Christian Mertes
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_17 |
| git_last_commit: 56d52a3 |
| git_last_commit_date: 2023-05-01 20:07:43 -0400 (Mon, 01 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:08 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1452/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.18.1 (landing page) Christian Mertes
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the OUTRIDER package: - 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: 1.18.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.18.1.tar.gz |
| StartedAt: 2023-10-18 13:10:57 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 13:21:56 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 659.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OUTRIDER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.18.1’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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 14.319 0.213 21.938
OUTRIDER 11.255 1.584 17.647
plotFunctions 9.546 0.330 14.994
results 4.119 0.053 6.386
getter_setter_functions 3.834 0.038 5.902
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -arch arm64 -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/opt/R/arm64/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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 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] "Wed Oct 18 13:20:01 2023: Initial PCA loss: 6.06664129156709"
[1] "Wed Oct 18 13:20:03 2023: Iteration: 1 loss: 4.19631163263512"
[1] "Wed Oct 18 13:20:04 2023: Iteration: 2 loss: 4.13261151068494"
[1] "Wed Oct 18 13:20:05 2023: Iteration: 3 loss: 4.1099739747096"
[1] "Wed Oct 18 13:20:06 2023: Iteration: 4 loss: 4.09795078821978"
[1] "Wed Oct 18 13:20:08 2023: Iteration: 5 loss: 4.09272917207559"
[1] "Wed Oct 18 13:20:09 2023: Iteration: 6 loss: 4.08323216501985"
Time difference of 6.905429 secs
[1] "Wed Oct 18 13:20:09 2023: 6 Final nb-AE loss: 4.08323216501985"
[1] "Wed Oct 18 13:20:11 2023: Initial PCA loss: 6.06664129156709"
[1] "Wed Oct 18 13:20:13 2023: Iteration: 1 loss: 4.19631163263512"
[1] "Wed Oct 18 13:20:14 2023: Iteration: 2 loss: 4.13261151068494"
[1] "Wed Oct 18 13:20:16 2023: Iteration: 3 loss: 4.1099739747096"
[1] "Wed Oct 18 13:20:17 2023: Iteration: 4 loss: 4.09795078821978"
[1] "Wed Oct 18 13:20:18 2023: Iteration: 5 loss: 4.09272917207559"
[1] "Wed Oct 18 13:20:19 2023: Iteration: 6 loss: 4.08323216501985"
Time difference of 7.634174 secs
[1] "Wed Oct 18 13:20:19 2023: 6 Final nb-AE loss: 4.08323216501985"
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 Oct 18 13:20:45 2023: Initial PCA loss: 4.45795031078478"
[1] "Wed Oct 18 13:20:47 2023: Iteration: 1 loss: 4.08900415441741"
[1] "Wed Oct 18 13:20:48 2023: Iteration: 2 loss: 4.07023146008605"
Time difference of 2.447924 secs
[1] "Wed Oct 18 13:20:48 2023: 2 Final nb-AE loss: 4.07023146008605"
[1] "Evaluation loss: 0.366772704532899 for q=3"
[1] "Wed Oct 18 13:20:50 2023: Initial PCA loss: 4.43177573999698"
[1] "Wed Oct 18 13:20:52 2023: Iteration: 1 loss: 4.02010540088301"
[1] "Wed Oct 18 13:20:53 2023: Iteration: 2 loss: 4.00135348528157"
Time difference of 2.680422 secs
[1] "Wed Oct 18 13:20:53 2023: 2 Final nb-AE loss: 4.00135348528157"
[1] "Evaluation loss: 0.411113358570366 for q=4"
[1] "Wed Oct 18 13:20:55 2023: Initial PCA loss: 4.41311049239545"
[1] "Wed Oct 18 13:20:57 2023: Iteration: 1 loss: 3.94290638473686"
[1] "Wed Oct 18 13:20:59 2023: Iteration: 2 loss: 3.91657250260896"
Time difference of 2.533919 secs
[1] "Wed Oct 18 13:20:59 2023: 2 Final nb-AE loss: 3.91657250260896"
[1] "Evaluation loss: 0.480352631833086 for q=5"
[1] "Wed Oct 18 13:21:16 2023: Initial PCA loss: 6.46616282459584"
[1] "Wed Oct 18 13:21:19 2023: Iteration: 1 loss: 4.81532204961095"
[1] "Wed Oct 18 13:21:21 2023: Iteration: 2 loss: 4.7902215575778"
Time difference of 3.276793 secs
[1] "Wed Oct 18 13:21:21 2023: 2 Final nb-AE loss: 4.7902215575778"
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
83.259 1.706 127.410
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 11.255 | 1.584 | 17.647 | |
| OutriderDataSet-class | 1.057 | 0.067 | 1.678 | |
| aberrant | 2.234 | 0.460 | 3.298 | |
| computeGeneLength | 1.805 | 0.140 | 2.940 | |
| computeLatentSpace | 0.996 | 0.011 | 1.534 | |
| computePvalues | 2.568 | 1.036 | 4.323 | |
| computeZscores | 1.118 | 0.114 | 1.906 | |
| controlForConfounders | 1.381 | 0.049 | 2.153 | |
| counts | 0.757 | 0.011 | 1.152 | |
| estimateBestQ | 0.500 | 0.005 | 0.771 | |
| filterExpression | 1.890 | 0.039 | 2.944 | |
| findEncodingDim | 14.319 | 0.213 | 21.938 | |
| fit | 1.074 | 0.015 | 1.668 | |
| fpkm | 1.016 | 0.013 | 1.563 | |
| getter_setter_functions | 3.834 | 0.038 | 5.902 | |
| makeExampleOutriderDataSet | 1.401 | 0.015 | 2.162 | |
| normalizationFactors | 0.951 | 0.011 | 1.481 | |
| plotFunctions | 9.546 | 0.330 | 14.994 | |
| results | 4.119 | 0.053 | 6.386 | |
| sampleExclusionMask | 0.592 | 0.007 | 0.912 | |
| sizeFactors | 0.801 | 0.010 | 1.248 | |