Multiple platform build/check report for BioC 3.13 - CHECK results for gCrisprTools on tokay2

Package: gCrisprTools

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gCrisprTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings gCrisprTools_1.20.0.tar.gz

StartedAt: 2021-10-14 23:24:48 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 23:39:43 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 895.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: gCrisprTools.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gCrisprTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings gCrisprTools_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/gCrisprTools.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.20.0'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  9.9Mb
  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               13.89  29.31   43.88
ct.PantherPathwayEnrichment 22.85   1.88   74.99
ct.makeContrastReport        8.08   5.86   14.86
ct.guideCDF                 12.90   0.16   13.06
ct.signalSummary             8.02   0.13    8.15
ct.makeQCReport              4.48   3.45    8.58
ct.GCbias                    7.33   0.18    7.51
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
ct.makeReport               14.46  27.81   42.91
ct.PantherPathwayEnrichment 22.81   0.83   24.55
ct.makeContrastReport        6.92   5.25   12.79
ct.guideCDF                 10.35   0.06   10.41
ct.GCbias                    7.78   0.11    7.89
ct.signalSummary             7.28   0.17    7.47
ct.makeQCReport              3.95   2.85    7.41
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/gCrisprTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/gCrisprTools_1.20.0.tar.gz && rm -rf gCrisprTools.buildbin-libdir && mkdir gCrisprTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gCrisprTools.buildbin-libdir gCrisprTools_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL gCrisprTools_1.20.0.zip && rm gCrisprTools_1.20.0.tar.gz gCrisprTools_1.20.0.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
  3 8836k    3  325k    0     0   575k      0  0:00:15 --:--:--  0:00:15  575k
 17 8836k   17 1567k    0     0  1000k      0  0:00:08  0:00:01  0:00:07 1000k
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 74 8836k   74 6603k    0     0  1854k      0  0:00:04  0:00:03  0:00:01 1854k
100 8836k  100 8836k    0     0  2131k      0  0:00:04  0:00:04 --:--:-- 2131k

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  
    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_1.20.0.zip
* DONE (gCrisprTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'gCrisprTools' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 Oct 14 23:39:25 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 
   7.73    0.59    8.31


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 Oct 14 23:39:35 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 
   8.96    0.50    9.45

name	user	system	elapsed
aln	0.02	0.00	0.01
ann	0.09	0.02	0.11
ct.CAT	0.18	0.00	0.19
ct.DirectionalTests	0.38	0.02	0.39
ct.GCbias	7.33	0.18	7.51
ct.PRC	1.04	0.03	1.08
ct.PantherPathwayEnrichment	22.85	1.88	74.99
ct.ROC	0.59	0.02	0.61
ct.RRAaPvals	0.50	0.03	0.53
ct.RRAalpha	0.36	0.01	0.37
ct.alignmentChart	0	0	0
ct.alphaBeta	0.01	0.00	0.01
ct.buildSE	0.58	0.05	0.63
ct.ecdf	0	0	0
ct.filterReads	0.37	0.01	0.39
ct.gRNARankByReplicate	0.65	0.02	0.65
ct.generateResults	0.56	0.00	0.57
ct.guideCDF	12.90	0.16	13.06
ct.inputCheck	0.11	0.00	0.11
ct.makeContrastReport	8.08	5.86	14.86
ct.makeQCReport	4.48	3.45	8.58
ct.makeReport	13.89	29.31	43.88
ct.multiGSEA	0.33	0.00	0.33
ct.normalizeBySlope	1.71	0.05	1.77
ct.normalizeFQ	1.04	0.03	1.06
ct.normalizeFactoredQuantiles	1.07	0.00	1.08
ct.normalizeGuides	4.11	0.03	4.14
ct.normalizeMedians	0.89	0.03	0.92
ct.normalizeNTC	1.41	0.02	1.42
ct.normalizeSpline	1.40	0.03	1.43
ct.prepareAnnotation	0.73	0.01	0.75
ct.preprocessFit	1.91	0.02	1.92
ct.rawCountDensities	0.17	0.00	0.17
ct.resultCheck	0.14	0.00	0.14
ct.signalSummary	8.02	0.13	8.15
ct.stackGuides	4.67	0.03	4.70
ct.targetSetEnrichment	0.15	0.00	0.15
ct.topTargets	0.69	0.01	0.71
ct.viewControls	0.36	0.00	0.36
ct.viewGuides	0.58	0.02	0.59
es	0.08	0.00	0.08
essential.genes	0.00	0.01	0.01
fit	0.23	0.00	0.24
resultsDF	0.14	0.02	0.16

name	user	system	elapsed
aln	0	0	0
ann	0.14	0.03	0.18
ct.CAT	0.23	0.02	0.25
ct.DirectionalTests	0.35	0.09	0.44
ct.GCbias	7.78	0.11	7.89
ct.PRC	1.45	0.02	1.47
ct.PantherPathwayEnrichment	22.81	0.83	24.55
ct.ROC	0.18	0.01	0.18
ct.RRAaPvals	0.50	0.03	0.53
ct.RRAalpha	0.25	0.02	0.27
ct.alignmentChart	0	0	0
ct.alphaBeta	0.01	0.00	0.02
ct.buildSE	0.44	0.01	0.45
ct.ecdf	0	0	0
ct.filterReads	1.09	0.02	1.11
ct.gRNARankByReplicate	0.43	0.03	0.45
ct.generateResults	0.46	0.03	0.50
ct.guideCDF	10.35	0.06	10.41
ct.inputCheck	0.11	0.00	0.11
ct.makeContrastReport	6.92	5.25	12.79
ct.makeQCReport	3.95	2.85	7.41
ct.makeReport	14.46	27.81	42.91
ct.multiGSEA	0.25	0.02	0.26
ct.normalizeBySlope	1.93	0.03	1.97
ct.normalizeFQ	0.92	0.04	0.97
ct.normalizeFactoredQuantiles	0.91	0.04	0.94
ct.normalizeGuides	3.83	0.04	3.87
ct.normalizeMedians	0.81	0.06	0.88
ct.normalizeNTC	1.05	0.02	1.06
ct.normalizeSpline	1.28	0.03	1.31
ct.prepareAnnotation	0.72	0.02	0.74
ct.preprocessFit	1.97	0.01	1.98
ct.rawCountDensities	0.14	0.00	0.14
ct.resultCheck	0.13	0.02	0.14
ct.signalSummary	7.28	0.17	7.47
ct.stackGuides	4.97	0.03	5.00
ct.targetSetEnrichment	0.11	0.00	0.11
ct.topTargets	0.36	0.00	0.35
ct.viewControls	0.25	0.00	0.25
ct.viewGuides	0.33	0.00	0.33
es	0.04	0.00	0.05
essential.genes	0	0	0
fit	0.17	0.00	0.17
resultsDF	0.10	0.02	0.11

CHECK results for gCrisprTools on tokay2

Summary

Command output

Installation output

Tests output

Example timings