Altuna Akalin
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/genomation |
| git_branch: RELEASE_3_13 |
| git_last_commit: 94f0278 |
| git_last_commit_date: 2021-05-19 12:09:55 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:37 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the genomation package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomation.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 735/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genomation 1.24.0 (landing page) Altuna Akalin
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2021-10-14 19:23:49 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:30:09 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 379.4 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/genomation.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.24.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/genomation.Rcheck/00install.out’ for details.
* 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: ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 6.225 2.966 9.070
enrichmentMatrix-ScoreMatrixList-method 5.922 2.702 8.588
* 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/library’ * installing *source* package ‘genomation’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/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++14 -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/4.1/Resources/library/00LOCK-genomation/00new/genomation/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** testing if installed package keeps a record of temporary installation path * DONE (genomation)
genomation.Rcheck/tests/genomation_unit_tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
> 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 ...
Rows: 2 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
RUNIT TEST PROTOCOL -- Thu Oct 14 19:29:59 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
44.837 1.436 46.175
genomation.Rcheck/genomation-Ex.timings
| name | user | system | elapsed | |
| AnnotationByGeneParts-methods | 1.284 | 0.089 | 1.296 | |
| ScoreMatrix-methods | 2.027 | 0.098 | 2.128 | |
| ScoreMatrixBin-methods | 3.361 | 0.067 | 3.361 | |
| ScoreMatrixList-methods | 1.573 | 0.049 | 1.623 | |
| annotateWithFeature-methods | 0.072 | 0.003 | 0.075 | |
| annotateWithFeatureFlank-methods | 0.543 | 0.004 | 0.547 | |
| annotateWithFeatures-methods | 1.210 | 0.041 | 1.163 | |
| annotateWithGeneParts-methods | 0.985 | 0.014 | 0.918 | |
| binMatrix-methods | 0.345 | 0.006 | 0.351 | |
| convertBed2Exons-methods | 0.098 | 0.001 | 0.100 | |
| convertBed2Introns-methods | 0.067 | 0.002 | 0.069 | |
| enrichmentMatrix-ScoreMatrix-method | 3.311 | 0.801 | 4.149 | |
| enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 6.225 | 2.966 | 9.070 | |
| enrichmentMatrix-ScoreMatrixList-method | 5.922 | 2.702 | 8.588 | |
| findFeatureComb-methods | 1.764 | 1.479 | 0.674 | |
| getFeatsWithTargetsStats-methods | 0.788 | 0.050 | 0.751 | |
| getFlanks-methods | 0.314 | 0.025 | 0.339 | |
| getRandomEnrichment-methods | 0.004 | 0.004 | 0.007 | |
| getTargetAnnotationStats-methods | 0.845 | 0.041 | 0.798 | |
| gffToGRanges | 0.132 | 0.007 | 0.139 | |
| heatMatrix | 0.348 | 0.022 | 0.370 | |
| heatMeta | 1.446 | 0.156 | 1.605 | |
| heatTargetAnnotation-methods | 1.210 | 0.023 | 1.148 | |
| intersectScoreMatrixList-methods | 0.514 | 0.029 | 0.544 | |
| multiHeatMatrix | 0.633 | 0.038 | 0.672 | |
| orderBy-methods | 0.921 | 0.044 | 0.966 | |
| patternMatrix-methods | 0.237 | 0.010 | 0.247 | |
| plotMeta | 0.735 | 0.043 | 0.779 | |
| plotTargetAnnotation-methods | 0.721 | 0.015 | 0.649 | |
| readBed | 0.305 | 0.015 | 0.315 | |
| readBroadPeak | 0.060 | 0.010 | 0.066 | |
| readFeatureFlank-methods | 0.460 | 0.010 | 0.468 | |
| readGeneric | 0.076 | 0.006 | 0.080 | |
| readNarrowPeak | 0.077 | 0.011 | 0.086 | |
| readTranscriptFeatures-methods | 0.585 | 0.013 | 0.520 | |
| scaleScoreMatrix-methods | 0.309 | 0.009 | 0.319 | |
| scaleScoreMatrixList | 0.979 | 0.036 | 1.018 | |