BioC 3.5: CHECK report for gCrisprTools on tokay2

Package: gCrisprTools

Version: 1.4.0

Command: rm -rf gCrisprTools.buildbin-libdir gCrisprTools.Rcheck && mkdir gCrisprTools.buildbin-libdir gCrisprTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCrisprTools.buildbin-libdir gCrisprTools_1.4.0.tar.gz >gCrisprTools.Rcheck\00install.out 2>&1 && cp gCrisprTools.Rcheck\00install.out gCrisprTools-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gCrisprTools.buildbin-libdir --install="check:gCrisprTools-install.out" --force-multiarch --no-vignettes --timings gCrisprTools_1.4.0.tar.gz

StartedAt: 2017-10-17 23:55:34 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-18 00:04:03 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 508.6 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf gCrisprTools.buildbin-libdir gCrisprTools.Rcheck && mkdir gCrisprTools.buildbin-libdir gCrisprTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCrisprTools.buildbin-libdir gCrisprTools_1.4.0.tar.gz >gCrisprTools.Rcheck\00install.out 2>&1 && cp gCrisprTools.Rcheck\00install.out gCrisprTools-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gCrisprTools.buildbin-libdir --install="check:gCrisprTools-install.out" --force-multiarch --no-vignettes --timings gCrisprTools_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.4.0'
* 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  8.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... 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 ... 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 or elapsed time > 5s
                             user system elapsed
ct.makeReport               14.90  32.56   48.19
ct.PantherPathwayEnrichment 40.03   0.99   47.85
ct.makeContrastReport       10.46   7.61   18.80
ct.guideCDF                 15.76   0.86   16.63
ct.makeQCReport              7.46   3.98   11.97
ct.GCbias                    8.11   0.23    8.34
ct.normalizeGuides           5.53   0.06    5.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
ct.makeReport               13.01  24.89   38.75
ct.PantherPathwayEnrichment 36.83   0.93   37.75
ct.makeContrastReport        8.95   5.03   14.68
ct.guideCDF                 11.68   0.23   11.93
ct.makeQCReport              4.77   2.49    7.79
ct.GCbias                    7.04   0.20    7.25
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'gCrisprTools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gCrisprTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gCrisprTools' as gCrisprTools_1.4.0.zip
* DONE (gCrisprTools)

name	user	system	elapsed
aln	0.01	0.00	0.02
ann	0.11	0.00	0.10
ct.DirectionalTests	0.36	0.08	0.44
ct.GCbias	8.11	0.23	8.34
ct.PRC	1.28	0.00	1.28
ct.PantherPathwayEnrichment	40.03	0.99	47.85
ct.ROC	0.28	0.01	0.29
ct.RRAaPvals	0.60	0.14	0.74
ct.RRAalpha	0.36	0.02	0.37
ct.alignmentChart	0	0	0
ct.alphaBeta	0.01	0.00	0.03
ct.ecdf	0	0	0
ct.filterReads	0.28	0.16	0.44
ct.gRNARankByReplicate	0.56	0.06	0.63
ct.generateResults	0.69	0.31	1.00
ct.guideCDF	15.76	0.86	16.63
ct.inputCheck	0.11	0.02	0.12
ct.makeContrastReport	10.46	7.61	18.80
ct.makeQCReport	7.46	3.98	11.97
ct.makeReport	14.90	32.56	48.19
ct.normalizeBySlope	1.9	0.1	2.0
ct.normalizeGuides	5.53	0.06	5.59
ct.normalizeMedians	1.27	0.01	1.28
ct.normalizeNTC	1.22	0.02	1.23
ct.normalizeSpline	1.59	0.02	1.61
ct.prepareAnnotation	0.97	0.01	0.98
ct.preprocessFit	2.60	0.00	2.61
ct.rawCountDensities	0.13	0.03	0.16
ct.resultCheck	0.13	0.02	0.14
ct.stackGuides	3.70	0.06	3.76
ct.targetSetEnrichment	0.15	0.00	0.14
ct.topTargets	0.45	0.02	0.47
ct.viewControls	0.26	0.03	0.30
ct.viewGuides	0.36	0.01	0.37
es	0.08	0.02	0.10
essential.genes	0.00	0.01	0.01
fit	0.22	0.00	0.22
resultsDF	0.13	0.02	0.14

name	user	system	elapsed
aln	0	0	0
ann	0.11	0.00	0.11
ct.DirectionalTests	0.35	0.07	0.41
ct.GCbias	7.04	0.20	7.25
ct.PRC	1.05	0.01	1.06
ct.PantherPathwayEnrichment	36.83	0.93	37.75
ct.ROC	0.16	0.04	0.20
ct.RRAaPvals	0.50	0.05	0.55
ct.RRAalpha	0.34	0.03	0.37
ct.alignmentChart	0	0	0
ct.alphaBeta	0.02	0.00	0.02
ct.ecdf	0	0	0
ct.filterReads	0.29	0.05	0.34
ct.gRNARankByReplicate	0.47	0.05	0.52
ct.generateResults	0.61	0.00	0.60
ct.guideCDF	11.68	0.23	11.93
ct.inputCheck	0.08	0.00	0.07
ct.makeContrastReport	8.95	5.03	14.68
ct.makeQCReport	4.77	2.49	7.79
ct.makeReport	13.01	24.89	38.75
ct.normalizeBySlope	1.51	0.03	1.55
ct.normalizeGuides	4.70	0.06	4.76
ct.normalizeMedians	0.89	0.03	0.92
ct.normalizeNTC	1.00	0.05	1.05
ct.normalizeSpline	1.11	0.03	1.14
ct.prepareAnnotation	0.53	0.03	0.56
ct.preprocessFit	2.41	0.00	2.41
ct.rawCountDensities	0.25	0.02	0.27
ct.resultCheck	0.17	0.00	0.17
ct.stackGuides	4.29	0.03	4.33
ct.targetSetEnrichment	0.13	0.01	0.14
ct.topTargets	0.53	0.02	0.55
ct.viewControls	0.44	0.01	0.45
ct.viewGuides	0.50	0.02	0.52
es	0.12	0.00	0.12
essential.genes	0.00	0.02	0.02
fit	0.28	0.00	0.28
resultsDF	0.14	0.00	0.14