Christian Mertes
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/OUTRIDER |
| Branch: master |
| Last Commit: 5245580 |
| Last Changed Date: 2019-03-18 13:51:05 -0400 (Mon, 18 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:20:48 -0400 (Tue, 09 Apr 2019).
| Package 1134/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OUTRIDER 1.1.4 Christian Mertes
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: OUTRIDER |
| Version: 1.1.4 |
| 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_1.1.4.tar.gz |
| StartedAt: 2019-04-09 04:10:22 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:19:29 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 546.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.1.4’
* 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 ... NOTE
Authors@R field gives more than one person with maintainer role:
Felix Brechtmann <brechtma@in.tum.de> [aut, cre]
Christian Mertes <mertes@in.tum.de> [aut, cre]
* 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 ... 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 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 or elapsed time > 5s
user system elapsed
aberrant 11.429 15.220 10.014
findEncodingDim 15.724 0.704 15.211
plotFunctions 9.820 2.994 6.719
OUTRIDER 4.324 2.005 4.122
* 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-3.9-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
loss_n_gradient_functions.cpp:41:19: warning: unused variable 'c' [-Wunused-variable]
double b, ll, c;
^
loss_n_gradient_functions.cpp:68:15: warning: unused variable 'c' [-Wunused-variable]
double b, c;
^
2 warnings generated.
clang++ -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 -fopenmp -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-darwin15/6.1.0 -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/3.6/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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] "Initial PCA loss: 6.70662273907173"
[1] "Tue Apr 9 04:18:04 2019: Iteration: 1 loss: 4.95977484689978"
[1] "Tue Apr 9 04:18:05 2019: Iteration: 2 loss: 4.88534536737843"
[1] "Tue Apr 9 04:18:06 2019: Iteration: 3 loss: 4.83334624373644"
[1] "Tue Apr 9 04:18:07 2019: Iteration: 4 loss: 4.80815653416493"
[1] "Tue Apr 9 04:18:07 2019: Iteration: 5 loss: 4.7952765190098"
[1] "Tue Apr 9 04:18:09 2019: Iteration: 6 loss: 4.78073515732517"
Time difference of 5.647855 secs
[1] "6 Final nb-AE loss: 4.78073515732517"
[1] "Initial PCA loss: 6.70662273907173"
[1] "Tue Apr 9 04:18:12 2019: Iteration: 1 loss: 4.95977484689978"
[1] "Tue Apr 9 04:18:13 2019: Iteration: 2 loss: 4.88534536737843"
[1] "Tue Apr 9 04:18:14 2019: Iteration: 3 loss: 4.83334624373644"
[1] "Tue Apr 9 04:18:14 2019: Iteration: 4 loss: 4.80815653416493"
[1] "Tue Apr 9 04:18:15 2019: Iteration: 5 loss: 4.7952765190098"
[1] "Tue Apr 9 04:18:16 2019: Iteration: 6 loss: 4.78073515732517"
Time difference of 5.008518 secs
[1] "6 Final nb-AE loss: 4.78073515732517"
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] "Initial PCA loss: 4.51030288124625"
[1] "Tue Apr 9 04:18:32 2019: Iteration: 1 loss: 4.14108582572827"
[1] "Tue Apr 9 04:18:33 2019: Iteration: 2 loss: 4.13290313295429"
[1] "Tue Apr 9 04:18:34 2019: Iteration: 3 loss: 4.12843259366419"
[1] "Tue Apr 9 04:18:34 2019: Iteration: 4 loss: 4.1249220398373"
[1] "Tue Apr 9 04:18:35 2019: Iteration: 5 loss: 4.12099486170901"
[1] "Tue Apr 9 04:18:36 2019: Iteration: 6 loss: 4.11670050355555"
[1] "Tue Apr 9 04:18:36 2019: Iteration: 7 loss: 4.11494044433622"
[1] "Tue Apr 9 04:18:37 2019: Iteration: 8 loss: 4.11437074231845"
[1] "Tue Apr 9 04:18:38 2019: Iteration: 9 loss: 4.11414081946281"
[1] "Tue Apr 9 04:18:38 2019: Iteration: 10 loss: 4.1135272567094"
[1] "Tue Apr 9 04:18:39 2019: Iteration: 11 loss: 4.11326859955664"
[1] "Tue Apr 9 04:18:40 2019: Iteration: 12 loss: 4.1129626928411"
[1] "Tue Apr 9 04:18:41 2019: Iteration: 13 loss: 4.11219823655559"
[1] "Tue Apr 9 04:18:41 2019: Iteration: 14 loss: 4.11156940426123"
[1] "Tue Apr 9 04:18:42 2019: Iteration: 15 loss: 4.10978515193197"
Time difference of 11.09414 secs
[1] "15 Final nb-AE loss: 4.10978515193197"
[1] "Evaluation loss: 0.480211886655605"
[1] "Initial PCA loss: 4.48708664267388"
[1] "Tue Apr 9 04:18:45 2019: Iteration: 1 loss: 4.04797713222014"
[1] "Tue Apr 9 04:18:46 2019: Iteration: 2 loss: 4.01790856545574"
[1] "Tue Apr 9 04:18:47 2019: Iteration: 3 loss: 3.97588122705879"
[1] "Tue Apr 9 04:18:47 2019: Iteration: 4 loss: 3.95592903398148"
[1] "Tue Apr 9 04:18:48 2019: Iteration: 5 loss: 3.94878969581082"
[1] "Tue Apr 9 04:18:49 2019: Iteration: 6 loss: 3.94848674743096"
[1] "Tue Apr 9 04:18:50 2019: Iteration: 7 loss: 3.94834590614953"
[1] "Tue Apr 9 04:18:51 2019: Iteration: 8 loss: 3.94834154593632"
Time difference of 6.430425 secs
[1] "8 Final nb-AE loss: 3.94834154593632"
[1] "Evaluation loss: 0.484053260680068"
[1] "Initial PCA loss: 4.45821086320487"
[1] "Tue Apr 9 04:18:53 2019: Iteration: 1 loss: 3.9725880694837"
[1] "Tue Apr 9 04:18:54 2019: Iteration: 2 loss: 3.93041671904735"
[1] "Tue Apr 9 04:18:54 2019: Iteration: 3 loss: 3.89033306039044"
[1] "Tue Apr 9 04:18:55 2019: Iteration: 4 loss: 3.8798254788317"
[1] "Tue Apr 9 04:18:56 2019: Iteration: 5 loss: 3.87268744987741"
[1] "Tue Apr 9 04:18:57 2019: Iteration: 6 loss: 3.86334203026905"
[1] "Tue Apr 9 04:18:57 2019: Iteration: 7 loss: 3.83990107770725"
[1] "Tue Apr 9 04:18:58 2019: Iteration: 8 loss: 3.81939547040031"
[1] "Tue Apr 9 04:18:59 2019: Iteration: 9 loss: 3.81621587680274"
[1] "Tue Apr 9 04:18:59 2019: Iteration: 10 loss: 3.81610688483597"
[1] "Tue Apr 9 04:19:00 2019: Iteration: 11 loss: 3.8161015458546"
Time difference of 8.013693 secs
[1] "11 Final nb-AE loss: 3.8161015458546"
[1] "Evaluation loss: 0.484462475678293"
[1] "Initial PCA loss: 6.46616282459584"
[1] "Tue Apr 9 04:19:11 2019: Iteration: 1 loss: 4.81518048146922"
[1] "Tue Apr 9 04:19:12 2019: Iteration: 2 loss: 4.78972706919211"
Time difference of 2.14176 secs
[1] "2 Final nb-AE loss: 4.78972706919211"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 108 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
167.828 57.128 97.962
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 4.324 | 2.005 | 4.122 | |
| OutriderDataSet-class | 1.290 | 0.168 | 1.460 | |
| aberrant | 11.429 | 15.220 | 10.014 | |
| computeGeneLength | 2.426 | 0.188 | 2.616 | |
| computeLatentSpace | 0.704 | 0.017 | 0.720 | |
| computePvalues | 1.576 | 1.250 | 1.865 | |
| computeZscores | 1.817 | 0.598 | 1.772 | |
| controlForConfounders | 1.506 | 0.186 | 1.691 | |
| counts | 0.739 | 0.009 | 0.748 | |
| estimateBestQ | 0.515 | 0.007 | 0.522 | |
| filterExpression | 2.108 | 0.042 | 2.150 | |
| findEncodingDim | 15.724 | 0.704 | 15.211 | |
| fit | 1.174 | 0.037 | 1.211 | |
| fpkm | 0.605 | 0.012 | 0.616 | |
| getter_setter_functions | 2.375 | 0.011 | 2.386 | |
| makeExampleOutriderDataSet | 1.079 | 0.005 | 1.084 | |
| normalizationFactors | 0.866 | 0.007 | 0.872 | |
| plotFunctions | 9.820 | 2.994 | 6.719 | |
| results | 3.071 | 0.145 | 3.058 | |
| sampleExclusionMask | 0.871 | 0.337 | 0.522 | |
| sizeFactors | 0.809 | 0.004 | 0.814 | |