| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:29:32 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 | ||||
| Package 2086/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TFEA.ChIP 1.25.0 (landing page) Laura Puente Santamaría
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the TFEA.ChIP package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: TFEA.ChIP |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TFEA.ChIP_1.25.0.tar.gz |
| StartedAt: 2024-05-31 08:55:26 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 09:02:25 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 419.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFEA.ChIP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TFEA.ChIP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TFEA.ChIP_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TFEA.ChIP.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘TFEA.ChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFEA.ChIP’ version ‘1.25.0’
* 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 ... NOTE
installed size is 5.2Mb
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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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
rankTFs 15.611 0.240 15.851
GSEA_run 11.635 0.267 11.903
plot_CM 6.920 0.128 7.048
getCMstats 5.838 0.032 5.870
contingency_matrix 5.581 0.160 5.742
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/TFEA.ChIP.Rcheck/00check.log’
for details.
TFEA.ChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TFEA.ChIP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘TFEA.ChIP’ ... ** using staged installation ** 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 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)
TFEA.ChIP.Rcheck/tests/runTests.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
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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! 16544 genes of 17527 successfully converted.
Couldn't find Entrez IDs for 983 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, aperm, 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, table, tapply,
union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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! 10428 genes of 11667 successfully converted.
Couldn't find Entrez IDs for 1239 genes.
Done! 16544 genes of 17527 successfully converted.
Couldn't find Entrez IDs for 983 genes.
Done! 10428 genes of 11667 successfully converted.
Couldn't find Entrez IDs for 1239 genes.
RUNIT TEST PROTOCOL -- Fri May 31 09:01:33 2024
***********************************************
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
47.365 1.209 48.565
TFEA.ChIP.Rcheck/TFEA.ChIP-Ex.timings
| name | user | system | elapsed | |
| GSEA_EnrichmentScore | 0.001 | 0.000 | 0.000 | |
| GSEA_run | 11.635 | 0.267 | 11.903 | |
| GeneID2entrez | 0.558 | 0.004 | 0.563 | |
| Select_genes | 0.093 | 0.007 | 0.100 | |
| contingency_matrix | 5.581 | 0.160 | 5.742 | |
| getCMstats | 5.838 | 0.032 | 5.870 | |
| get_chip_index | 0.026 | 0.000 | 0.026 | |
| makeChIPGeneDB | 0.081 | 0.016 | 0.097 | |
| matrixDB_to_listDB | 0.001 | 0.000 | 0.001 | |
| plot_CM | 6.920 | 0.128 | 7.048 | |
| plot_ES | 0.364 | 0.008 | 0.372 | |
| plot_RES | 0.536 | 0.015 | 0.535 | |
| preprocessInputData | 1.497 | 0.080 | 1.577 | |
| rankTFs | 15.611 | 0.240 | 15.851 | |
| set_user_data | 1.103 | 0.004 | 1.106 | |
| txt2GR | 0.03 | 0.00 | 0.03 | |