Altuna Akalin
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/genomation |
| Branch: master |
| Last Commit: 24210b0 |
| Last Changed Date: 2019-10-29 13:38:40 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:40:57 -0500 (Thu, 16 Jan 2020).
| Package 673/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genomation 1.19.0 Altuna Akalin
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: genomation |
| Version: 1.19.0 |
| 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_1.19.0.tar.gz |
| StartedAt: 2020-01-16 04:48:32 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 04:56:59 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 507.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genomation.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/genomation.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.19.0’
* 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 9.396 2.008 11.177
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 8.437 1.141 9.647
enrichmentMatrix-ScoreMatrix-method 5.283 1.078 6.692
ScoreMatrixBin-methods 4.706 0.649 4.477
* 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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -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/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c binSum.cpp -o binSum.o 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 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 Under development (unstable) (2019-12-14 r77572) -- "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.
> (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
Loading required package: BiocParallel
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 ...
Parsed with 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()
)
Parsed with 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 -- Thu Jan 16 04:56:44 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
55.919 4.423 55.037
genomation.Rcheck/genomation-Ex.timings
| name | user | system | elapsed | |
| AnnotationByGeneParts-methods | 1.438 | 0.052 | 1.492 | |
| ScoreMatrix-methods | 4.657 | 0.186 | 4.907 | |
| ScoreMatrixBin-methods | 4.706 | 0.649 | 4.477 | |
| ScoreMatrixList-methods | 0.992 | 0.091 | 1.083 | |
| annotateWithFeature-methods | 0.087 | 0.003 | 0.090 | |
| annotateWithFeatureFlank-methods | 0.666 | 0.004 | 0.670 | |
| annotateWithFeatures-methods | 1.749 | 0.362 | 1.545 | |
| annotateWithGeneParts-methods | 0.923 | 0.161 | 0.788 | |
| binMatrix-methods | 0.447 | 0.017 | 0.463 | |
| convertBed2Exons-methods | 0.160 | 0.002 | 0.162 | |
| convertBed2Introns-methods | 0.126 | 0.002 | 0.127 | |
| enrichmentMatrix-ScoreMatrix-method | 5.283 | 1.078 | 6.692 | |
| enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 8.437 | 1.141 | 9.647 | |
| enrichmentMatrix-ScoreMatrixList-method | 9.396 | 2.008 | 11.177 | |
| findFeatureComb-methods | 1.522 | 1.136 | 1.216 | |
| getFeatsWithTargetsStats-methods | 0.972 | 0.173 | 1.145 | |
| getFlanks-methods | 0.524 | 0.077 | 0.601 | |
| getRandomEnrichment-methods | 0.005 | 0.004 | 0.009 | |
| getTargetAnnotationStats-methods | 1.756 | 0.487 | 2.243 | |
| gffToGRanges | 0.146 | 0.009 | 0.157 | |
| heatMatrix | 1.514 | 0.114 | 1.628 | |
| heatMeta | 1.158 | 0.095 | 1.254 | |
| heatTargetAnnotation-methods | 2.029 | 0.834 | 1.371 | |
| intersectScoreMatrixList-methods | 0.960 | 0.319 | 0.722 | |
| multiHeatMatrix | 1.027 | 0.067 | 1.094 | |
| orderBy-methods | 1.055 | 0.085 | 1.141 | |
| patternMatrix-methods | 0.300 | 0.010 | 0.309 | |
| plotMeta | 1.035 | 0.056 | 1.091 | |
| plotTargetAnnotation-methods | 0.668 | 0.021 | 0.688 | |
| readBed | 0.082 | 0.027 | 0.109 | |
| readBroadPeak | 0.041 | 0.011 | 0.053 | |
| readFeatureFlank-methods | 0.432 | 0.015 | 0.448 | |
| readGeneric | 0.061 | 0.015 | 0.078 | |
| readNarrowPeak | 0.056 | 0.014 | 0.071 | |
| readTranscriptFeatures-methods | 0.417 | 0.044 | 0.461 | |
| scaleScoreMatrix-methods | 0.378 | 0.008 | 0.386 | |
| scaleScoreMatrixList | 1.024 | 0.062 | 1.087 | |