Bohdan Khomtchouk
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/geneXtendeR |
| Branch: RELEASE_3_8 |
| Last Commit: ea67de7 |
| Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:00 -0400 (Tue, 16 Apr 2019).
| Package 614/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| geneXtendeR 1.8.0 Bohdan Khomtchouk
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: geneXtendeR |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geneXtendeR_1.8.0.tar.gz |
| StartedAt: 2019-04-16 00:10:53 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:26:25 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 932.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: geneXtendeR.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:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geneXtendeR_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘geneXtendeR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.4Mb
sub-directories of 1Mb or more:
data 5.8Mb
doc 1.9Mb
extdata 3.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘rtracklayer’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.geneXtender: no visible binding for global variable ‘type’
.geneXtender: no visible binding for global variable ‘seqid’
.geneXtender: no visible binding for global variable ‘gene_id’
.geneXtender: no visible binding for global variable ‘gene_name’
annotate_n: no visible binding for global variable ‘..I’
annotate_n: no visible binding for global variable ‘seqid’
diffGO: no visible binding for global variable ‘rat’
gene_annotate: no visible global function definition for ‘.’
gene_annotate: no visible binding for global variable
‘Distance-of-Gene-to-Nearest-Peak’
gene_annotate: no visible global function definition for ‘sd’
gene_annotate: no visible binding for global variable ‘Chromosome’
gene_annotate: no visible binding for global variable ‘Gene-Start’
gene_annotate: no visible binding for global variable ‘Gene-End’
gene_annotate: no visible binding for global variable ‘Gene-ID’
gene_annotate: no visible binding for global variable ‘Gene-Name’
gene_annotate: no visible binding for global variable
‘Peaks-on-Gene-Body’
gene_annotate: no visible binding for global variable
‘Number-of-Peaks-Associated-with-Gene’
gene_lookup: no visible binding for global variable ‘gene_name_id’
gene_lookup: no visible binding for global variable ‘gene_id’
gene_lookup : internal_find: no visible binding for global variable
‘Chromosome’
gene_lookup : internal_find: no visible binding for global variable
‘distance’
gene_lookup : internal_find: no visible global function definition for
‘na.omit’
gene_lookup: no visible binding for global variable ‘..I’
gene_lookup: no visible binding for global variable ‘distance’
makeWordCloud: no visible binding for global variable ‘rat’
meanPeakLength: no visible binding for global variable ‘rat’
peaksInput: no visible binding for global variable ‘chr’
peaksInput: no visible global function definition for ‘na.omit’
peaksMerge: no visible binding for global variable ‘chr’
peaksMerge: no visible binding for global variable ‘g’
peaksMerge: no visible global function definition for ‘.’
plotWordFreq : geneXtender: no visible binding for global variable
‘type’
plotWordFreq : geneXtender: no visible binding for global variable
‘seqid’
plotWordFreq : geneXtender: no visible binding for global variable
‘gene_id’
plotWordFreq : geneXtender: no visible binding for global variable
‘gene_name’
Undefined global functions or variables:
. ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID
Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene
Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id
na.omit rat sd seqid type
Consider adding
importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
‘vignettes/geneXtendeR.Rnw’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
meanPeakLengthPlot 47.842 5.937 56.859
hotspotPlot 29.845 6.456 34.410
barChart 25.573 2.251 30.910
cumlinePlot 25.363 2.206 31.010
gene_annotate 21.789 5.324 24.487
linePlot 23.202 2.914 27.835
annotate 21.883 1.878 26.137
diffGO 20.791 2.076 24.849
distinct 20.693 1.739 22.614
makeWordCloud 20.086 2.141 24.758
makeNetwork 20.721 1.399 23.210
plotWordFreq 18.336 2.007 22.472
meanPeakLength 18.394 1.212 20.904
peakLengthBoxplot 16.329 2.186 20.449
gene_lookup 15.738 0.571 19.099
rat 5.565 0.425 6.097
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.
geneXtendeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘geneXtendeR’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c annotate.c -o annotate.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c extract_number.c -o extract_number.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c extract_peaks.c -o extract_peaks.o clang -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 geneXtendeR.so annotate.o extract_number.o extract_peaks.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/geneXtendeR/libs ** 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 * DONE (geneXtendeR)
geneXtendeR.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> library(testthat)
> library(geneXtendeR)
Loading required package: rtracklayer
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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: GO.db
Loading required package: AnnotationDbi
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")'.
>
> test_check("geneXtendeR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 86 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
538.697 306.724 256.504
geneXtendeR.Rcheck/geneXtendeR-Ex.timings
| name | user | system | elapsed | |
| allPeakLengths | 0.028 | 0.005 | 0.035 | |
| annotate | 21.883 | 1.878 | 26.137 | |
| annotate_n | 0.001 | 0.000 | 0.001 | |
| barChart | 25.573 | 2.251 | 30.910 | |
| cumlinePlot | 25.363 | 2.206 | 31.010 | |
| diffGO | 20.791 | 2.076 | 24.849 | |
| distinct | 20.693 | 1.739 | 22.614 | |
| gene_annotate | 21.789 | 5.324 | 24.487 | |
| gene_lookup | 15.738 | 0.571 | 19.099 | |
| hotspotPlot | 29.845 | 6.456 | 34.410 | |
| linePlot | 23.202 | 2.914 | 27.835 | |
| makeNetwork | 20.721 | 1.399 | 23.210 | |
| makeWordCloud | 20.086 | 2.141 | 24.758 | |
| meanPeakLength | 18.394 | 1.212 | 20.904 | |
| meanPeakLengthPlot | 47.842 | 5.937 | 56.859 | |
| peakLengthBoxplot | 16.329 | 2.186 | 20.449 | |
| peaksInput | 0.970 | 1.030 | 0.406 | |
| peaksMerge | 2.403 | 0.656 | 0.339 | |
| plotWordFreq | 18.336 | 2.007 | 22.472 | |
| rat | 5.565 | 0.425 | 6.097 | |
| samplepeaksinput | 0.013 | 0.001 | 0.012 | |