Altuna Akalin
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/genomation |
| Branch: RELEASE_3_11 |
| Last Commit: 31de677 |
| Last Changed Date: 2020-04-27 14:45:32 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:34 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE genomation PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 702/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genomation 1.20.0 Altuna Akalin
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: genomation |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genomation_1.20.0.tar.gz |
| StartedAt: 2020-10-17 01:29:39 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:36:38 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 418.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genomation.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genomation_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/genomation.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.20.0’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 3.6Mb
extdata 1.2Mb
* 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
Namespace in Imports field not imported from: ‘RUnit’
All declared Imports should be used.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
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 ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
definition for ‘:=’
Undefined global functions or variables:
:= id
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘cache’
Please remove from your package.
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichmentMatrix-ScoreMatrixList-method 7.028 4.024 8.414
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 6.832 4.139 10.904
enrichmentMatrix-ScoreMatrix-method 4.492 1.320 5.851
ScoreMatrixBin-methods 4.458 0.746 5.206
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘genomation_unit_tests.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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/genomation.Rcheck/00check.log’
for details.
genomation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genomation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘genomation’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c binSum.cpp -o binSum.o clang++ -mmacosx-version-min=10.13 -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 genomation.so RcppExports.o binSum.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-genomation/00new/genomation/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘GenomationManual.Rmd’ using ‘UTF-8’ ** 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 (genomation)
genomation.Rcheck/tests/genomation_unit_tests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
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, 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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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: 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: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
> genomation:::.test()
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
testing:min
testing:max
testing:median
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
── Column specification ────────────────────────────────────────────────────────
cols(
X1 = col_character(),
X2 = col_double(),
X3 = col_double(),
X4 = col_character(),
X5 = col_double(),
X6 = col_character(),
X7 = col_double(),
X8 = col_double(),
X9 = col_number()
)
── Column specification ────────────────────────────────────────────────────────
cols(
X1 = col_character(),
X2 = col_double(),
X3 = col_double(),
X4 = col_character(),
X5 = col_double(),
X6 = col_character(),
X7 = col_double(),
X8 = col_double(),
X9 = col_number()
)
RUNIT TEST PROTOCOL -- Sat Oct 17 01:36:27 2020
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
genomation RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(target, windows, strand.aware) :
1 windows fall off the target
2: In .local(target, windows, strand.aware) :
2 windows fall off the target
3: In .local(target, windows, strand.aware) :
2 windows fall off the target
4: In .local(target, windows, strand.aware) :
2 windows fall off the target
5: In .local(target, windows, strand.aware) :
2 windows fall off the target
6: In .local(target, windows, strand.aware) :
2 windows fall off the target
7: In .local(target, windows, bin.num, bin.op, strand.aware) :
2 windows fall off the target
8: In .local(target, windows, bin.num, bin.op, strand.aware) :
2 windows fall off the target
>
> proc.time()
user system elapsed
43.622 1.396 44.955
genomation.Rcheck/genomation-Ex.timings
| name | user | system | elapsed | |
| AnnotationByGeneParts-methods | 1.096 | 0.022 | 1.121 | |
| ScoreMatrix-methods | 3.523 | 0.108 | 3.634 | |
| ScoreMatrixBin-methods | 4.458 | 0.746 | 5.206 | |
| ScoreMatrixList-methods | 0.760 | 0.041 | 0.802 | |
| annotateWithFeature-methods | 0.070 | 0.002 | 0.072 | |
| annotateWithFeatureFlank-methods | 0.571 | 0.022 | 0.594 | |
| annotateWithFeatures-methods | 1.047 | 0.025 | 1.076 | |
| annotateWithGeneParts-methods | 0.690 | 0.021 | 0.714 | |
| binMatrix-methods | 0.288 | 0.009 | 0.299 | |
| convertBed2Exons-methods | 0.087 | 0.001 | 0.089 | |
| convertBed2Introns-methods | 0.088 | 0.002 | 0.090 | |
| enrichmentMatrix-ScoreMatrix-method | 4.492 | 1.320 | 5.851 | |
| enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 6.832 | 4.139 | 10.904 | |
| enrichmentMatrix-ScoreMatrixList-method | 7.028 | 4.024 | 8.414 | |
| findFeatureComb-methods | 0.610 | 0.088 | 0.699 | |
| getFeatsWithTargetsStats-methods | 0.684 | 0.099 | 0.784 | |
| getFlanks-methods | 0.400 | 0.036 | 0.437 | |
| getRandomEnrichment-methods | 0.003 | 0.002 | 0.006 | |
| getTargetAnnotationStats-methods | 0.649 | 0.063 | 0.713 | |
| gffToGRanges | 0.118 | 0.007 | 0.126 | |
| heatMatrix | 0.342 | 0.034 | 0.376 | |
| heatMeta | 0.608 | 0.048 | 0.657 | |
| heatTargetAnnotation-methods | 1.150 | 0.037 | 1.190 | |
| intersectScoreMatrixList-methods | 0.453 | 0.014 | 0.468 | |
| multiHeatMatrix | 1.470 | 0.216 | 1.692 | |
| orderBy-methods | 0.784 | 0.024 | 0.808 | |
| patternMatrix-methods | 0.239 | 0.038 | 0.277 | |
| plotMeta | 0.621 | 0.024 | 0.644 | |
| plotTargetAnnotation-methods | 0.608 | 0.016 | 0.625 | |
| readBed | 0.258 | 0.028 | 0.286 | |
| readBroadPeak | 0.044 | 0.010 | 0.054 | |
| readFeatureFlank-methods | 0.436 | 0.021 | 0.456 | |
| readGeneric | 0.055 | 0.015 | 0.070 | |
| readNarrowPeak | 0.035 | 0.011 | 0.046 | |
| readTranscriptFeatures-methods | 0.394 | 0.045 | 0.439 | |
| scaleScoreMatrix-methods | 0.246 | 0.007 | 0.252 | |
| scaleScoreMatrixList | 0.830 | 0.030 | 0.862 | |