| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:51 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the TFEA.ChIP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFEA.ChIP.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 1953/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TFEA.ChIP 1.15.2 (landing page) Laura Puente Santamaría
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TFEA.ChIP |
| Version: 1.15.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFEA.ChIP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.15.2.tar.gz |
| StartedAt: 2022-03-17 20:28:07 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:33:04 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 296.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFEA.ChIP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFEA.ChIP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.15.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TFEA.ChIP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFEA.ChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFEA.ChIP' version '1.15.2'
* 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 whether package 'TFEA.ChIP' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 5.0Mb
* 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 ... NOTE
rankTFs: no visible binding for global variable 'arg.ES'
rankTFs: no visible binding for global variable 'ES'
rankTFs: no visible binding for global variable 'TF'
Undefined global functions or variables:
ES TF arg.ES
* 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
GSEA_run 12.02 2.18 14.20
rankTFs 12.67 0.50 13.18
plot_CM 5.77 0.52 6.28
getCMstats 4.89 0.13 5.02
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/TFEA.ChIP.Rcheck/00check.log'
for details.
TFEA.ChIP.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TFEA.ChIP
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'TFEA.ChIP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TFEA.ChIP'
finding HTML links ... done
ARNT.metadata html
ARNT.peaks.bed html
ChIPDB html
DnaseHS_db html
Entrez.gene.IDs html
GSEA.result html
GSEA_ESpermutations html
GSEA_EnrichmentScore html
GSEA_run html
GeneID2entrez html
Genes.Upreg html
MetaData html
Select_genes html
contingency_matrix html
getCMstats html
get_LFC_bar html
get_chip_index html
gr.list html
highlight_TF html
hypoxia html
hypoxia_DESeq html
log2.FC html
makeChIPGeneDB html
matrixDB_to_listDB html
plot_CM html
plot_ES html
plot_RES html
preprocessInputData html
rankTFs html
set_user_data html
txt2GR html
** 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 (TFEA.ChIP)
Making 'packages.html' ... done
TFEA.ChIP.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from cell types in ENCODE's tiers 1, 2, and 2.5.
To download the full ReMap2022 database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Done! 2 genes of 2 successfully converted.
Done! 1 genes of 1 successfully converted.
Done! 1 genes of 1 successfully converted.
Done! 2 genes of 2 successfully converted.
Done! 16646 genes of 17527 successfully converted.
Couldn't find Entrez IDs for 881 genes.
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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
Done! 10484 genes of 11667 successfully converted.
Couldn't find Entrez IDs for 1183 genes.
Done! 16646 genes of 17527 successfully converted.
Couldn't find Entrez IDs for 881 genes.
Done! 10484 genes of 11667 successfully converted.
Couldn't find Entrez IDs for 1183 genes.
RUNIT TEST PROTOCOL -- Thu Mar 17 20:32:55 2022
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
TFEA.ChIP RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
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
44.28 3.51 47.78
TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings
| name | user | system | elapsed | |
| GSEA_EnrichmentScore | 0 | 0 | 0 | |
| GSEA_run | 12.02 | 2.18 | 14.20 | |
| GeneID2entrez | 0.24 | 0.00 | 0.23 | |
| Select_genes | 0.06 | 0.06 | 0.13 | |
| contingency_matrix | 3.95 | 0.23 | 4.18 | |
| getCMstats | 4.89 | 0.13 | 5.02 | |
| get_chip_index | 0.05 | 0.01 | 0.06 | |
| makeChIPGeneDB | 0.07 | 0.00 | 0.08 | |
| matrixDB_to_listDB | 0 | 0 | 0 | |
| plot_CM | 5.77 | 0.52 | 6.28 | |
| plot_ES | 0.33 | 0.09 | 0.42 | |
| plot_RES | 0.50 | 0.07 | 0.56 | |
| preprocessInputData | 1.11 | 0.11 | 1.22 | |
| rankTFs | 12.67 | 0.50 | 13.18 | |
| set_user_data | 0.77 | 0.04 | 0.81 | |
| txt2GR | 0.01 | 0.02 | 0.03 | |