Russell Bainer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/gCrisprTools |
| Branch: RELEASE_3_12 |
| Last Commit: e6168b2 |
| Last Changed Date: 2020-10-27 11:17:28 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:40 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the gCrisprTools package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 669/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 1.18.0 (landing page) Russell Bainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: gCrisprTools |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings gCrisprTools_1.18.0.tar.gz |
| StartedAt: 2021-05-06 01:44:17 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:52:20 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 483.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gCrisprTools.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings gCrisprTools_1.18.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘1.18.0’
* 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 ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
data 2.3Mb
doc 1.4Mb
* 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 ... WARNING
'::' or ':::' imports not declared from:
‘methods’ ‘multiGSEA’
Missing object imported by a ':::' call: ‘multiGSEA:::GeneSetDb.list’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ct.GCbias: no visible global function definition for ‘is’
ct.GREATdb: no visible global function definition for
‘getMSigGeneSetDb’
ct.buildSE: no visible global function definition for ‘is’
ct.inputCheck: no visible global function definition for ‘is’
ct.multiGSEA: no visible global function definition for ‘is’
ct.multiGSEA: no visible binding for global variable ‘sig’
ct.multiGSEA: no visible global function definition for
‘hyperGeometricTest’
ct.multiGSEA: no visible binding for global variable ‘genesetDB’
ct.multiGSEA: no visible binding for global variable ‘up’
ct.multiGSEA: no visible binding for global variable ‘universe’
ct.normalizeBySlope: no visible global function definition for ‘is’
Undefined global functions or variables:
genesetDB getMSigGeneSetDb hyperGeometricTest is sig universe up
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ct.PantherPathwayEnrichment 28.628 0.568 41.188
ct.makeReport 28.792 0.292 29.207
ct.makeContrastReport 13.120 0.420 15.762
ct.guideCDF 12.860 0.016 12.900
ct.signalSummary 8.308 0.096 8.429
ct.stackGuides 8.008 0.024 8.093
ct.makeQCReport 7.544 0.220 7.863
ct.GCbias 7.600 0.128 7.748
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘unit.tests.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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.
gCrisprTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL gCrisprTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
RUNIT TEST PROTOCOL -- Thu May 6 01:52:15 2021
***********************************************
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
11.236 0.196 11.640
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.004 | 0.000 | 0.003 | |
| ann | 0.084 | 0.004 | 0.087 | |
| ct.CAT | 0.144 | 0.000 | 0.142 | |
| ct.DirectionalTests | 0.352 | 0.112 | 0.465 | |
| ct.GCbias | 7.600 | 0.128 | 7.748 | |
| ct.PRC | 1.184 | 0.012 | 1.205 | |
| ct.PantherPathwayEnrichment | 28.628 | 0.568 | 41.188 | |
| ct.ROC | 0.216 | 0.004 | 0.217 | |
| ct.RRAaPvals | 0.464 | 0.008 | 0.482 | |
| ct.RRAalpha | 0.392 | 0.000 | 0.394 | |
| ct.alignmentChart | 0.008 | 0.000 | 0.007 | |
| ct.alphaBeta | 0.024 | 0.000 | 0.021 | |
| ct.buildSE | 0.660 | 0.004 | 0.663 | |
| ct.ecdf | 0.000 | 0.000 | 0.001 | |
| ct.filterReads | 0.396 | 0.004 | 0.403 | |
| ct.gRNARankByReplicate | 0.732 | 0.008 | 0.741 | |
| ct.generateResults | 0.924 | 0.020 | 0.945 | |
| ct.guideCDF | 12.860 | 0.016 | 12.900 | |
| ct.inputCheck | 0.116 | 0.000 | 0.114 | |
| ct.makeContrastReport | 13.120 | 0.420 | 15.762 | |
| ct.makeQCReport | 7.544 | 0.220 | 7.863 | |
| ct.makeReport | 28.792 | 0.292 | 29.207 | |
| ct.multiGSEA | 0.272 | 0.016 | 0.286 | |
| ct.normalizeBySlope | 1.920 | 0.040 | 1.961 | |
| ct.normalizeFQ | 1.212 | 0.044 | 1.257 | |
| ct.normalizeFactoredQuantiles | 1.120 | 0.024 | 1.148 | |
| ct.normalizeGuides | 4.412 | 0.068 | 4.510 | |
| ct.normalizeMedians | 1.120 | 0.024 | 1.153 | |
| ct.normalizeNTC | 1.208 | 0.016 | 1.230 | |
| ct.normalizeSpline | 1.260 | 0.008 | 1.276 | |
| ct.prepareAnnotation | 0.712 | 0.016 | 0.730 | |
| ct.preprocessFit | 2.440 | 0.032 | 2.472 | |
| ct.rawCountDensities | 0.216 | 0.004 | 0.221 | |
| ct.resultCheck | 0.136 | 0.000 | 0.134 | |
| ct.signalSummary | 8.308 | 0.096 | 8.429 | |
| ct.stackGuides | 8.008 | 0.024 | 8.093 | |
| ct.targetSetEnrichment | 0.188 | 0.004 | 0.193 | |
| ct.topTargets | 0.660 | 0.004 | 0.665 | |
| ct.viewControls | 0.432 | 0.000 | 0.431 | |
| ct.viewGuides | 0.496 | 0.004 | 0.499 | |
| es | 0.052 | 0.000 | 0.051 | |
| essential.genes | 0.000 | 0.000 | 0.001 | |
| fit | 0.168 | 0.004 | 0.174 | |
| resultsDF | 0.108 | 0.000 | 0.117 | |