Juan Pablo Romero
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/EventPointer |
| Branch: RELEASE_3_11 |
| Last Commit: fe43f2b |
| Last Changed Date: 2020-04-27 15:05:39 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:27 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE EventPointer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 568/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EventPointer 2.6.0 Juan Pablo Romero
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: EventPointer |
| Version: 2.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EventPointer_2.6.0.tar.gz |
| StartedAt: 2020-10-17 01:01:16 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:10:31 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 554.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EventPointer.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EventPointer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EventPointer_2.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/EventPointer.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 ‘EventPointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EventPointer’ version ‘2.6.0’
* 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 ‘EventPointer’ can be installed ... OK
* 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 objects imported by ':::' calls:
‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’ ‘SGSeq:::edges’
‘SGSeq:::exonGraph’ ‘SGSeq:::feature2name’ ‘SGSeq:::matchSGFeatures’
‘SGSeq:::nodes’ ‘SGSeq:::propagateAnnotation’
‘SGSeq:::splitCharacterList’
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
annotate2: no visible global function definition for
‘addDummySpliceSites’
annotate2: no visible global function definition for ‘annotatePaths’
annotateFeatures2: no visible global function definition for
‘matchTxFeatures’
Undefined global functions or variables:
addDummySpliceSites annotatePaths matchTxFeatures
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CDFfromGTF 10.369 0.188 10.656
EventsGTFfromTrancriptomeGTF 8.587 0.035 8.793
CDFfromGTF_Multipath 8.314 0.061 8.672
EventPointer_RNASeq_IGV 6.864 0.048 6.936
EventPointer_IGV 5.369 0.023 5.418
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/EventPointer.Rcheck/00check.log’
for details.
EventPointer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EventPointer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘EventPointer’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (EventPointer)
EventPointer.Rcheck/tests/runTests.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.
> BiocGenerics:::testPackage("EventPointer")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Creating SG Information...Creating SG Information...
Obtaining Events
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Obtaining Events
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Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Creating SG Information...Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
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Creating .txt ...
.txt created
Creating .GTF ...
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.txt created
Creating the sparseMatrix of paths x transcripts...
******FINISHED******
RUNIT TEST PROTOCOL -- Sat Oct 17 01:10:22 2020
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
EventPointer RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
36.029 1.248 40.350
EventPointer.Rcheck/EventPointer-Ex.timings
| name | user | system | elapsed | |
| CDFfromGTF | 10.369 | 0.188 | 10.656 | |
| CDFfromGTF_Multipath | 8.314 | 0.061 | 8.672 | |
| EventDetection | 3.398 | 0.033 | 3.537 | |
| EventDetectionMultipath | 1.815 | 0.010 | 1.848 | |
| EventPointer | 0.065 | 0.005 | 0.071 | |
| EventPointer_IGV | 5.369 | 0.023 | 5.418 | |
| EventPointer_RNASeq | 0.107 | 0.003 | 0.110 | |
| EventPointer_RNASeq_IGV | 6.864 | 0.048 | 6.936 | |
| EventPointer_RNASeq_TranRef | 0.023 | 0.006 | 0.029 | |
| EventsGTFfromTrancriptomeGTF | 8.587 | 0.035 | 8.793 | |
| FindPrimers | 0.000 | 0.001 | 0.001 | |
| GetPSI_FromTranRef | 0.028 | 0.005 | 0.074 | |
| PSI_Statistic | 0.152 | 0.004 | 0.157 | |
| PrepareBam_EP | 0.001 | 0.001 | 0.001 | |
| getbootstrapkallisto | 0.338 | 0.034 | 0.380 | |