Leonard Goldstein
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SGSeq |
| Branch: RELEASE_3_11 |
| Last Commit: 446fe43 |
| Last Changed Date: 2020-04-27 14:44:44 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:44 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SGSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1642/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SGSeq 1.22.0 Leonard Goldstein
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: SGSeq |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SGSeq_1.22.0.tar.gz |
| StartedAt: 2020-10-17 05:26:53 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:39:39 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 765.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SGSeq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SGSeq_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SGSeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGSeq’ version ‘1.22.0’
* 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 ‘SGSeq’ 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:
‘GenomicRanges:::extraColumnSlotNames’
‘GenomicRanges:::extraColumnSlotsAsDF’
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 ... OK
* 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
predictVariantEffects 62.050 0.096 62.157
analyzeFeatures 28.154 0.356 28.631
predictTxFeatures 20.140 0.180 20.334
getSGVariantCounts 10.995 0.152 11.156
getSGFeatureCounts 7.197 0.108 7.304
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.11-bioc/meat/SGSeq.Rcheck/00check.log’
for details.
SGSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SGSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘SGSeq’ ... ** 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 (SGSeq)
SGSeq.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-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.
> BiocGenerics:::testPackage("SGSeq")
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
Predict features...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Process features...
Obtain counts...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Find segments...
Find variants...
Annotate variants...
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Predicting effect of 2 variants on 3 coding transcripts...
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Predicting effect of 3 variants on 3 coding transcripts...
RUNIT TEST PROTOCOL -- Sat Oct 17 05:39:35 2020
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
SGSeq RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
261.004 1.531 265.827
SGSeq.Rcheck/SGSeq-Ex.timings
| name | user | system | elapsed | |
| SGFeatureCounts | 0.158 | 0.000 | 0.157 | |
| SGFeatures | 0.047 | 0.000 | 0.047 | |
| SGVariantCounts | 0.212 | 0.008 | 0.220 | |
| SGVariants | 0.133 | 0.008 | 0.140 | |
| TxFeatures | 0.054 | 0.004 | 0.058 | |
| analyzeFeatures | 28.154 | 0.356 | 28.631 | |
| analyzeVariants | 2.001 | 0.004 | 2.005 | |
| annotate | 2.419 | 0.000 | 2.419 | |
| assays | 0.029 | 0.000 | 0.028 | |
| convertToSGFeatures | 1.843 | 0.000 | 1.842 | |
| convertToTxFeatures | 0.889 | 0.000 | 0.889 | |
| exportFeatures | 0 | 0 | 0 | |
| findSGVariants | 2.465 | 0.000 | 2.466 | |
| getBamInfo | 2.044 | 0.296 | 2.340 | |
| getSGFeatureCounts | 7.197 | 0.108 | 7.304 | |
| getSGVariantCounts | 10.995 | 0.152 | 11.156 | |
| importTranscripts | 0 | 0 | 0 | |
| makeSGFeatureCounts | 0.087 | 0.000 | 0.087 | |
| makeVariantNames | 0.031 | 0.000 | 0.032 | |
| mergeTxFeatures | 0.494 | 0.000 | 0.493 | |
| plotCoverage | 0.000 | 0.000 | 0.001 | |
| plotFeatures | 0 | 0 | 0 | |
| plotSpliceGraph | 0.001 | 0.000 | 0.000 | |
| plotVariants | 0.000 | 0.000 | 0.001 | |
| predictTxFeatures | 20.140 | 0.180 | 20.334 | |
| predictVariantEffects | 62.050 | 0.096 | 62.157 | |
| processTerminalExons | 0.488 | 0.000 | 0.489 | |
| slots | 0.000 | 0.003 | 0.003 | |