Christian Mertes
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/FRASER |
| git_branch: RELEASE_3_17 |
| git_last_commit: 72d97bf |
| git_last_commit_date: 2023-05-01 20:07:22 -0400 (Mon, 01 May 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:09 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 739/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FRASER 1.12.1 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the FRASER package: - 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 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: FRASER |
| Version: 1.12.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FRASER.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FRASER_1.12.1.tar.gz |
| StartedAt: 2023-10-16 02:18:28 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:29:35 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 667.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FRASER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FRASER.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FRASER_1.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/FRASER.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FRASER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FRASER' version '1.12.1'
* 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 whether package 'FRASER' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 startup messages can be suppressed ... 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-3.17-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 nor [v]sprintf. 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 51.45 0.67 52.14
FRASER 48.03 1.07 56.33
counts 22.10 0.25 22.37
optimHyperParams 10.45 0.14 10.61
injectOutliers 7.10 0.07 7.16
annotateRanges 6.14 0.42 27.44
results 5.28 0.08 5.36
* 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
'F:/biocbuild/bbs-3.17-bioc/meat/FRASER.Rcheck/00check.log'
for details.
FRASER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL FRASER ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'FRASER' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"C:/rtools43/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-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"C:/rtools43/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-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
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 object is masked from 'package:utils':
findMatches
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 2.14.2
//========================== 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-3.17-bioc/tmpdir/RtmpaSkG7e ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11520 ... ||
|| 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 2.14.2
//========================== 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-3.17-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_pid11520 ... ||
|| 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 2.14.2
//========================== 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-3.17-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_pid11520 ... ||
|| 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 2.14.2
//========================== 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-3.17-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_pid11520 ... ||
|| 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
104.25 3.35 112.37
FRASER.Rcheck/FRASER-Ex.timings
| name | user | system | elapsed | |
| FRASER | 48.03 | 1.07 | 56.33 | |
| FraserDataSet | 0.51 | 0.01 | 0.61 | |
| annotateRanges | 6.14 | 0.42 | 27.44 | |
| calculatePSIValues | 2.64 | 0.03 | 2.69 | |
| countRNA | 0.63 | 0.04 | 0.72 | |
| counts | 22.10 | 0.25 | 22.37 | |
| createTestFraserDataSet | 0.36 | 0.00 | 0.38 | |
| fds-methods | 1.35 | 0.06 | 1.61 | |
| filtering | 1.59 | 0.04 | 1.64 | |
| getter_setter_functions | 0.31 | 0.00 | 0.31 | |
| injectOutliers | 7.10 | 0.07 | 7.16 | |
| loadFraserDataSet | 0.31 | 0.01 | 0.32 | |
| makeSimulatedFraserDataSet | 3.77 | 0.00 | 3.77 | |
| mergeExternalData | 3.39 | 0.13 | 3.77 | |
| optimHyperParams | 10.45 | 0.14 | 10.61 | |
| plotFunctions | 51.45 | 0.67 | 52.14 | |
| psiTypes | 0 | 0 | 0 | |
| results | 5.28 | 0.08 | 5.36 | |
| subset | 0.75 | 0.00 | 0.75 | |