Russell Bainer
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/gCrisprTools |
| git_branch: devel |
| git_last_commit: 5d5f6da |
| git_last_commit_date: 2023-10-24 10:52:32 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:44 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 776/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.9.0 (landing page) Russell Bainer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the gCrisprTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gCrisprTools.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: gCrisprTools |
| Version: 2.9.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings gCrisprTools_2.9.0.tar.gz |
| StartedAt: 2024-03-28 05:29:52 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:37:43 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 470.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gCrisprTools.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings gCrisprTools_2.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.9.0’
* 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 ‘gCrisprTools’ 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 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RobustRankAggreg’
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 ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'ct.targetSetEnrichment.Rd':
‘pvalue.cutoff’ ‘organism’ ‘db.cut’ ‘species’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
ct.guideCDF 40.773 0.112 40.962
ct.GREATdb 38.693 0.567 38.981
ct.makeReport 28.166 0.207 28.432
ct.compareContrasts 15.580 0.171 15.784
ct.makeContrastReport 14.111 0.284 14.416
ct.upSet 12.945 0.407 13.380
ct.seas 11.262 0.926 11.696
ct.contrastBarchart 9.865 0.064 9.950
ct.makeQCReport 7.174 0.089 7.282
ct.stackGuides 6.185 0.515 6.713
ct.rankSimple 5.913 0.004 5.927
ct.GCbias 5.426 0.103 5.540
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘unit.tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
‘/home/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.
gCrisprTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL gCrisprTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘gCrisprTools’ ... ** 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 (gCrisprTools)
gCrisprTools.Rcheck/tests/unit.tests.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
RUNIT TEST PROTOCOL -- Thu Mar 28 05:37:38 2024
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
9.496 0.348 9.847
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.003 | 0.000 | 0.003 | |
| ann | 0.062 | 0.000 | 0.063 | |
| ct.CAT | 2.857 | 0.152 | 3.015 | |
| ct.DirectionalTests | 0.237 | 0.051 | 0.289 | |
| ct.GCbias | 5.426 | 0.103 | 5.540 | |
| ct.GREATdb | 38.693 | 0.567 | 38.981 | |
| ct.PRC | 2.614 | 0.152 | 2.773 | |
| ct.ROC | 2.116 | 0.012 | 2.133 | |
| ct.RRAaPvals | 0.360 | 0.004 | 0.365 | |
| ct.RRAalpha | 0.234 | 0.004 | 0.239 | |
| ct.alignmentChart | 0.006 | 0.000 | 0.006 | |
| ct.alphaBeta | 0 | 0 | 0 | |
| ct.applyAlpha | 0.001 | 0.000 | 0.002 | |
| ct.buildSE | 0.407 | 0.008 | 0.416 | |
| ct.compareContrasts | 15.580 | 0.171 | 15.784 | |
| ct.contrastBarchart | 9.865 | 0.064 | 9.950 | |
| ct.expandAnnotation | 0.071 | 0.000 | 0.071 | |
| ct.filterReads | 0.424 | 0.000 | 0.425 | |
| ct.gRNARankByReplicate | 0.449 | 0.000 | 0.450 | |
| ct.generateResults | 0.586 | 0.008 | 0.596 | |
| ct.guideCDF | 40.773 | 0.112 | 40.962 | |
| ct.keyCheck | 0.108 | 0.004 | 0.113 | |
| ct.makeContrastReport | 14.111 | 0.284 | 14.416 | |
| ct.makeQCReport | 7.174 | 0.089 | 7.282 | |
| ct.makeReport | 28.166 | 0.207 | 28.432 | |
| ct.makeRhoNull | 0.001 | 0.000 | 0.000 | |
| ct.normalizeBySlope | 1.125 | 0.012 | 1.138 | |
| ct.normalizeFQ | 0.796 | 0.012 | 0.809 | |
| ct.normalizeGuides | 3.059 | 0.064 | 3.128 | |
| ct.normalizeMedians | 0.687 | 0.008 | 0.696 | |
| ct.normalizeNTC | 0.783 | 0.004 | 0.789 | |
| ct.normalizeSpline | 0.985 | 0.012 | 0.999 | |
| ct.parseGeneSymbol | 0.002 | 0.000 | 0.002 | |
| ct.prepareAnnotation | 0.673 | 0.008 | 0.682 | |
| ct.preprocessFit | 2.569 | 0.016 | 2.590 | |
| ct.rankSimple | 5.913 | 0.004 | 5.927 | |
| ct.rawCountDensities | 0.153 | 0.008 | 0.162 | |
| ct.regularizeContrasts | 0.116 | 0.000 | 0.117 | |
| ct.resultCheck | 0.054 | 0.004 | 0.058 | |
| ct.scatter | 0.554 | 0.000 | 0.555 | |
| ct.seas | 11.262 | 0.926 | 11.696 | |
| ct.seasPrep | 3.276 | 0.291 | 3.575 | |
| ct.signalSummary | 2.270 | 0.200 | 2.473 | |
| ct.simpleResult | 2.097 | 0.083 | 2.186 | |
| ct.softLog | 0.000 | 0.000 | 0.001 | |
| ct.stackGuides | 6.185 | 0.515 | 6.713 | |
| ct.targetSetEnrichment | 2.027 | 0.104 | 2.134 | |
| ct.topTargets | 0.327 | 0.007 | 0.336 | |
| ct.upSet | 12.945 | 0.407 | 13.380 | |
| ct.viewControls | 0.304 | 0.000 | 0.305 | |
| ct.viewGuides | 0.344 | 0.012 | 0.357 | |
| es | 0.048 | 0.004 | 0.053 | |
| essential.genes | 0.001 | 0.000 | 0.002 | |
| fit | 0.164 | 0.004 | 0.168 | |
| resultsDF | 0.060 | 0.004 | 0.064 | |