Laura Puente Santamaría
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/TFEA.ChIP |
| Branch: RELEASE_3_7 |
| Last Commit: c1a3cf4 |
| Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:59:19 -0400 (Wed, 17 Oct 2018).
| Package 1477/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFEA.ChIP 1.0.0 Laura Puente Santamaría
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: TFEA.ChIP |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFEA.ChIP_1.0.0.tar.gz |
| StartedAt: 2018-10-17 00:23:44 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:33:25 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 580.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFEA.ChIP.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:TFEA.ChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFEA.ChIP_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/TFEA.ChIP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TFEA.ChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFEA.ChIP’ version ‘1.0.0’
* 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 ‘TFEA.ChIP’ 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 ... OK
* 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 ... NOTE
Failed with error: 'package 'DelayedArray' could not be loaded'
Error in .requirePackage(package) :
unable to find required package 'DESeq2'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GSEA_run 88.301 14.966 104.357
contingency_matrix 11.481 0.864 12.433
set_user_data 6.345 0.167 6.557
* 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
‘/Users/biocbuild/bbs-3.7-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.
TFEA.ChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFEA.ChIP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘TFEA.ChIP’ ... ** R ** data ** 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 (TFEA.ChIP)
TFEA.ChIP.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.
> BiocGenerics:::testPackage(pkgname = "TFEA.ChIP")
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
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:dplyr':
combine, intersect, setdiff, union
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:dplyr':
select
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Done! 2 genes of 2 successfully translated.
Done! 1 genes of 1 successfully translated.
Done! 1 genes of 1 successfully translated.
Done! 2 genes of 2 successfully translated.
Done! 0 genes of 1 successfully translated.
Couldn't find Entrez IDs for 1 genes (NAs returned instead).
Done! 17027 genes of 17527 successfully translated.
Couldn't find Entrez IDs for 500 genes.
Done! 10493 genes of 11667 successfully translated.
Couldn't find Entrez IDs for 1174 genes.
Done! 17027 genes of 17527 successfully translated.
Couldn't find Entrez IDs for 500 genes.
Done! 10493 genes of 11667 successfully translated.
Couldn't find Entrez IDs for 1174 genes.
RUNIT TEST PROTOCOL -- Wed Oct 17 00:33:19 2018
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
TFEA.ChIP RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
>
> proc.time()
user system elapsed
172.554 15.630 205.867
TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings
| name | user | system | elapsed | |
| GR2tfbs_db | 0.794 | 0.046 | 0.849 | |
| GSEA_EnrichmentScore | 0.001 | 0.000 | 0.001 | |
| GSEA_run | 88.301 | 14.966 | 104.357 | |
| GeneID2entrez | 2.974 | 0.065 | 3.064 | |
| Select_genes | 0.151 | 0.018 | 0.171 | |
| contingency_matrix | 11.481 | 0.864 | 12.433 | |
| getCMstats | 0.050 | 0.002 | 0.054 | |
| get_chip_index | 0.047 | 0.006 | 0.053 | |
| makeTFBSmatrix | 0.058 | 0.039 | 0.099 | |
| plot_CM | 0.524 | 0.039 | 0.573 | |
| plot_ES | 1.058 | 0.116 | 1.204 | |
| plot_RES | 1.289 | 0.080 | 1.395 | |
| preprocessInputData | 4.597 | 0.258 | 4.895 | |
| set_user_data | 6.345 | 0.167 | 6.557 | |
| txt2GR | 0.026 | 0.001 | 0.027 | |