Altuna Akalin
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/genomation |
| Branch: RELEASE_3_12 |
| Last Commit: 4ab56f3 |
| Last Changed Date: 2020-10-27 11:01:16 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:43 -0400 (Thu, 06 May 2021).
|
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 710/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genomation 1.22.0 (landing page) Altuna Akalin
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: genomation |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:genomation.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings genomation_1.22.0.tar.gz |
| StartedAt: 2021-05-06 01:52:48 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:58:29 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 341.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genomation.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:genomation.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings genomation_1.22.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/genomation.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 7.6Mb
sub-directories of 1Mb or more:
doc 3.6Mb
extdata 1.2Mb
libs 1.5Mb
* 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 4.640 0.680 4.868
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 4.544 0.216 5.296
enrichmentMatrix-ScoreMatrix-method 3.744 0.060 5.487
* 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
‘/home/biocbuild/bbs-3.12-bioc/meat/genomation.Rcheck/00check.log’
for details.
genomation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL genomation ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘genomation’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c binSum.cpp -o binSum.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o genomation.so RcppExports.o binSum.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.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: 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
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 -- Thu May 6 01:58:24 2021
***********************************************
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
37.260 0.936 38.140
genomation.Rcheck/genomation-Ex.timings
| name | user | system | elapsed | |
| AnnotationByGeneParts-methods | 1.736 | 0.008 | 1.758 | |
| ScoreMatrix-methods | 2.136 | 0.100 | 2.252 | |
| ScoreMatrixBin-methods | 3.220 | 0.080 | 3.304 | |
| ScoreMatrixList-methods | 0.604 | 0.000 | 0.605 | |
| annotateWithFeature-methods | 0.044 | 0.000 | 0.042 | |
| annotateWithFeatureFlank-methods | 0.340 | 0.000 | 0.339 | |
| annotateWithFeatures-methods | 0.756 | 0.008 | 0.750 | |
| annotateWithGeneParts-methods | 0.744 | 0.004 | 0.747 | |
| binMatrix-methods | 0.360 | 0.004 | 0.365 | |
| convertBed2Exons-methods | 0.096 | 0.000 | 0.093 | |
| convertBed2Introns-methods | 0.092 | 0.000 | 0.091 | |
| enrichmentMatrix-ScoreMatrix-method | 3.744 | 0.060 | 5.487 | |
| enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 4.544 | 0.216 | 5.296 | |
| enrichmentMatrix-ScoreMatrixList-method | 4.640 | 0.680 | 4.868 | |
| findFeatureComb-methods | 0.884 | 0.224 | 0.635 | |
| getFeatsWithTargetsStats-methods | 0.520 | 0.040 | 0.563 | |
| getFlanks-methods | 0.240 | 0.016 | 0.254 | |
| getRandomEnrichment-methods | 0.004 | 0.000 | 0.003 | |
| getTargetAnnotationStats-methods | 0.628 | 0.012 | 0.643 | |
| gffToGRanges | 0.116 | 0.000 | 0.131 | |
| heatMatrix | 0.304 | 0.044 | 0.348 | |
| heatMeta | 0.544 | 0.020 | 0.565 | |
| heatTargetAnnotation-methods | 0.996 | 0.012 | 0.990 | |
| intersectScoreMatrixList-methods | 0.540 | 0.000 | 0.544 | |
| multiHeatMatrix | 1.360 | 0.080 | 1.439 | |
| orderBy-methods | 0.616 | 0.004 | 0.619 | |
| patternMatrix-methods | 0.212 | 0.004 | 0.217 | |
| plotMeta | 0.516 | 0.008 | 0.524 | |
| plotTargetAnnotation-methods | 0.600 | 0.012 | 0.612 | |
| readBed | 0.232 | 0.020 | 0.251 | |
| readBroadPeak | 0.052 | 0.012 | 0.100 | |
| readFeatureFlank-methods | 0.384 | 0.012 | 0.397 | |
| readGeneric | 0.056 | 0.008 | 0.062 | |
| readNarrowPeak | 0.052 | 0.008 | 0.076 | |
| readTranscriptFeatures-methods | 0.356 | 0.012 | 0.385 | |
| scaleScoreMatrix-methods | 0.344 | 0.008 | 0.356 | |
| scaleScoreMatrixList | 0.836 | 0.004 | 0.848 | |