Christian Mertes
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/FRASER |
| git_branch: RELEASE_3_16 |
| git_last_commit: 411304e |
| git_last_commit_date: 2023-01-19 11:17:01 -0400 (Thu, 19 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:33 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 FRASER package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FRASER.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 717/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FRASER 1.10.2 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FRASER |
| Version: 1.10.2 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FRASER.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings FRASER_1.10.2.tar.gz |
| StartedAt: 2023-04-11 01:37:25 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:48:15 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 649.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FRASER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FRASER.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings FRASER_1.10.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/FRASER.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FRASER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FRASER' version '1.10.2'
* 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 whether package 'FRASER' 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
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/FRASER/libs/x64/FRASER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
plotFunctions 52.67 0.25 52.99
FRASER 50.05 1.14 52.66
counts 23.80 0.23 24.04
optimHyperParams 11.25 0.09 11.34
injectOutliers 8.32 0.03 8.36
annotateRanges 5.53 0.30 20.63
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/FRASER.Rcheck/00check.log'
for details.
FRASER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL FRASER ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'FRASER' ... ** using staged installation ** libs g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -shared -s -static-libgcc -o FRASER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-FRASER/00new/FRASER/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FRASER)
FRASER.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(FRASER)
Loading required package: BiocParallel
Loading required package: data.table
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
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:data.table':
first, second
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
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
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'FRASER'
The following object is masked from 'package:Biobase':
samples
The following object is masked from 'package:GenomeInfoDb':
mapSeqlevels
>
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+ register(SerialParam())
+ }
>
> test_check("FRASER")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| sample3.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : R data.frame ||
|| Dir for temp files : F:/biocbuild/bbs-3.16-bioc/tmpdir/RtmpcDo37b ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid12760 ... ||
|| Features : 87 ||
|| Meta-features : 87 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample3.bam... ||
|| Strand specific : stranded ||
|| Paired-end reads are included. ||
|| Total alignments : 1918 ||
|| Successfully assigned alignments : 241 (12.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| sample1.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : R data.frame ||
|| Dir for temp files : F:/biocbuild/bbs-3.16-bioc/meat/FRASER.Rchec ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid12760 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample1.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 474 ||
|| Successfully assigned alignments : 145 (30.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| sample2.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : R data.frame ||
|| Dir for temp files : F:/biocbuild/bbs-3.16-bioc/meat/FRASER.Rchec ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid12760 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample2.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 2455 ||
|| Successfully assigned alignments : 826 (33.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| sample3.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : R data.frame ||
|| Dir for temp files : F:/biocbuild/bbs-3.16-bioc/meat/FRASER.Rchec ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid12760 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample3.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 1918 ||
|| Successfully assigned alignments : 703 (36.7%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 55 ]
>
> proc.time()
user system elapsed
108.07 2.79 113.96
FRASER.Rcheck/FRASER-Ex.timings
| name | user | system | elapsed | |
| FRASER | 50.05 | 1.14 | 52.66 | |
| FraserDataSet | 0.42 | 0.03 | 0.57 | |
| annotateRanges | 5.53 | 0.30 | 20.63 | |
| calculatePSIValues | 1.41 | 0.02 | 1.42 | |
| countRNA | 0.78 | 0.03 | 0.82 | |
| counts | 23.80 | 0.23 | 24.04 | |
| createTestFraserDataSet | 0.34 | 0.00 | 0.36 | |
| fds-methods | 1.14 | 0.03 | 1.17 | |
| filtering | 1.87 | 0.04 | 1.91 | |
| getter_setter_functions | 0.25 | 0.00 | 0.25 | |
| injectOutliers | 8.32 | 0.03 | 8.36 | |
| loadFraserDataSet | 0.31 | 0.00 | 0.31 | |
| makeSimulatedFraserDataSet | 3.72 | 0.04 | 3.77 | |
| mergeExternalData | 3.14 | 0.16 | 3.47 | |
| optimHyperParams | 11.25 | 0.09 | 11.34 | |
| plotFunctions | 52.67 | 0.25 | 52.99 | |
| psiTypes | 0 | 0 | 0 | |
| results | 4.61 | 0.02 | 4.60 | |
| subset | 0.69 | 0.02 | 0.71 | |