"
Time difference of 8.184952 secs
[1] "Wed Apr 12 08:17:41 2023: 2 Final nb-AE loss: 4.15368393818793"
[1] "Evaluation loss: 0.609667740384938 for q=3"
[1] "Wed Apr 12 08:17:46 2023: Initial PCA loss: 4.48540814083504"
[1] "Wed Apr 12 08:17:50 2023: Iteration: 1 loss: 4.09996623712493"
[1] "Wed Apr 12 08:17:52 2023: Iteration: 2 loss: 4.08061067739643"
Time difference of 3.180661 secs
[1] "Wed Apr 12 08:17:52 2023: 2 Final nb-AE loss: 4.08061067739643"
[1] "Evaluation loss: 0.493835263798132 for q=4"
[1] "Wed Apr 12 08:17:53 2023: Initial PCA loss: 4.43995837612952"
[1] "Wed Apr 12 08:17:54 2023: Iteration: 1 loss: 4.01104522431846"
[1] "Wed Apr 12 08:17:56 2023: Iteration: 2 loss: 3.99351194329728"
Time difference of 2.610379 secs
[1] "Wed Apr 12 08:17:56 2023: 2 Final nb-AE loss: 3.99351194329728"
[1] "Evaluation loss: 0.557367128348542 for q=5"
[1] "Wed Apr 12 08:18:17 2023: Initial PCA loss: 6.46616282459584"
[1] "Wed Apr 12 08:18:21 2023: Iteration: 1 loss: 4.81520071473822"
[1] "Wed Apr 12 08:18:23 2023: Iteration: 2 loss: 4.78981527904659"
Time difference of 5.020362 secs
[1] "Wed Apr 12 08:18:23 2023: 2 Final nb-AE loss: 4.78981527904659"
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
133.030 2.357 170.025
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 11.826 | 2.759 | 13.093 | |
| OutriderDataSet-class | 1.626 | 0.061 | 2.137 | |
| aberrant | 3.469 | 1.332 | 4.815 | |
| computeGeneLength | 2.567 | 0.165 | 2.877 | |
| computeLatentSpace | 0.785 | 0.019 | 0.805 | |
| computePvalues | 2.589 | 2.884 | 3.683 | |
| computeZscores | 1.747 | 0.202 | 5.114 | |
| controlForConfounders | 2.543 | 0.194 | 7.680 | |
| counts | 1.645 | 0.094 | 4.871 | |
| estimateBestQ | 0.838 | 0.039 | 2.616 | |
| filterExpression | 4.052 | 0.196 | 9.313 | |
| findEncodingDim | 19.380 | 0.971 | 25.104 | |
| fit | 0.823 | 0.040 | 0.863 | |
| fpkm | 0.728 | 0.028 | 0.756 | |
| getter_setter_functions | 2.863 | 0.041 | 2.904 | |
| makeExampleOutriderDataSet | 1.068 | 0.016 | 1.084 | |
| normalizationFactors | 0.916 | 0.016 | 0.932 | |
| plotFunctions | 11.897 | 0.406 | 13.681 | |
| results | 6.984 | 0.132 | 9.329 | |
| sampleExclusionMask | 1.099 | 0.032 | 1.133 | |
| sizeFactors | 1.590 | 0.000 | 1.591 | |