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 12:31:23 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gCrisprTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gCrisprTools_1.18.0.tar.gz |
| StartedAt: 2021-05-06 02:57:35 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:11:47 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 852.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gCrisprTools.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gCrisprTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gCrisprTools_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'gCrisprTools' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp0CyFHa/R.INSTALL15b4261f54c4/gCrisprTools/man/ct.getPanther.Rd:16: file link 'PANTHER.db' in package 'PANTHER.db' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.8Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ct.makeReport 15.98 26.50 43.14
ct.PantherPathwayEnrichment 24.45 1.89 91.39
ct.makeContrastReport 7.44 5.47 13.54
ct.guideCDF 12.14 0.33 12.46
ct.GCbias 10.61 0.28 10.89
ct.signalSummary 8.21 0.31 8.52
ct.makeQCReport 3.78 3.17 7.43
ct.stackGuides 5.22 0.01 5.23
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ct.makeReport 17.49 31.69 49.89
ct.PantherPathwayEnrichment 27.65 1.11 29.34
ct.makeContrastReport 7.39 6.80 14.95
ct.guideCDF 12.18 0.14 12.33
ct.signalSummary 9.97 0.32 10.30
ct.stackGuides 7.94 0.04 7.98
ct.GCbias 7.81 0.12 7.94
ct.makeQCReport 3.87 3.34 7.64
ct.normalizeGuides 5.68 0.17 5.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'unit.tests.R'
OK
** running tests for arch 'x64' ...
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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck/00check.log'
for details.
gCrisprTools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/gCrisprTools_1.18.0.tar.gz && rm -rf gCrisprTools.buildbin-libdir && mkdir gCrisprTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gCrisprTools.buildbin-libdir gCrisprTools_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL gCrisprTools_1.18.0.zip && rm gCrisprTools_1.18.0.tar.gz gCrisprTools_1.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 8837k 100 8837k 0 0 70.9M 0 --:--:-- --:--:-- --:--:-- 71.3M
install for i386
* installing *source* package 'gCrisprTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gCrisprTools'
finding HTML links ... done
aln html
ann html
appendDateAndExt html
ct.CAT html
ct.DirectionalTests html
ct.GCbias html
ct.GREATdb html
ct.PRC html
ct.PantherPathwayEnrichment html
ct.ROC html
ct.RRAaPvals html
ct.RRAalpha html
ct.RRAalphaBatch html
ct.alignmentChart html
ct.alphaBeta html
ct.applyAlpha html
ct.buildSE html
ct.drawColorLegend html
ct.drawFlat html
ct.ecdf html
ct.exprsColor html
ct.filterReads html
ct.gRNARankByReplicate html
ct.generateResults html
ct.getPanther html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp0CyFHa/R.INSTALL15b4261f54c4/gCrisprTools/man/ct.getPanther.Rd:16: file link 'PANTHER.db' in package 'PANTHER.db' does not exist and so has been treated as a topic
ct.guideCDF html
ct.inputCheck html
ct.makeContrastReport html
ct.makeQCReport html
ct.makeReport html
ct.makeRhoNull html
ct.multiGSEA html
ct.normalizeBySlope html
ct.normalizeFQ html
ct.normalizeFactoredQuantiles html
ct.normalizeGuides html
ct.normalizeMedians html
ct.normalizeNTC html
ct.normalizeSpline html
ct.numcores html
ct.prepareAnnotation html
ct.preprocessFit html
ct.rawCountDensities html
ct.resultCheck html
ct.signalSummary html
ct.stackGuides html
ct.targetSetEnrichment html
ct.topTargets html
ct.viewControls html
ct.viewGuides html
dir.writable html
es html
essential.genes html
fit html
gCrisprTools-package html
initOutDir html
renderReport html
resultsDF 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
install for x64
* installing *source* package 'gCrisprTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gCrisprTools' as gCrisprTools_1.18.0.zip
* DONE (gCrisprTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'gCrisprTools' successfully unpacked and MD5 sums checked
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gCrisprTools.Rcheck/tests_i386/unit.tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 06 03:11:31 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
7.32 0.48 7.85
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gCrisprTools.Rcheck/tests_x64/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-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.
> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
RUNIT TEST PROTOCOL -- Thu May 06 03:11:39 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
7.81 0.34 8.25
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gCrisprTools.Rcheck/examples_i386/gCrisprTools-Ex.timings
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gCrisprTools.Rcheck/examples_x64/gCrisprTools-Ex.timings
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